SBMLBioModels: B - C

B


Bordbar2011_MultiTissueType_MetabolicNetwork: MODEL1111070003v0.0.1

This model is from the article: A multi-tissue type genome-scale metabolic network for analysis of whole-body systems…

Details

Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconstructed allowing the systems analysis of human metabolic physiology and pathology. Utilizing high-throughput data, Recon 1 has recently been tailored to different cells and tissues, including the liver, kidney, brain, and alveolar macrophage. These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done.To describe tissue-specific functions, Recon 1 was tailored to describe metabolism in three human cells: adipocytes, hepatocytes, and myocytes. These cell-specific networks were manually curated and validated based on known cellular metabolic functions. To study intercellular interactions, a novel multi-tissue type modeling approach was developed to integrate the metabolic functions for the three cell types, and subsequently used to simulate known integrated metabolic cycles. In addition, the multi-tissue model was used to study diabetes: a pathology with systemic properties. High-throughput data was integrated with the network to determine differential metabolic activity between obese and type II obese gastric bypass patients in a whole-body context.The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. link: http://identifiers.org/pubmed/22041191

Bordbar2011_TissueSpecific-Adipocyte_MetabolicNetwork: MODEL1111070000v0.0.1

This model is from the article: A multi-tissue type genome-scale metabolic network for analysis of whole-body systems…

Details

Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconstructed allowing the systems analysis of human metabolic physiology and pathology. Utilizing high-throughput data, Recon 1 has recently been tailored to different cells and tissues, including the liver, kidney, brain, and alveolar macrophage. These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done.To describe tissue-specific functions, Recon 1 was tailored to describe metabolism in three human cells: adipocytes, hepatocytes, and myocytes. These cell-specific networks were manually curated and validated based on known cellular metabolic functions. To study intercellular interactions, a novel multi-tissue type modeling approach was developed to integrate the metabolic functions for the three cell types, and subsequently used to simulate known integrated metabolic cycles. In addition, the multi-tissue model was used to study diabetes: a pathology with systemic properties. High-throughput data was integrated with the network to determine differential metabolic activity between obese and type II obese gastric bypass patients in a whole-body context.The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. link: http://identifiers.org/pubmed/22041191

Bordbar2011_TissueSpecific-Hepatocyte_MetabolicNetwork: MODEL1111070001v0.0.1

This model is from the article: A multi-tissue type genome-scale metabolic network for analysis of whole-body systems…

Details

Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconstructed allowing the systems analysis of human metabolic physiology and pathology. Utilizing high-throughput data, Recon 1 has recently been tailored to different cells and tissues, including the liver, kidney, brain, and alveolar macrophage. These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done.To describe tissue-specific functions, Recon 1 was tailored to describe metabolism in three human cells: adipocytes, hepatocytes, and myocytes. These cell-specific networks were manually curated and validated based on known cellular metabolic functions. To study intercellular interactions, a novel multi-tissue type modeling approach was developed to integrate the metabolic functions for the three cell types, and subsequently used to simulate known integrated metabolic cycles. In addition, the multi-tissue model was used to study diabetes: a pathology with systemic properties. High-throughput data was integrated with the network to determine differential metabolic activity between obese and type II obese gastric bypass patients in a whole-body context.The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. link: http://identifiers.org/pubmed/22041191

Bordbar2011_TissueSpecific-Myocyte_MetablicNetwork: MODEL1111070002v0.0.1

This model is from the article: A multi-tissue type genome-scale metabolic network for analysis of whole-body systems…

Details

Genome-scale metabolic reconstructions provide a biologically meaningful mechanistic basis for the genotype-phenotype relationship. The global human metabolic network, termed Recon 1, has recently been reconstructed allowing the systems analysis of human metabolic physiology and pathology. Utilizing high-throughput data, Recon 1 has recently been tailored to different cells and tissues, including the liver, kidney, brain, and alveolar macrophage. These models have shown utility in the study of systems medicine. However, no integrated analysis between human tissues has been done.To describe tissue-specific functions, Recon 1 was tailored to describe metabolism in three human cells: adipocytes, hepatocytes, and myocytes. These cell-specific networks were manually curated and validated based on known cellular metabolic functions. To study intercellular interactions, a novel multi-tissue type modeling approach was developed to integrate the metabolic functions for the three cell types, and subsequently used to simulate known integrated metabolic cycles. In addition, the multi-tissue model was used to study diabetes: a pathology with systemic properties. High-throughput data was integrated with the network to determine differential metabolic activity between obese and type II obese gastric bypass patients in a whole-body context.The multi-tissue type modeling approach presented provides a platform to study integrated metabolic states. As more cell and tissue-specific models are released, it is critical to develop a framework in which to study their interdependencies. link: http://identifiers.org/pubmed/22041191

Bordel2018 - GSMM for Human Metabolic Reactions (HMR database): MODEL1707250000v0.0.1

Bordel2018 - GSMM for Human Metabolic Reactions (HMR database)This model is described in the article: [Constraint based…

Details

In order to choose optimal personalized anticancer treatments, transcriptomic data should be analyzed within the frame of biological networks. The best known human biological network (in terms of the interactions between its different components) is metabolism. Cancer cells have been known to have specific metabolic features for a long time and currently there is a growing interest in characterizing new cancer specific metabolic hallmarks. In this article it is presented a method to find personalized therapeutic windows using RNA-seq data and Genome Scale Metabolic Models. This method is implemented in the python library, pyTARG. Our predictions showed that the most anticancer selective (affecting 27 out of 34 considered cancer cell lines and only 1 out of 6 healthy mesenchymal stem cell lines) single metabolic reactions are those involved in cholesterol biosynthesis. Excluding cholesterol biosynthesis, all the considered cell lines can be selectively affected by targeting different combinations (from 1 to 5 reactions) of only 18 metabolic reactions, which suggests that a small subset of drugs or siRNAs combined in patient specific manners could be at the core of metabolism based personalized treatments. link: http://identifiers.org/doi/10.18632/oncotarget.24805

Borghans1997 - Calcium Oscillation - Model 1: BIOMD0000000043v0.0.1

Borghans1997 - Calcium Oscillation - Model 1A theoretical expoloration of possible mechanisms of intracellular calcium o…

Details

Intracellular Ca(2+) oscillations are commonly observed in a large number of cell types in response to stimulation by an extracellular agonist. In most cell types the mechanism of regular spiking is well understood and models based on Ca(2+)-induced Ca(2+) release (CICR) can account for many experimental observations. However, cells do not always exhibit simple Ca(2+) oscillations. In response to given agonists, some cells show more complex behaviour in the form of bursting, i.e. trains of Ca(2+) spikes separated by silent phases. Here we develop several theoretical models, based on physiologically plausible assumptions, that could account for complex intracellular Ca(2+) oscillations. The models are all based on one- or two-pool models based on CICR. We extend these models by (i) considering the inhibition of the Ca(2+)-release channel on a unique intracellular store at high cytosolic Ca(2+) concentrations, (ii) taking into account the Ca(2+)-activated degradation of inositol 1,4,5-trisphosphate (IP(3)), or (iii) considering explicity the evolution of the Ca(2+) concentration in two different pools, one sensitive and the other one insensitive to IP(3). Besides simple periodic oscillations, these three models can all account for more complex oscillatory behaviour in the form of bursting. Moreover, the model that takes the kinetics of IP(3) into account shows chaotic behaviour. link: http://identifiers.org/pubmed/17029867

Parameters:

NameDescription
Kf=1.0Reaction: Y => Z, Rate Law: cytosol*Kf*Y
beta = 1.0; v1=1.0; v0=1.0Reaction: EC => Z, Rate Law: cytosol*(v0+v1*beta)
Ky=0.2; a = 40000.0; d = 100.0; beta = 1.0; Vm3=50.0Reaction: Y => Z; Rho, Rate Law: cytosol*beta*Rho*a/d*Z^4/(1+a/d*Z^4)*Vm3*Y^2/(Ky^2+Y^2)
K=10.0Reaction: Z => EC, Rate Law: extracellular*K*Z
Kd=5000.0Reaction: Rho => Fraction_Inactive_Channels; Z, Rate Law: cytosol*Kd*Z^4*Rho
Kr=5.0Reaction: Fraction_Inactive_Channels => Rho, Rate Law: cytosol*Kr*(1-Rho)
K2=0.1; Vm2=6.5Reaction: Z => Y, Rate Law: intravesicular*Vm2*Z^2/(K2^2+Z^2)

States:

NameDescription
Z[calcium(2+); Calcium cation]
Y[calcium(2+); Calcium cation]
EC[calcium(2+); Calcium cation]
Fraction Inactive Channels[IPR000493; PIRSF002433]
Rho[IPR016093; IPR000493]

Borghans1997 - Calcium Oscillation - Model 2: BIOMD0000000044v0.0.1

Borghans1997 - Calcium Oscillation - Model 2A theoretical expoloration of possible mechanisms of intracellular calcium o…

Details

Intracellular Ca(2+) oscillations are commonly observed in a large number of cell types in response to stimulation by an extracellular agonist. In most cell types the mechanism of regular spiking is well understood and models based on Ca(2+)-induced Ca(2+) release (CICR) can account for many experimental observations. However, cells do not always exhibit simple Ca(2+) oscillations. In response to given agonists, some cells show more complex behaviour in the form of bursting, i.e. trains of Ca(2+) spikes separated by silent phases. Here we develop several theoretical models, based on physiologically plausible assumptions, that could account for complex intracellular Ca(2+) oscillations. The models are all based on one- or two-pool models based on CICR. We extend these models by (i) considering the inhibition of the Ca(2+)-release channel on a unique intracellular store at high cytosolic Ca(2+) concentrations, (ii) taking into account the Ca(2+)-activated degradation of inositol 1,4,5-trisphosphate (IP(3)), or (iii) considering explicity the evolution of the Ca(2+) concentration in two different pools, one sensitive and the other one insensitive to IP(3). Besides simple periodic oscillations, these three models can all account for more complex oscillatory behaviour in the form of bursting. Moreover, the model that takes the kinetics of IP(3) into account shows chaotic behaviour. link: http://identifiers.org/pubmed/17029867

Parameters:

NameDescription
Kf=1.0Reaction: Y => Z, Rate Law: cytosol*Kf*Y
epsilon=0.1Reaction: A =>, Rate Law: cytosol*epsilon*A
beta = 0.5; v1=1.0; v0=2.0Reaction: EC => Z, Rate Law: cytosol*(v0+v1*beta)
Vp=2.5; beta = 0.5Reaction: => A, Rate Law: cytosol*beta*Vp
K=10.0Reaction: Z => EC, Rate Law: extracellular*K*Z
Ka=0.2; Ky=0.2; Vm3=19.5; Kz=0.3Reaction: Y => Z; A, Rate Law: cytosol*Vm3*A^4*Y^2*Z^4/((Ka^4+A^4)*(Ky^2+Y^2)*(Kz^4+Z^4))
Kp=1.0; Vd=80.0; Kd=0.4; n=4.0Reaction: A => ; Z, Rate Law: cytosol*Vd*A^2*Z^n/((Kp^2+A^2)*(Kd^n+Z^n))
K2=0.1; Vm2=6.5Reaction: Z => Y, Rate Law: intravesicular*Vm2*Z^2/(K2^2+Z^2)

States:

NameDescription
Y[calcium(2+); Calcium cation]
Z[calcium(2+); Calcium cation]
A[1D-myo-inositol 1,4,5-trisphosphate; D-myo-Inositol 1,4,5-trisphosphate]
EC[calcium(2+); Calcium cation]

Borghans1997 - Calcium Oscillation - Model 3: BIOMD0000000045v0.0.1

Borghans1997 - Calcium Oscillation - Model 3A theoretical expoloration of possible mechanisms of intracellular calcium o…

Details

Intracellular Ca(2+) oscillations are commonly observed in a large number of cell types in response to stimulation by an extracellular agonist. In most cell types the mechanism of regular spiking is well understood and models based on Ca(2+)-induced Ca(2+) release (CICR) can account for many experimental observations. However, cells do not always exhibit simple Ca(2+) oscillations. In response to given agonists, some cells show more complex behaviour in the form of bursting, i.e. trains of Ca(2+) spikes separated by silent phases. Here we develop several theoretical models, based on physiologically plausible assumptions, that could account for complex intracellular Ca(2+) oscillations. The models are all based on one- or two-pool models based on CICR. We extend these models by (i) considering the inhibition of the Ca(2+)-release channel on a unique intracellular store at high cytosolic Ca(2+) concentrations, (ii) taking into account the Ca(2+)-activated degradation of inositol 1,4,5-trisphosphate (IP(3)), or (iii) considering explicity the evolution of the Ca(2+) concentration in two different pools, one sensitive and the other one insensitive to IP(3). Besides simple periodic oscillations, these three models can all account for more complex oscillatory behaviour in the form of bursting. Moreover, the model that takes the kinetics of IP(3) into account shows chaotic behaviour. link: http://identifiers.org/pubmed/17029867

Parameters:

NameDescription
Vm2s=1.5; K2s=0.0265Reaction: Z => X, Rate Law: intravesicular1*Vm2s*Z^2/(K2s^2+Z^2)
beta = 1.0; Vm3s=0.169; K3s=0.1Reaction: X => Z, Rate Law: cytosol*beta*Vm3s*X^2/(K3s^2+X^2)
K=1.0Reaction: Z => EC, Rate Law: extracellular*K*Z
v0=0.015; beta = 1.0; v1=0.012Reaction: EC => Z, Rate Law: cytosol*(v0+v1*beta)
K3z=0.022; K3y=0.065; Vm3i=25.0Reaction: Y => Z, Rate Law: cytosol*Vm3i*Y^2*Z^2/((K3y^2+Y^2)*(K3z^2+Z^2))
Vm2i=3.1; K2i=0.005Reaction: Z => Y, Rate Law: intravesicular2*Vm2i*Z^2/(K2i^2+Z^2)
Kf=0.5Reaction: Y => Z, Rate Law: cytosol*Kf*Y

States:

NameDescription
Z[calcium(2+); Calcium cation]
Y[calcium(2+); Calcium cation]
X[calcium(2+); Calcium cation]
EC[calcium(2+); Calcium cation]

Borisov2009_EGF_Insulin_Crosstalk: BIOMD0000000223v0.0.1

described in: **Systems-level interactions between insulin-EGF networks amplify mitogenic signaling.** Borisov N, A…

Details

Crosstalk mechanisms have not been studied as thoroughly as individual signaling pathways. We exploit experimental and computational approaches to reveal how a concordant interplay between the insulin and epidermal growth factor (EGF) signaling networks can potentiate mitogenic signaling. In HEK293 cells, insulin is a poor activator of the Ras/ERK (extracellular signal-regulated kinase) cascade, yet it enhances ERK activation by low EGF doses. We find that major crosstalk mechanisms that amplify ERK signaling are localized upstream of Ras and at the Ras/Raf level. Computational modeling unveils how critical network nodes, the adaptor proteins GAB1 and insulin receptor substrate (IRS), Src kinase, and phosphatase SHP2, convert insulin-induced increase in the phosphatidylinositol-3,4,5-triphosphate (PIP(3)) concentration into enhanced Ras/ERK activity. The model predicts and experiments confirm that insulin-induced amplification of mitogenic signaling is abolished by disrupting PIP(3)-mediated positive feedback via GAB1 and IRS. We demonstrate that GAB1 behaves as a non-linear amplifier of mitogenic responses and insulin endows EGF signaling with robustness to GAB1 suppression. Our results show the feasibility of using computational models to identify key target combinations and predict complex cellular responses to a mixture of external cues. link: http://identifiers.org/pubmed/19357636

Parameters:

NameDescription
V72 = 33.3 nM per sec; Km72 = 500.0 nM; Km73 = 500.0 nMReaction: ppErk => pErk, Rate Law: V72*ppErk/(Km72+ppErk+pErk*Km72/Km73)*cell
k_10 = NaN per second; k10 = 4.0E-4 per nM per sReaction: Rp_pShc_GS => Rp + pShc_GS, Rate Law: (k_10*Rp_pShc_GS-k10*Rp*pShc_GS)*cell
k118 = 0.001 per secondReaction: imGABp => imGAB, Rate Law: k118*imGABp*cell
k_9 = NaN per second; k9 = 0.00666 per nM per sReaction: GS + Rp_pShc => Rp_pShc_GS, Rate Law: (k9*Rp_pShc*GS-k_9*Rp_pShc_GS)*cell
k59 = 0.01 per nM per s; k_59 = NaN per secondReaction: GS + mGABp_pSHP2 => mGABp_pSHP2_GS, Rate Law: (k59*mGABp_pSHP2*GS-k_59*mGABp_pSHP2_GS)*cell
k_54 = NaN per second; k54 = 1.0E-5 per nM per sReaction: RasGAP + mGABp => mGABp_RasGAP, Rate Law: (k54*mGABp*RasGAP-k_54*mGABp_RasGAP)*cell
V8 = 200.0 nM per sec; Km8 = 100.0 nMReaction: pShc => Shc, Rate Law: V8*pShc/(Km8+pShc)*cell
k_2 = NaN per second; k2 = 0.033 per nM per sReaction: RE => Rd, Rate Law: (k2*RE*RE-k_2*Rd)*cell
Km43 = 150.0 nM; alpha43 = 0.05 dimensionless; kcat43 = 33.3 per secondReaction: mIRS => mIRSp; Rp, IRp, Rate Law: kcat43*mIRS*(IRp+alpha43*Rp)/(Km43+mIRS)*cell
k13 = 6.66E-6 per nM per s; k_13 = NaN per secondReaction: Rp + RasGAP => Rp_RasGAP, Rate Law: (k13*Rp*RasGAP-k_13*Rp_RasGAP)*cell
k_28 = NaN per second; k28 = 0.1066 per nM per sReaction: IRp + IRS => IRp_IRS, Rate Law: (k28*IRp*IRS-k_28*IRp_IRS)*cell
kcat77 = 0.666 per second; alpha77 = 0.5 dimensionless; Km77 = 100.0 nM; k_77 = 0.666 per secondReaction: mTOR => amTOR; pAkt, ppAkt, Rate Law: (kcat77*mTOR*(alpha77*pAkt+ppAkt)/(Km77+mTOR)-k_77*amTOR)*cell
k24 = 0.011322 per nM per s; k_24 = NaN per secondReaction: I + IR => IRL, Rate Law: (k24*IR*I-k_24*IRL)*cell
k3 = 0.4 per secondReaction: Rd => Rp, Rate Law: k3*Rd*cell
V31 = 333.0 nM per sec; Km31 = 143.3 nMReaction: mIRSp => mIRS, Rate Law: V31*mIRSp/(Km31+mIRSp)*cell
V51 = 333.0 nM per sec; Km51 = 130.0 nMReaction: GABp => GAB, Rate Law: V51*GABp/(Km51+GABp)*cell
k85 = 0.0166 per secondReaction: IRi => IRL, Rate Law: k85*IRi*cell
k48 = 0.666 per secondReaction: mIRSp_SHP2 => mIRS + SHP2, Rate Law: k48*mIRSp_SHP2*cell
V_82 = 133.0 nM per sec; Km82 = 50.0 nMReaction: Rp => Ri, Rate Law: V_82*Rp/(Km82+Rp)*cell
Km81 = 300.0 nM; k_81 = 6.66E-5 per second; kcat81 = 0.166 per secondReaction: mIRS => imIRS; amTOR, Rate Law: (kcat81*mIRS*amTOR/(Km81+mIRS)-k_81*imIRS)*cell
k_74 = NaN per second; k74 = 0.00666 per nM per sReaction: PIP3 + PDK1 => mPDK1, Rate Law: (k74*PDK1*PIP3-k_74*mPDK1)*cell
k6 = 0.333 per secondReaction: Rp_Shc => Rp_pShc, Rate Law: k6*Rp_Shc*cell
k_12 = NaN per second; k12 = 0.00933 per nM per sReaction: Rp + PI3K => Rp_PI3K, Rate Law: (k12*Rp*PI3K-k_12*Rp_PI3K)*cell
V_84 = 333.0 nM per sec; Km84 = 266.0 nMReaction: IRp => IRi, Rate Law: V_84*IRp/(Km84+IRp)*cell
k_27 = NaN per second; k27 = 6.66E-8 per nM per sReaction: RasGAP + IRp => IRp_RasGAP, Rate Law: (k27*IRp*RasGAP-k_27*IRp_RasGAP)*cell
kcat62 = 5.33 per second; Km62 = 50.0 nMReaction: dRas => tRas; Rp_GS, Rp_pShc_GS, mIRSp_GS, mGABp_GS, mGABp_pSHP2_GS, Rate Law: kcat62*dRas*(Rp_GS+Rp_pShc_GS+mIRSp_GS+mGABp_GS+mGABp_pSHP2_GS)/(Km62+dRas)*cell
k5 = 0.0133 per nM per s; k_5 = NaN per secondReaction: Rp + Shc => Rp_Shc, Rate Law: (k5*Rp*Shc-k_5*Rp_Shc)*cell
Km70 = 500.0 nM; kcat71 = 0.666 per second; Km71 = 500.0 nMReaction: pErk => ppErk; Erk, ppMek, Rate Law: kcat71*pErk*ppMek/(Km71+pErk+Erk*Km71/Km70)*cell
Km78 = 100.0 nM; k_78 = 0.666 per second; kcat78 = 0.666 per secondReaction: pAkt => ppAkt; amTOR, Rate Law: (kcat78*amTOR*pAkt/(Km78+pAkt)-k_78*ppAkt)*cell
k1 = 0.068 per nM per s; k_1 = NaN per secondReaction: R + EGF => RE, Rate Law: (k1*R*EGF-k_1*RE)*cell
V41 = 6.66 nM per sec; Km41 = 50.0 nMReaction: aSrc => iSrc, Rate Law: V41*aSrc/(Km41+aSrc)*cell
k64 = 0.0 per nM per s; k_64 = 2.5 per secondReaction: PI3K + tRas => tRas_PI3K, Rate Law: (k64*tRas*PI3K-k_64*tRas_PI3K)*cell
Km69 = 675.299 nM; V69 = 16.6 nM per secReaction: ppMek => Mek, Rate Law: V69*ppMek/(Km69+ppMek)*cell
alpha67 = 1.0E-6 per nM per s; kcat67 = 0.666 per second; Km67 = 10000.0 nM; beta67 = 2.0 dimensionlessReaction: aaRaf => Raf; pAkt, PKA, ppAkt, Rate Law: (kcat67*aaRaf*PKA/(Km67+aaRaf)+alpha67*aaRaf*(pAkt+beta67*ppAkt))*cell
Km68 = 50.0 nM; kcat68 = 0.133 per secondReaction: Mek => ppMek; aaRaf, Rate Law: kcat68*aaRaf*Mek/(Km68+Mek)*cell
k_52 = NaN per second; k52 = 0.002 per nM per sReaction: GS + mGABp => mGABp_GS, Rate Law: (k52*mGABp*GS-k_52*mGABp_GS)*cell
kcat66 = 3.33 per second; Km66 = 10.0 nMReaction: aRaf => aaRaf; aSrc, Rate Law: kcat66*aSrc*aRaf/(Km66+aRaf)*cell
Km63 = 50.0 nM; kcat63 = 20000.0 per secondReaction: tRas => dRas; Rp_RasGAP, IRp_RasGAP, mGABp_RasGAP, bRasGAP, Rate Law: kcat63*tRas*(bRasGAP+mGABp_RasGAP+Rp_RasGAP+IRp_RasGAP)/(Km63+tRas)*cell
k46 = 0.00666 per nM per s; k_46 = NaN per secondReaction: PI3K + mIRSp => mIRSp_PI3K, Rate Law: (k46*mIRSp*PI3K-k_46*mIRSp_PI3K)*cell
k111 = 0.0133 per nM per sReaction: Rp_RasGAP => Rp + RasGAP; mGABp_SHP2, mGABp_pSHP2, mGABp_pSHP2_GS, Rate Law: k111*(mGABp_SHP2+mGABp_pSHP2+mGABp_pSHP2_GS)*Rp_RasGAP*cell
k17 = 1.85E-4 per secondReaction: Rp => Null, Rate Law: k17*Rp*cell
k_11 = NaN per second; k11 = 0.0 per nM per sReaction: pShc_GS => GS + pShc, Rate Law: (k_11*pShc_GS-k11*pShc*GS)*cell
k47 = 6.66E-4 per nM per s; k_47 = NaN per secondReaction: mIRSp + SHP2 => mIRSp_SHP2, Rate Law: (k47*mIRSp*SHP2-k_47*mIRSp_SHP2)*cell
k56 = 0.666 per secondReaction: GABp_pSHP2_GS => GS + SHP2 + GAB, Rate Law: k56*GABp_pSHP2_GS*cell
k83 = 0.0166 per secondReaction: Ri => Rd, Rate Law: k83*Ri*cell
Km79 = 5000.0 nM; k_79 = 6.66E-5 per second; kcat79 = 0.0466 per secondReaction: GS => iGS; ppErk, Rate Law: (kcat79*ppErk*GS/(Km79+GS)-k_79*iGS)*cell
k_4 = NaN per second; k4 = 6.66E-4 per nM per sReaction: Rp + GS => Rp_GS, Rate Law: (k4*Rp*GS-k_4*Rp_GS)*cell
k_42 = NaN per second; k42 = 0.00666 per nM per sReaction: IRS + PIP3 => mIRS, Rate Law: (k42*IRS*PIP3-k_42*mIRS)*cell
k_7 = NaN per second; k7 = 6.66E-4 per nM per sReaction: Rp_pShc => Rp + pShc, Rate Law: (k_7*Rp_pShc-k7*Rp*pShc)*cell
k49 = 6.66E-4 per nM per s; k_42 = NaN per secondReaction: mGABp_RasGAP => PIP3 + GABp_RasGAP, Rate Law: (k_42*mGABp_RasGAP-k49*PIP3*GABp_RasGAP)*cell
k61 = 3.33 per secondReaction: PIP3 => Null, Rate Law: k61*PIP3*cell
k45 = 6.66E-4 per nM per s; k_45 = NaN per secondReaction: GS + mIRSp => mIRSp_GS, Rate Law: (k45*mIRSp*GS-k_45*mIRSp_GS)*cell

States:

NameDescription
RasGAPRasGAP
SHP2SHP2
mGABp RasGAPmGABp_RasGAP
IRp RasGAPIRp_RasGAP
tRas PI3KtRas_PI3K
mIRSpmIRSp
ShcShc
Rp Shc[Epidermal growth factor receptor]
ppAktppAkt
RiRi
Rd[Pro-epidermal growth factor; Epidermal growth factor receptor]
IRiIRi
Rp pShc GSRp_pShc_GS
ppErkppErk
mTORmTOR
pShc GSpShc_GS
IRIR
ppMekppMek
Rp PI3KRp_PI3K
mIRSmIRS
imIRSimIRS
GABGAB
PI3KPI3K
mGABp pSHP2 GSmGABp_pSHP2_GS
mPDK1mPDK1
IRSIRS
GSGS
Rp GS[Epidermal growth factor receptor]
mIRSp SHP2mIRSp_SHP2
I[Insulin; Insulin [extracellular region]]
aaRafaaRaf
imGABimGAB
IRpIRp
mIRSp PI3KmIRSp_PI3K
NullNull
iSrciSrc
Rp pShcRp_pShc
tRastRas
RR
Rp[Pro-epidermal growth factor; Epidermal growth factor receptor]

Bornheimer2004_GTPaseCycle: BIOMD0000000086v0.0.1

This model is according to the paper *Computational modeling reveals how interplay between components of a GTPase-cycle…

Details

Heterotrimeric G protein signaling is regulated by signaling modules composed of heterotrimeric G proteins, active G protein-coupled receptors (Rs), which activate G proteins, and GTPase-activating proteins (GAPs), which deactivate G proteins. We term these modules GTPase-cycle modules. The local concentrations of these proteins are spatially regulated between plasma membrane microdomains and between the plasma membrane and cytosol, but no data or models are available that quantitatively explain the effect of such regulation on signaling. We present a computational model of the GTPase-cycle module that predicts that the interplay of local G protein, R, and GAP concentrations gives rise to 16 distinct signaling regimes and numerous intermediate signaling phenomena. The regimes suggest alternative modes of the GTPase-cycle module that occur based on defined local concentrations of the component proteins. In one mode, signaling occurs while G protein and receptor are unclustered and GAP eliminates signaling; in another, G protein and receptor are clustered and GAP can rapidly modulate signaling but does not eliminate it. Experimental data from multiple GTPase-cycle modules is interpreted in light of these predictions. The latter mode explains previously paradoxical data in which GAP does not alter maximal current amplitude of G protein-activated ion channels, but hastens signaling. The predictions indicate how variations in local concentrations of the component proteins create GTPase-cycle modules with distinctive phenotypes. They provide a quantitative framework for investigating how regulation of local concentrations of components of the GTPase-cycle module affects signaling. link: http://identifiers.org/pubmed/15520372

Parameters:

NameDescription
k2=0.00297; k1=25.0Reaction: species_15 => species_16 + species_7, Rate Law: compartment_0*(k1*species_15-k2*species_16*species_7)
k2=2.22E-9; k1=0.013Reaction: species_10 => species_13 + species_7, Rate Law: compartment_0*(k1*species_10-k2*species_13*species_7)
k1=6200000.0; k2=0.0433Reaction: species_11 + species_4 => species_15, Rate Law: compartment_0*(k1*species_11*species_4-k2*species_15)
k2=8.0; k1=8780000.0Reaction: species_1 + species_0 => species_2, Rate Law: compartment_0*(k1*species_1*species_0-k2*species_2)
k2=0.478; k1=6300000.0Reaction: species_10 + species_0 => species_15, Rate Law: compartment_0*(k1*species_10*species_0-k2*species_15)
k1=2.0; k2=1470000.0Reaction: species_13 => species_9 + species_8, Rate Law: compartment_0*(k1*species_13-k2*species_9*species_8)
k2=8.38E-6; k1=529000.0Reaction: species_1 + species_3 => species_5, Rate Law: compartment_0*(k1*species_1*species_3-k2*species_5)
k1=4.94E7; k2=0.00421Reaction: species_12 + species_4 => species_16, Rate Law: compartment_0*(k1*species_12*species_4-k2*species_16)
k2=0.685; k1=13000.0Reaction: species_13 + species_0 => species_16, Rate Law: compartment_0*(k1*species_13*species_0-k2*species_16)
k1=64100.0; k2=0.95Reaction: species_6 + species_0 => species_12, Rate Law: compartment_0*(k1*species_6*species_0-k2*species_12)
k1=1620000.0; k2=0.00875Reaction: species_14 + species_3 => species_15, Rate Law: compartment_0*(k1*species_14*species_3-k2*species_15)
k1=9.47E7; k2=0.00227Reaction: species_6 + species_4 => species_13, Rate Law: compartment_0*(k1*species_6*species_4-k2*species_13)
k2=0.00572; k1=74300.0Reaction: species_9 + species_0 => species_14, Rate Law: compartment_0*(k1*species_9*species_0-k2*species_14)
k2=1.28; k1=1.32E8Reaction: species_5 + species_4 => species_10, Rate Law: compartment_0*(k1*species_5*species_4-k2*species_10)
k2=9.03E-7; k1=0.013Reaction: species_5 => species_6 + species_7, Rate Law: compartment_0*(k1*species_5-k2*species_6*species_7)
k1=853000.0; k2=0.00468Reaction: species_9 + species_3 => species_10, Rate Law: compartment_0*(k1*species_9*species_3-k2*species_10)
k1=386000.0; k2=0.0408Reaction: species_5 + species_0 => species_11, Rate Law: compartment_0*(k1*species_5*species_0-k2*species_11)
k1=2.28E7; k2=5.43E-5Reaction: species_2 + species_4 => species_14, Rate Law: compartment_0*(k1*species_2*species_4-k2*species_14)
k2=2940.0; k1=2.75Reaction: species_16 => species_14 + species_8, Rate Law: compartment_0*(k1*species_16-k2*species_14*species_8)
k1=1.0E-4; k2=3.83Reaction: species_12 => species_2 + species_8, Rate Law: compartment_0*(k1*species_12-k2*species_2*species_8)
k1=44700.0; k2=8.32E-8Reaction: species_2 + species_3 => species_11, Rate Law: compartment_0*(k1*species_2*species_3-k2*species_11)
k1=6.36E8; k2=0.0179Reaction: species_1 + species_4 => species_9, Rate Law: compartment_0*(k1*species_1*species_4-k2*species_9)
k2=62.3; k1=1.0E-4Reaction: species_6 => species_1 + species_8, Rate Law: compartment_0*(k1*species_6-k2*species_1*species_8)
k1=25.0; k2=0.244Reaction: species_11 => species_12 + species_7, Rate Law: compartment_0*(k1*species_11-k2*species_12*species_7)

States:

NameDescription
species 9[receptor complex; heterotrimeric G-protein complex]
species 2[IPR000342; heterotrimeric G-protein complex]
species 6[GDP; heterotrimeric G-protein complex]
species 10[GTP; receptor complex; heterotrimeric G-protein complex]
species 11[GTP; IPR000342; heterotrimeric G-protein complex]
species 1[heterotrimeric G-protein complex]
species 4[IPR000337; receptor complex]
species 16[GDP; IPR000342; receptor complex; heterotrimeric G-protein complex]
species 14[IPR000342; receptor complex; heterotrimeric G-protein complex]
species 3[GTP; GTP]
species 0[IPR000342]
species 8[GDP; GDP]
species 12[GDP; IPR000342; heterotrimeric G-protein complex]
species 7[phosphate(3-)]
species 5[GTP; heterotrimeric G-protein complex]
species 15[GTP; IPR000342; receptor complex; heterotrimeric G-protein complex]
species 13[GDP; receptor complex; heterotrimeric G-protein complex]

Borodina2005 - Genome-scale metabolic network of Streptomyces coelicolor (iIB711): MODEL1507180049v0.0.1

Borodina2005 - Genome-scale metabolic network of Streptomyces coelicolor (iIB711)This model is described in the article:…

Details

Streptomyces are filamentous soil bacteria that produce more than half of the known microbial antibiotics. We present the first genome-scale metabolic model of a representative of this group–Streptomyces coelicolor A3(2). The metabolism reconstruction was based on annotated genes, physiological and biochemical information. The stoichiometric model includes 819 biochemical conversions and 152 transport reactions, accounting for a total of 971 reactions. Of the reactions in the network, 700 are unique, while the rest are iso-reactions. The network comprises 500 metabolites. A total of 711 open reading frames (ORFs) were included in the model, which corresponds to 13% of the ORFs with assigned function in the S. coelicolor A3(2) genome. In a comparative analysis with the Streptomyces avermitilis genome, we showed that the metabolic genes are highly conserved between these species and therefore the model is suitable for use with other Streptomycetes. Flux balance analysis was applied for studies of the reconstructed metabolic network and to assess its metabolic capabilities for growth and polyketides production. The model predictions of wild-type and mutants' growth on different carbon and nitrogen sources agreed with the experimental data in most cases. We estimated the impact of each reaction knockout on the growth of the in silico strain on 62 carbon sources and two nitrogen sources, thereby identifying the "core" of the essential reactions. We also illustrated how reconstruction of a metabolic network at the genome level can be used to fill gaps in genome annotation. link: http://identifiers.org/pubmed/15930493

Bose2011 - Noise-assisted interactions of tumor and immune cells: BIOMD0000000894v0.0.1

Noise-assisted interactions of tumor and immune cells. Bose T1, Trimper S. Author information 1 Institute of Physics,…

Details

We consider a three-state model comprising tumor cells, effector cells, and tumor-detecting cells under the influence of noises. It is demonstrated that inevitable stochastic forces existing in all three cell species are able to suppress tumor cell growth completely. Whereas the deterministic model does not reveal a stable tumor-free state, the auto-correlated noise combined with cross-correlation functions can either lead to tumor-dormant states, tumor progression, as well as to an elimination of tumor cells. The auto-correlation function exhibits a finite correlation time τ, while the cross-correlation functions shows a white-noise behavior. The evolution of each of the three kinds of cells leads to a multiplicative noise coupling. The model is investigated by means of a multivariate Fokker-Planck equation for small τ. The different behavior of the system is, above all, determined by the variation of the correlation time and the strength of the cross-correlation between tumor and tumor-detecting cells. The theoretical model is based on a biological background discussed in detail, and the results are tested using realistic parameters from experimental observations. link: http://identifiers.org/pubmed/21929038

Parameters:

NameDescription
Dy = 0.01; p = 0.06Reaction: y =>, Rate Law: compartment*(p-Dy)*y
R = 1.0; Dz = 1.2; Dx = 2.1; tau = 0.3; mu = 20.0Reaction: z =>, Rate Law: compartment*(mu-(R*(1+Dx*tau)+Dx*(1+0.5*Dz*tau)))*z
R = 1.0; Dz = 1.2; Dx = 2.1; tau = 0.3Reaction: => x; z, Rate Law: compartment*((1+R*(1-Dx*tau)+0.5*Dx*Dz*tau)*x+Dx*(1+R*tau)*z)

States:

NameDescription
x[Neoplastic Cell]
z[Lymphocyte]
y[Effector Immune Cell]

Bouchnita2019 - A multiscale model to design therapeutic strategies that overcome drug resistance to tyrosine kinase inhibitors in multiple myeloma: MODEL1912170004v0.0.1

Drug resistance (DR) is a phenomenon characterized by the tolerance of a disease to pharmaceutical treatment. In cancer…

Details

Drug resistance (DR) is a phenomenon characterized by the tolerance of a disease to pharmaceutical treatment. In cancer patients, DR is one of the main challenges that limit the therapeutic potential of the existing treatments. Therefore, overcoming DR by restoring the sensitivity of cancer cells would be greatly beneficial. In this context, mathematical modeling can be used to provide novel therapeutic strategies that maximize the efficiency of anti-cancer agents and potentially overcome DR. In this paper, we present a new multiscale model devoted to the interaction of potential treatments with multiple myeloma (MM) development. In this model, MM cells are represented as individual objects that move, divide, and die by apoptosis. The fate of each cell depends on intracellular and extracellular regulation, as well as the administered treatment. The model is used to explore the combined effects of a tyrosine-kinase inhibitor (TKI) with a pentose phosphate pathway (PPP) inhibitor. We use numerical simulations to tailor effective and safe treatment regimens that may eradicate the MM tumors. The model suggests that an interval for the daily dose of the PPP inhibitor can maximize the responsiveness of MM cells to the treatment with TKIs. Then, it demonstrates that the combination of high-dose pulsatile TKI treatment with high-dose daily PPP inhibitor therapy can potentially eradicate the tumor.The predictions of numerical simulations using such a model can be considered as testable hypotheses in future pre-clinical experiments and clinical studies. link: http://identifiers.org/pubmed/31809782

Brands2002 - Monosaccharide-casein systems: BIOMD0000000052v0.0.1

In the present study, a kinetic model of the Maillard reaction occurring in heated monosaccharide-casein systems was pro…

Details

Brands2002 - Monosaccharide-casein systems

A kinetic model of the Maillard reaction occurring in heated monosaccharide-casein system.

This model is described in the article: Kinetic modeling of reactions in heated monosaccharide-casein systems., Brands CM, van Boekel MA,Journal of Agricultural and Food Chemistry. 2002, 50(23):6725-6739

Abstract: In the present study, a kinetic model of the Maillard reaction occurring in heated monosaccharide-casein systems was proposed. Its parameters, the reaction rate constants, were estimated via multiresponse modeling. The determinant criterion was used as the statistical fit criterion instead of the familiar least squares to avoid statistical problems. The kinetic model was extensively tested by varying the reaction conditions. Different sugars (glucose, fructose, galactose, and tagatose) were studied regarding their effect on the reaction kinetics. This study has shown the power of multiresponse modeling for the unraveling of complicated reaction routes as occur in the Maillard reaction. The iterative process of proposing a model, confronting it with experiments, and criticizing the model was passed through four times to arrive at a model that was largely consistent with all results obtained. A striking difference was found between aldose and ketose sugars as suggested by the modeling results: not the ketoses themselves but only their reaction products were found to be reactive in the Maillard reaction.

This model is hosted on BioModels Database and identified by MODEL8177704759.

To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Parameters:

NameDescription
K6=0.00439Reaction: Triose => Cn + Acetic_acid, Rate Law: K6*Triose
K3=4.7E-4Reaction: Glu => C5 + Formic_acid, Rate Law: K3*Glu
K10=1.5E-4Reaction: lys_R + Fru => AMP, Rate Law: K10*Fru*lys_R
K2=0.00509Reaction: Fru => Glu, Rate Law: K2*Fru
K7=1.8E-4Reaction: lys_R + Glu => Amadori, Rate Law: K7*Glu*lys_R
K8=0.11134Reaction: Amadori => Acetic_acid + lys_R, Rate Law: K8*Amadori
K9=0.14359Reaction: Amadori => AMP, Rate Law: K9*Amadori
K4=0.0011Reaction: Fru => C5 + Formic_acid, Rate Law: K4*Fru
K11=0.12514Reaction: AMP => Melanoidin, Rate Law: K11*AMP
K1=0.01Reaction: Glu => Fru, Rate Law: K1*Glu
K5=0.00712Reaction: Fru => Triose, Rate Law: K5*Fru

States:

NameDescription
AMPAMP
Formic acid[formic acid; Formate]
Acetic acid[acetic acid; Acetate]
lys R[lysine residue]
TrioseTriose
CnCn
Glu[glucose; C00293]
MelanoidinMelanoidin
Fru[fructose; Fructose]
C5C5
AmadoriAmadori

Brannmark2010_InsulinSignalling_Mifamodel: BIOMD0000000343v0.0.1

This model is from the article: Mass and information feedbacks through receptor endocytosis govern insulin signaling…

Details

Insulin and other hormones control target cells through a network of signal-mediating molecules. Such networks are extremely complex due to multiple feedback loops in combination with redundancy, shared signal mediators, and cross-talk between signal pathways. We present a novel framework that integrates experimental work and mathematical modeling to quantitatively characterize the role and relation between co-existing submechanisms in complex signaling networks. The approach is independent of knowing or uniquely estimating model parameters because it only relies on (i) rejections and (ii) core predictions (uniquely identified properties in unidentifiable models). The power of our approach is demonstrated through numerous iterations between experiments, model-based data analyses, and theoretical predictions to characterize the relative role of co-existing feedbacks governing insulin signaling. We examined phosphorylation of the insulin receptor and insulin receptor substrate-1 and endocytosis of the receptor in response to various different experimental perturbations in primary human adipocytes. The analysis revealed that receptor endocytosis is necessary for two identified feedback mechanisms involving mass and information transfer, respectively. Experimental findings indicate that interfering with the feedback may substantially increase overall signaling strength, suggesting novel therapeutic targets for insulin resistance and type 2 diabetes. Because the central observations are present in other signaling networks, our results may indicate a general mechanism in hormonal control. link: http://identifiers.org/pubmed/20421297

Parameters:

NameDescription
k1d = 1580.6782649401Reaction: V1d = k1d*IRp, Rate Law: missing
k1g = 286.6994648072Reaction: V1g = k1g*IRp, Rate Law: missing
k1b = 0.02000224505Reaction: V1b = k1b*IRins, Rate Law: missing
km3 = 0.1131073982Reaction: Vm3 = km3*Xp, Rate Law: missing
k1c = 0.3635167928Reaction: V1c = k1c*IRins, Rate Law: missing
k21 = 1.6722503302; k22 = 0.036381619Reaction: V2 = k21*(IRp+k22*IRip)*IRS, Rate Law: missing
k1f = 20.0726035037; k1e = 4.38334E-5Reaction: V1e = IRip*(k1e+k1f*Xp/(1+Xp)), Rate Law: missing
k1r = 3.6327773442Reaction: V1r = k1r*IRi, Rate Law: missing
k3 = 1.6286590231Reaction: V3 = k3*X*IRSip, Rate Law: missing
kyanna = 16760.1203140926Reaction: measanna = kyanna*IRSip, Rate Law: missing
kyDosR = 13740.4321729991Reaction: measdosR = kyDosR*IRSip, Rate Law: missing
k1abasic = 0.012452744; ins = 100.0; k1a = 0.3892881852Reaction: V1a = k1a*ins*IR+k1abasic*IR, Rate Law: missing
km2 = 32.5942371891Reaction: Vm2 = km2*IRSip, Rate Law: missing
ky2 = 8936.219557405Reaction: measdoublestep = ky2*IRSip, Rate Law: missing

States:

NameDescription
Vm3Vm3
V3V3
V1bV1b
measdosRmeasdosR
IRi[Insulin receptor]
Vm2Vm2
measdoublestepmeasdoublestep
IRip[Insulin receptor; Phosphoprotein]
V2V2
IR[Insulin receptor]
V1gV1g
simXPsimXp
IRSip[Insulin receptor substrate 1; Phosphoprotein]
X[protein; Intermediate]
intamountintamount
IRS[Insulin receptor substrate 1]
V1aV1a
V1eV1e
V1rv1r
V1cV1c
IRp[Insulin receptor; Phosphoprotein]
IRins[Insulin receptor; Insulin]
V1dV1d
measannameasanna
Xp[protein; Intermediate]

Bravo2012 - Modelling blood coagulation factor Va inactivation by APC: BIOMD0000000739v0.0.1

Mathematical model of blood coagulation factor Va and Va fragment inactivation by APC, reactions with Xa and prothrombin…

Details

Because understanding of the inventory, connectivity and dynamics of the components characterizing the process of coagulation is relatively mature, it has become an attractive target for physiochemical modeling. Such models can potentially improve the design of therapeutics. The prothrombinase complex (composed of the protease factor (F)Xa and its cofactor FVa) plays a central role in this network as the main producer of thrombin, which catalyses both the activation of platelets and the conversion of fibrinogen to fibrin, the main substances of a clot. A key negative feedback loop that prevents clot propagation beyond the site of injury is the thrombin-dependent generation of activated protein C (APC), an enzyme that inactivates FVa, thus neutralizing the prothrombinase complex. APC inactivation of FVa is complex, involving the production of partially active intermediates and "protection" of FVa from APC by both FXa and prothrombin. An empirically validated mathematical model of this process would be useful in advancing the predictive capacity of comprehensive models of coagulation.A model of human APC inactivation of prothrombinase was constructed in a stepwise fashion by analyzing time courses of FVa inactivation in empirical reaction systems with increasing number of interacting components and generating corresponding model constructs of each reaction system. Reaction mechanisms, rate constants and equilibrium constants informing these model constructs were initially derived from various research groups reporting on APC inactivation of FVa in isolation, or in the presence of FXa or prothrombin. Model predictions were assessed against empirical data measuring the appearance and disappearance of multiple FVa degradation intermediates as well as prothrombinase activity changes, with plasma proteins derived from multiple preparations. Our work integrates previously published findings and through the cooperative analysis of in vitro experiments and mathematical constructs we are able to produce a final validated model that includes 24 chemical reactions and interactions with 14 unique rate constants which describe the flux in concentrations of 24 species.This study highlights the complexity of the inactivation process and provides a module of equations describing the Protein C pathway that can be integrated into existing comprehensive mathematical models describing tissue factor initiated coagulation. link: http://identifiers.org/pubmed/22607732

Parameters:

NameDescription
R16_kdis = 0.0035Reaction: Xa_Va_i_306_506 => Xa + Va_1_306_Va_LC + Va_307_506 + Va_507_679_709, Rate Law: compartment*R16_kdis*Xa_Va_i_306_506
R01_koff = 0.7; R01_kon = 1.0E8Reaction: APC + Va => APC_Va, Rate Law: compartment*(R01_kon*APC*Va-R01_koff*APC_Va)
R09_kdis = 0.028Reaction: Va_i_306_506 => Va_1_306_Va_LC + Va_307_506 + Va_507_679_709, Rate Law: compartment*R09_kdis*Va_i_306_506
R05_kon = 1.0E8; R05_koff = 0.7Reaction: APC + Va_i_306 => APC_Va_i_306, Rate Law: compartment*(R05_kon*APC*Va_i_306-R05_koff*APC_Va_i_306)
R20_koff = 103.0; R20_kon = 1.0E8Reaction: Xa_Va_i_506 + PT => Xa_Va_i_506_PT, Rate Law: compartment*(R20_kon*Xa_Va_i_506*PT-R20_koff*Xa_Va_i_506_PT)
R15_kdis = 0.0035Reaction: Xa_Va_i_306 => Xa + Va_1_306_Va_LC + Va_307_679_709, Rate Law: compartment*R15_kdis*Xa_Va_i_306
R21_koff = 103.0; R21_kon = 1.0E8Reaction: Xa_Va_i_306 + PT => Xa_Va_i_306_PT, Rate Law: compartment*(R21_kon*Xa_Va_i_306*PT-R21_koff*Xa_Va_i_306_PT)
R23_dis = 0.0035Reaction: Xa_Va_i_306_PT => Xa + Va_1_306_Va_LC + Va_307_679_709 + PT, Rate Law: compartment*R23_dis*Xa_Va_i_306_PT
R10_kon = 1.0E8; R10_koff = 0.7Reaction: APC + Va_1_306_Va_LC => APC_Va_1_306_Va_LC, Rate Law: compartment*(R10_kon*APC*Va_1_306_Va_LC-R10_koff*APC_Va_1_306_Va_LC)
R11_kon = 1.5E8; R11_koff = 0.075Reaction: Xa + Va => Xa_Va, Rate Law: compartment*(R11_kon*Xa*Va-R11_koff*Xa_Va)
R24_dis = 0.0035Reaction: Xa_Va_i_306_506_PT => Xa + PT + Va_1_306_Va_LC + Va_307_506 + Va_507_679_709, Rate Law: compartment*R24_dis*Xa_Va_i_306_506_PT
R17_koff = 70.0; R17_kon = 1.0E8Reaction: Va + PT => Va_PT, Rate Law: compartment*(R17_kon*Va*PT-R17_koff*Va_PT)
R14_kon = 1.5E8; R14_koff = 0.15Reaction: Xa + Va_i_306_506 => Xa_Va_i_306_506, Rate Law: compartment*(R14_kon*Xa*Va_i_306_506-R14_koff*Xa_Va_i_306_506)
R13_koff = 0.15; R13_kon = 1.5E8Reaction: Xa + Va_i_306 => Xa_Va_i_306, Rate Law: compartment*(R13_kon*Xa*Va_i_306-R13_koff*Xa_Va_i_306)
R02_kcat = 1.0Reaction: APC_Va => APC + Va_i_506, Rate Law: compartment*R02_kcat*APC_Va
R08_kdis = 0.028Reaction: Va_i_306 => Va_1_306_Va_LC + Va_307_679_709, Rate Law: compartment*R08_kdis*Va_i_306
R03_kcat = 0.192Reaction: APC_Va => APC + Va_i_306, Rate Law: compartment*R03_kcat*APC_Va
R06_kcat = 0.192Reaction: APC_Va_i_506 => APC + Va_i_306_506, Rate Law: compartment*R06_kcat*APC_Va_i_506
R19_kon = 1.0E8; R19_koff = 103.0Reaction: Xa_Va + PT => Xa_Va_PT, Rate Law: compartment*(R19_kon*Xa_Va*PT-R19_koff*Xa_Va_PT)
R12_koff = 0.15; R12_kon = 1.5E8Reaction: Xa + Va_i_506 => Xa_Va_i_506, Rate Law: compartment*(R12_kon*Xa*Va_i_506-R12_koff*Xa_Va_i_506)
R04_koff = 0.7; R04_kon = 1.0E8Reaction: APC + Va_i_506 => APC_Va_i_506, Rate Law: compartment*(R04_kon*APC*Va_i_506-R04_koff*APC_Va_i_506)
R07_kcat = 1.0Reaction: APC_Va_i_306 => APC + Va_i_306_506, Rate Law: compartment*R07_kcat*APC_Va_i_306
R22_kon = 1.0E8Reaction: Xa_Va_i_306_506 + PT => Xa_Va_i_306_506_PT, Rate Law: compartment*(R22_kon*Xa_Va_i_306_506*PT-R22_kon*Xa_Va_i_306_506_PT)

States:

NameDescription
Va 307 679 709[Coagulation Factor V]
Va PT[Prothrombin; Coagulation Factor V]
Va 1 306 Va LC[Coagulation Factor V]
Xa[Factor X Measurement]
Va 507 679 709[Coagulation Factor V]
Va i 306[Coagulation Factor V]
APC Va i 506[Vitamin K-Dependent Protein C; Coagulation Factor V]
Xa Va i 306 506[Factor X Measurement; Coagulation Factor V]
Xa Va i 306[Coagulation Factor V; Factor X Measurement]
Va 307 506[Coagulation Factor V]
APC Va 1 306 Va LC[Vitamin K-Dependent Protein C; Coagulation Factor V]
Xa Va i 306 PT[Prothrombin; Factor X Measurement; Coagulation Factor V]
Xa Va[Coagulation Factor V; Factor X Measurement]
PT[Prothrombin]
APC Va i 306[Vitamin K-Dependent Protein C; Coagulation Factor V]
Xa Va i 506[Factor X Measurement; Coagulation Factor V]
Xa Va i 306 506 PT[Factor X Measurement; Coagulation Factor V; Prothrombin]
APC Va[Coagulation Factor V; Vitamin K-Dependent Protein C]
Va[Coagulation Factor V]
APC[Vitamin K-Dependent Protein C]
Xa Va i 506 PT[Factor X Measurement; Prothrombin; Coagulation Factor V]
Xa Va PT[Coagulation Factor V; Factor X Measurement; Prothrombin]
Va i 506[Coagulation Factor V]
Va i 306 506[Coagulation Factor V]

Bray1993_chemotaxis: BIOMD0000000404v0.0.1

This version of the model is very close to the version described in the paper with one exception: the binding of asparta…

Details

We have developed a computer program that simulates the intracellular reactions mediating the rapid (nonadaptive) chemotactic response of Escherichia coli bacteria to the attractant aspartate and the repellent Ni2+ ions. The model is built from modular units representing the molecular components involved, which are each assigned a known value of intracellular concentration and enzymatic rate constant wherever possible. The components are linked into a network of coupled biochemical reactions based on a compilation of widely accepted mechanisms but incorporating several novel features. The computer motor shows the same pattern of runs, tumbles and pauses seen in actual bacteria and responds in the same way as living bacteria to sudden changes in concentration of aspartate or Ni2+. The simulated network accurately reproduces the phenotype of more than 30 mutants in which components of the chemotactic pathway are deleted and/or expressed in excess amounts and shows a rapidity of response to a step change in aspartate concentration similar to living bacteria. Discrepancies between the simulation and real bacteria in the phenotype of certain mutants and in the gain of the chemotactic response to aspartate suggest the existence of additional as yet unidentified interactions in the in vivo signal processing pathway. link: http://identifiers.org/pubmed/8334303

Parameters:

NameDescription
k1=1.0Reaction: Bp => B, Rate Law: cell*k1*Bp
ka = 0.1; kappa = 2.25E-7Reaction: M + Yp => MYp, Rate Law: cell*ka*(M*Yp-kappa/4*MYp)/cell
alpha = 0.14; ka = 0.1; kappa = 2.25E-7Reaction: MYpYp + Yp => MYpYpYp, Rate Law: cell*ka*(MYpYp*Yp-3*alpha*alpha*kappa/2*MYpYpYp)/cell
kcat=75000.0; parameter_2 = 0.997008973080758Reaction: A => Ap; TWA, Rate Law: cell*TWA*A*kcat*parameter_2
k1=10000.0; k2=1.0Reaction: T + A => TA, Rate Law: cell*(k1*T*A-k2*TA)
k1=400000.0; k2=1.0Reaction: Tasp + WA => Tasp_WA, Rate Law: cell*(k1*Tasp*WA-k2*Tasp_WA)
k1=1000000.0Reaction: Ap + B => A + Bp, Rate Law: cell*k1*Ap*B
k1=500000.0Reaction: Yp + Z => Y + Z, Rate Law: cell*k1*Yp*Z
k1=200000.0Reaction: Ap + Y => A + Yp, Rate Law: cell*k1*Ap*Y
parameter_2 = 0.997008973080758; kcat=200000.0Reaction: A => Ap; Tni_WA, Rate Law: cell*Tni_WA*A*kcat*parameter_2
k1=0.4; k2=1.0Reaction: Tni + WA => Tni_WA, Rate Law: cell*(k1*Tni*WA-k2*Tni_WA)
parameter_2 = 0.997008973080758; kcat=0.001Reaction: A => Ap, Rate Law: cell*kcat*parameter_2*A
k1=1.0E8Reaction: Tasp_WA + Yp => Tasp_WA + Y, Rate Law: cell*k1*Tasp_WA*Yp
k1=0.037Reaction: Yp => Y, Rate Law: cell*k1*Yp
k1=1000000.0; k2=1.0Reaction: T + asp => Tasp, Rate Law: cell*(k1*T*asp-k2*Tasp)
k1=1000.0; k2=1.0Reaction: T + ni => Tni, Rate Law: cell*(k1*T*ni-k2*Tni)
k1=0.01; k2=1.0Reaction: Tni + A => Tni_A, Rate Law: cell*(k1*Tni*A-k2*Tni_A)
k1=0.1; k2=1.0Reaction: Tni + W => Tni_W, Rate Law: cell*(k1*Tni*W-k2*Tni_W)
k1=100000.0; k2=1.0Reaction: T + W => TW, Rate Law: cell*(k1*T*W-k2*TW)
parameter_2 = 0.997008973080758; kcat=0.0Reaction: Y => Yp, Rate Law: cell*kcat*parameter_2*Y

States:

NameDescription
MYp[Flagellar motor switch protein FliM; Chemotaxis protein CheY]
TWA[Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA; Chemotaxis protein CheW]
Z[Protein phosphatase CheZ]
W[Chemotaxis protein CheW]
T[Methyl-accepting chemotaxis protein II]
Tasp[aspartate(1-); Methyl-accepting chemotaxis protein II]
B[Chemotaxis response regulator protein-glutamate methylesterase]
Bp[phosphorylated residue; Chemotaxis response regulator protein-glutamate methylesterase]
M[Flagellar motor switch protein FliM]
Tni[nickel(2+); Methyl-accepting chemotaxis protein II]
A[Chemotaxis protein CheA]
Tasp WA[aspartate(1-); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA; Chemotaxis protein CheW]
Tasp A[aspartate(1-); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA]
Tasp W[aspartate(1-); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheW]
TA[Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA]
WA[Chemotaxis protein CheA; Chemotaxis protein CheW]
Y[Chemotaxis protein CheY]
MYpYp[Chemotaxis protein CheY; Flagellar motor switch protein FliM]
Ap[phosphorylated residue; Chemotaxis protein CheA]
asp[aspartate(1-)]
Yp[phosphorylated residue; Chemotaxis protein CheY]
Tni A[nickel(2+); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA]
ni[nickel(2+)]
TW[Chemotaxis protein CheW; Methyl-accepting chemotaxis protein II]
Tni W[nickel(2+); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheW]
Tni WA[nickel(2+); Methyl-accepting chemotaxis protein II; Chemotaxis protein CheA; Chemotaxis protein CheW]
MYpYpYp[Chemotaxis protein CheY; Flagellar motor switch protein FliM]
MYpYpYpYp[Flagellar motor switch protein FliM; Chemotaxis protein CheY]

Bray1995_chemotaxis_receptorlinkedcomplex: BIOMD0000000200v0.0.1

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 T…

Details

The chemotactic response of bacteria is mediated by complexes containing two molecules each of a transmembrane receptor and the intracellular signaling proteins CheA and CheW. Mutants in which one or the other of the proteins of this complex are absent, inactive, or expressed at elevated amounts show altered chemotactic behavior and the phenotypes are difficult to interpret for some overexpression mutants. We have examined the possibility that these unexpected phenotypes might arise from the binding steps that lead to active complex formation. A limited genetic algorithm was used to search for sets of binding reactions and associated binding constants expected to give mutant phenotypes in accord with experimental data. Different sets of binding equilibria and different assumptions about the activity of particular receptor complexes were tried. Computer analysis demonstrated that it is possible to obtain sets of binding equilibria consistent with the observed phenotypes and provided a simple explanation for these phenotypes in terms of the distribution of active and inactive complexes formed under various conditions. Optimization methods of this kind offer a unique way to analyze reactions taking place inside living cells based on behavioral data. link: http://identifiers.org/pubmed/8573792

Parameters:

NameDescription
k1=0.0511 persec; k2=1000000.0 perMpersecReaction: TTWW => TTW + W, Rate Law: cell*(k1*TTWW-k2*TTW*W)
k1=0.35 persecReaction: Bp => B, Rate Law: cell*k1*Bp
k2=1000000.0 perMpersec; k1=297.0 persecReaction: TTWAA => TT + WAA, Rate Law: cell*(k1*TTWAA-k2*TT*WAA)
k1=0.64 persec; k2=1000000.0 perMpersecReaction: TTWWAA => TTW + WAA, Rate Law: cell*(k1*TTWWAA-k2*TTW*WAA)
k1=727.0 persec; k2=1000000.0 perMpersecReaction: TTWAA => TTW + AA, Rate Law: cell*(k1*TTWAA-k2*TTW*AA)
k1=3.0E7 perMpersecReaction: Y + TTWWAAp => Yp + TTWWAA, Rate Law: cell*k1*Y*TTWWAAp
k1=7.87E-6 persec; k2=1000000.0 perMpersecReaction: TTWWAA => TTWAA + W, Rate Law: cell*(k1*TTWWAA-k2*TTWAA*W)
k1=0.0227 persecReaction: TTAA => TTAAp, Rate Law: cell*k1*TTAA
k1=0.0229 persec; k2=1000000.0 perMpersecReaction: TTWWAA => TT + WWAA, Rate Law: cell*(k1*TTWWAA-k2*TT*WWAA)
k1=500000.0 perMpersecReaction: Yp + Z => Y + Z, Rate Law: cell*k1*Yp*Z
k1=0.00894 persec; k2=1000000.0 perMpersecReaction: WAA => W + AA, Rate Law: cell*(k1*WAA-k2*W*AA)
k1=0.102 persec; k2=1000000.0 perMpersecReaction: WWAA => W + WAA, Rate Law: cell*(k1*WWAA-k2*W*WAA)
k1=6000000.0 perMpersecReaction: B + TTAAp => Bp + TTAA, Rate Law: cell*k1*B*TTAAp
k1=0.0676 persec; k2=1000000.0 perMpersecReaction: TTWAA => TTAA + W, Rate Law: cell*(k1*TTWAA-k2*TTAA*W)
k1=0.037 persecReaction: Yp => Y, Rate Law: cell*k1*Yp
k1=0.112 persec; k2=1000000.0 perMpersecReaction: TTWWAA => TTWW + AA, Rate Law: cell*(k1*TTWWAA-k2*TTWW*AA)
k1=0.00365 persec; k2=1000000.0 perMpersecReaction: TTW => TT + W, Rate Law: cell*(k1*TTW-k2*TT*W)
k1=15.5 persecReaction: TTWWAA => TTWWAAp, Rate Law: cell*k1*TTWWAA
k1=39.3 persec; k2=1000000.0 perMpersecReaction: TTAA => TT + AA, Rate Law: cell*(k1*TTAA-k2*TT*AA)
k1=0.00124 persecReaction: Y => Yp, Rate Law: cell*k1*Y

States:

NameDescription
Z[Protein phosphatase CheZ]
TTAAp[Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
W[Chemotaxis protein CheW]
TTAA[Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
TTWAAp[Chemotaxis protein CheW; Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
TTWWAA[Chemotaxis protein CheW; Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
TTWAA[Chemotaxis protein CheW; Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
TT[Methyl-accepting chemotaxis protein II]
TTWW[Chemotaxis protein CheW; Methyl-accepting chemotaxis protein II]
WWAAp[Chemotaxis protein CheW; Chemotaxis protein CheA]
B[Chemotaxis response regulator protein-glutamate methylesterase]
Bp[Chemotaxis response regulator protein-glutamate methylesterase]
TTW[Chemotaxis protein CheW; Methyl-accepting chemotaxis protein II]
Y[Chemotaxis protein CheY]
Yp[Chemotaxis protein CheY]
TTWWAAp[Chemotaxis protein CheW; Chemotaxis protein CheA; Methyl-accepting chemotaxis protein II]
AA[Chemotaxis protein CheA]
AAp[Chemotaxis protein CheA]
WAA[Chemotaxis protein CheA; Chemotaxis protein CheW]
WWAA[Chemotaxis protein CheW; Chemotaxis protein CheA]
WAAp[Chemotaxis protein CheA; Chemotaxis protein CheW]

Brown1997 - Plasma Melatonin Levels: BIOMD0000000672v0.0.1

Brown1997 - Plasma Melatonin LevelsA mathematical model that incorporates a piecewise function for NAT activity to predi…

Details

Studies in animals and humans suggest that the diurnal pattern in plasma melatonin levels is due to the hormone's rates of synthesis, circulatory infusion and clearance, circadian control of synthesis onset and offset, environmental lighting conditions, and error in the melatonin immunoassay. A two-dimensional linear differential equation model of the hormone is formulated and is used to analyze plasma melatonin levels in 18 normal healthy male subjects during a constant routine. Recently developed Bayesian statistical procedures are used to incorporate correctly the magnitude of the immunoassay error into the analysis. The estimated parameters [median (range)] were clearance half-life of 23.67 (14.79-59.93) min, synthesis onset time of 2206 (1940-0029), synthesis offset time of 0621 (0246-0817), and maximum N-acetyltransferase activity of 7.17(2.34-17.93) pmol x l(-1) x min(-1). All were in good agreement with values from previous reports. The difference between synthesis offset time and the phase of the core temperature minimum was 1 h 15 min (-4 h 38 min-2 h 43 min). The correlation between synthesis onset and the dim light melatonin onset was 0.93. Our model provides a more physiologically plausible estimate of the melatonin synthesis onset time than that given by the dim light melatonin onset and the first reliable means of estimating the phase of synthesis offset. Our analysis shows that the circadian and pharmacokinetics parameters of melatonin can be reliably estimated from a single model. link: http://identifiers.org/pubmed/9124558

Brown2004 - NGF and EGF signaling: BIOMD0000000033v0.0.1

Brown2004 - NGF and EGF signalingThis model is described in the article: [The statistical mechanics of complex signalin…

Details

The inherent complexity of cellular signaling networks and their importance to a wide range of cellular functions necessitates the development of modeling methods that can be applied toward making predictions and highlighting the appropriate experiments to test our understanding of how these systems are designed and function. We use methods of statistical mechanics to extract useful predictions for complex cellular signaling networks. A key difficulty with signaling models is that, while significant effort is being made to experimentally measure the rate constants for individual steps in these networks, many of the parameters required to describe their behavior remain unknown or at best represent estimates. To establish the usefulness of our approach, we have applied our methods toward modeling the nerve growth factor (NGF)-induced differentiation of neuronal cells. In particular, we study the actions of NGF and mitogenic epidermal growth factor (EGF) in rat pheochromocytoma (PC12) cells. Through a network of intermediate signaling proteins, each of these growth factors stimulates extracellular regulated kinase (Erk) phosphorylation with distinct dynamical profiles. Using our modeling approach, we are able to predict the influence of specific signaling modules in determining the integrated cellular response to the two growth factors. Our methods also raise some interesting insights into the design and possible evolution of cellular systems, highlighting an inherent property of these systems that we call 'sloppiness.' link: http://identifiers.org/pubmed/16204838

Parameters:

NameDescription
KmRasGap = 1432410.0; kRasGap = 1509.36Reaction: RasActive => RasInactive; RasGapActive, Rate Law: cell*kRasGap*RasGapActive*RasActive/(RasActive+KmRasGap)
kPI3KRas = 0.0771067; KmPI3KRas = 272056.0Reaction: PI3KInactive => PI3KActive; RasActive, Rate Law: cell*kPI3KRas*RasActive*PI3KInactive/(PI3KInactive+KmPI3KRas)
KmPI3K = 184912.0; kPI3K = 10.6737Reaction: PI3KInactive => PI3KActive; boundEGFReceptor, Rate Law: cell*kPI3K*boundEGFReceptor*PI3KInactive/(PI3KInactive+KmPI3K)
KmNGF = 2112.66; kNGF = 389.428Reaction: SosInactive => SosActive; boundNGFReceptor, Rate Law: cell*kNGF*boundNGFReceptor*SosInactive/(SosInactive+KmNGF)
KmdSos = 896896.0; kdSos = 1611.97Reaction: SosActive => SosInactive; P90RskActive, Rate Law: cell*kdSos*P90RskActive*SosActive/(SosActive+KmdSos)
kpP90Rsk = 0.0213697; KmpP90Rsk = 763523.0Reaction: P90RskInactive => P90RskActive; ErkActive, Rate Law: cell*kpP90Rsk*ErkActive*P90RskInactive/(P90RskInactive+KmpP90Rsk)
kruEGF = 0.0121008Reaction: boundEGFReceptor => EGF + freeEGFReceptor, Rate Law: cell*kruEGF*boundEGFReceptor
KmpBRaf = 157948.0; kpBRaf = 125.089Reaction: MekInactive => MekActive; BRafActive, Rate Law: cell*kpBRaf*BRafActive*MekInactive/(MekInactive+KmpBRaf)
krbEGF = 2.18503E-5Reaction: EGF + freeEGFReceptor => boundEGFReceptor, Rate Law: cell*krbEGF*EGF*freeEGFReceptor
KmEGF = 6086070.0; kEGF = 694.731Reaction: SosInactive => SosActive; boundEGFReceptor, Rate Law: cell*kEGF*boundEGFReceptor*SosInactive/(SosInactive+KmEGF)
kC3GNGF = 146.912; KmC3GNGF = 12876.2Reaction: C3GInactive => C3GActive; boundNGFReceptor, Rate Law: cell*kC3GNGF*boundNGFReceptor*C3GInactive/(C3GInactive+KmC3GNGF)
KmRapGap = 295990.0; kRapGap = 27.265Reaction: Rap1Active => Rap1Inactive; RapGapActive, Rate Law: cell*kRapGap*RapGapActive*Rap1Active/(Rap1Active+KmRapGap)
kdBRaf = 441.287; KmdBRaf = 1.08795E7Reaction: BRafActive => BRafInactive; Raf1PPtase, Rate Law: cell*kdBRaf*Raf1PPtase*BRafActive/(BRafActive+KmdBRaf)
kpRaf1 = 185.759; KmpRaf1 = 4768350.0Reaction: MekInactive => MekActive; Raf1Active, Rate Law: cell*kpRaf1*Raf1Active*MekInactive/(MekInactive+KmpRaf1)
KmAkt = 653951.0; kAkt = 0.0566279Reaction: AktInactive => AktActive; PI3KActive, Rate Law: cell*kAkt*PI3KActive*AktInactive/(AktInactive+KmAkt)
KmRasToRaf1 = 62464.6; kRasToRaf1 = 0.884096Reaction: Raf1Inactive => Raf1Active; RasActive, Rate Law: cell*kRasToRaf1*RasActive*Raf1Inactive/(Raf1Inactive+KmRasToRaf1)
kdErk = 8.8912; KmdErk = 3496490.0Reaction: ErkActive => ErkInactive; PP2AActive, Rate Law: cell*kdErk*PP2AActive*ErkActive/(ErkActive+KmdErk)
kdRaf1 = 0.126329; KmdRaf1 = 1061.71Reaction: Raf1Active => Raf1Inactive; Raf1PPtase, Rate Law: cell*kdRaf1*Raf1PPtase*Raf1Active/(Raf1Active+KmdRaf1)
kSos = 32.344; KmSos = 35954.3Reaction: RasInactive => RasActive; SosActive, Rate Law: cell*kSos*SosActive*RasInactive/(RasInactive+KmSos)
kruNGF = 0.00723811Reaction: boundNGFReceptor => NGF + freeNGFReceptor, Rate Law: kruNGF*boundNGFReceptor*cell
kdMek = 2.83243; KmdMek = 518753.0Reaction: MekActive => MekInactive; PP2AActive, Rate Law: cell*kdMek*PP2AActive*MekActive/(MekActive+KmdMek)
krbNGF = 1.38209E-7Reaction: NGF + freeNGFReceptor => boundNGFReceptor, Rate Law: krbNGF*NGF*freeNGFReceptor*cell
kpMekCytoplasmic = 9.85367; KmpMekCytoplasmic = 1007340.0Reaction: ErkInactive => ErkActive; MekActive, Rate Law: cell*kpMekCytoplasmic*MekActive*ErkInactive/(ErkInactive+KmpMekCytoplasmic)
kdRaf1ByAkt = 15.1212; KmRaf1ByAkt = 119355.0Reaction: Raf1Active => Raf1Inactive; AktActive, Rate Law: cell*kdRaf1ByAkt*AktActive*Raf1Active/(Raf1Active+KmRaf1ByAkt)
kRap1ToBRaf = 2.20995; KmRap1ToBRaf = 1025460.0Reaction: BRafInactive => BRafActive; Rap1Active, Rate Law: cell*kRap1ToBRaf*Rap1Active*BRafInactive/(BRafInactive+KmRap1ToBRaf)
kC3G = 1.40145; KmC3G = 10965.6Reaction: Rap1Inactive => Rap1Active; C3GActive, Rate Law: cell*kC3G*C3GActive*Rap1Inactive/(Rap1Inactive+KmC3G)

States:

NameDescription
freeEGFReceptor[Receptor protein-tyrosine kinase]
boundEGFReceptor[Receptor protein-tyrosine kinase; Pro-epidermal growth factor]
MekActive[Dual specificity mitogen-activated protein kinase kinase 1; Dual specificity mitogen-activated protein kinase kinase 2]
C3GActive[C3G protein]
RasInactive[IPR003577]
EGF[Pro-epidermal growth factor]
C3GInactive[C3G protein]
Rap1Inactive[Ras-related protein Rap-1ARas-related protein Rap-1ARas-related protein Rap-1ARas-related protein Rap-1A; Ras-related protein Rap-1b]
SosInactive[ENSRNOP00000009359; Son of sevenless 1]
Raf1Inactive[RAF proto-oncogene serine/threonine-protein kinase]
boundNGFReceptor[High affinity nerve growth factor receptor; Beta-nerve growth factor]
AktInactive[RAC-alpha serine/threonine-protein kinase; RAC-beta serine/threonine-protein kinase; RAC-gamma serine/threonine-protein kinase]
PI3KActive[IPR015433; phosphatidylinositol 3-kinase complex]
MekInactive[Dual specificity mitogen-activated protein kinase kinase 1; Dual specificity mitogen-activated protein kinase kinase 2]
SosActive[ENSRNOP00000009359; Son of sevenless 1]
Raf1Active[RAF proto-oncogene serine/threonine-protein kinase]
Rap1Active[Ras-related protein Rap-1ARas-related protein Rap-1ARas-related protein Rap-1ARas-related protein Rap-1A; Ras-related protein Rap-1b]
BRafActive[V-raf murine sarcoma viral oncogene B1-like protein]
RasActive[IPR003577]
NGF[Beta-nerve growth factor]
freeNGFReceptor[High affinity nerve growth factor receptor]
ErkInactive[Mitogen-activated protein kinase 3; Mitogen-activated protein kinase 1]
AktActive[RAC-alpha serine/threonine-protein kinase; RAC-beta serine/threonine-protein kinase; RAC-gamma serine/threonine-protein kinase]
PI3KInactive[IPR015433; phosphatidylinositol 3-kinase complex]
ErkActive[Mitogen-activated protein kinase 3; Mitogen-activated protein kinase 1]
BRafInactive[V-raf murine sarcoma viral oncogene B1-like protein]
P90RskActive[p90 S6 kinase; Ribosomal protein S6 kinase alpha-1]
P90RskInactive[p90 S6 kinase; Ribosomal protein S6 kinase alpha-1]

Bruck2008_Glycolysis: MODEL1011010000v0.0.1

**Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis** Jozsef Bruck, Wolfra…

Details

Metabolism is one of the best studied fields of biochemistry, but its regulation involves processes on many different levels, some of which are still not understood well enough to allow for quantitative modeling and prediction. Glycolysis in yeast is a good example: although high-quality quantitative data are available, well-established mathematical models typically only cover direct regulation of the involved enzymes by metabolite binding. The effect of various metabolites on the enzyme kinetics is summarized in carefully developed mathematical formulae. However, this approach implicitly assumes that the enzyme concentrations themselves are constant, thus neglecting other regulatory levels–e.g. transcriptional and translational regulation–involved in the regulation of enzyme activities. It is believed, however, that different experimental conditions result in different enzyme activities regulated by the above mechanisms. Detailed modeling of all regulatory levels is still out of reach since some of the necessary data–e.g. quantitative large scale enzyme concentration data sets–are lacking or rare. Nevertheless, a viable approach is to include the regulation of enzyme concentrations into an established model and to investigate whether this improves the predictive capabilities. Proteome data are usually hard to obtain, but levels of mRNA transcripts may be used instead as clues for changes in enzyme concentrations. Here we investigate whether including mRNA data into an established model of yeast glycolysis allows to predict the steady state metabolic concentrations for different experimental conditions. To this end, we modified an established ODE model for the glycolytic pathway of yeast to include changes of enzyme concentrations. Presumable changes were inferred from mRNA transcript level measurement data. We investigate how this approach can be used to predict metabolite concentrations for steady-state yeast cultures at five different oxygen levels ranging from anaerobic to fully aerobic conditions. We were partly able to reproduce the experimental data and present a number of changes that were necessary to improve the modeling result. link: http://identifiers.org/pubmed/19425118

Bruggeman2005_AmmoniumAssimilation: BIOMD0000000217v0.0.1

This a model from the article: The multifarious short-term regulation of ammonium assimilation of Escherichia coli: di…

Details

Ammonium assimilation in Escherichia coli is regulated through multiple mechanisms (metabolic, signal transduction leading to covalent modification, transcription, and translation), which (in-)directly affect the activities of its two ammonium-assimilating enzymes, i.e. glutamine synthetase (GS) and glutamate dehydrogenase (GDH). Much is known about the kinetic properties of the components of the regulatory network that these enzymes are part of, but the ways in which, and the extents to which the network leads to subtle and quasi-intelligent regulation are unappreciated. To determine whether our present knowledge of the interactions between and the kinetic properties of the components of this network is complete - to the extent that when integrated in a kinetic model it suffices to calculate observed physiological behaviour - we now construct a kinetic model of this network, based on all of the kinetic data on the components that is available in the literature. We use this model to analyse regulation of ammonium assimilation at various carbon statuses for cells that have adapted to low and high ammonium concentrations. We show how a sudden increase in ammonium availability brings about a rapid redirection of the ammonium assimilation flux from GS/glutamate synthase (GOGAT) to GDH. The extent of redistribution depends on the nitrogen and carbon status of the cell. We develop a method to quantify the relative importance of the various regulators in the network. We find the importance is shared among regulators. We confirm that the adenylylation state of GS is the major regulator but that a total of 40% of the regulation is mediated by ADP (22%), glutamate (10%), glutamine (7%) and ATP (1%). The total steady-state ammonium assimilation flux is remarkably robust against changes in the ammonium concentration, but the fluxes through GS and GDH are completely nonrobust. Gene expression of GOGAT above a threshold value makes expression of GS under ammonium-limited conditions, and of GDH under glucose-limited conditions, sufficient for ammonium assimilation. link: http://identifiers.org/pubmed/15819889

Parameters:

NameDescription
Kadp = 0.5; Vadp = 100.0Reaction: ADP => ATP, Rate Law: compartment*Vadp*ADP/(Kadp+ADP)
Kgludemglu = 8.0; Vgludem = 120.0; Kgludemazglu = 0.5; Kgludemeq = 1.0E10Reaction: GLU => AZGLU, Rate Law: compartment*Vgludem*((-AZGLU/Kgludemeq)+GLU)/(Kgludemglu*(1+AZGLU/Kgludemazglu+GLU/Kgludemglu))
Kglndemeq = 1.0E10; Kglndemazgln = 0.25; Kglndemgln = 2.0; Vglndem = 70.0Reaction: GLN => AZGLN, Rate Law: compartment*Vglndem*((-AZGLN/Kglndemeq)+GLN)/(Kglndemgln*(1+AZGLN/Kglndemazgln+GLN/Kglndemgln))
Kgogglu = 11.0; Vgog = 85.0; Kgoggln = 0.175; Kgogkg = 0.007; Kgognadp = 0.0037; Kgognadph = 0.0015; Kgogaz = 0.65Reaction: GLN + NADPH + KG => GLU + NADP; AZGLU, Rate Law: compartment*KG*NADPH*Vgog*GLN/(Kgoggln*Kgogkg*Kgognadph*(1+NADP/Kgognadp+NADPH/Kgognadph)*(1+AZGLU/Kgogaz)*(1+KG/Kgogkg+GLU/Kgogglu)*(1+GLN/Kgoggln+GLU/Kgogglu))
camp = 0.1012; n2amp = 19.2166; bamp = 2.3667; Kgsatp = 0.35; Kgsglu = 4.1; Kgsadp = 0.0585; n1amp = 1.1456; Kgsgln = 5.65; Keq = 460.0 dimensionless; Kgspi = 3.7; damp = 10.8688; aamp = 10.0; Kgsnh = 0.1; Vgs = 600.0; GStot = 0.014Reaction: GLU + ATP + NH4 => P_i + GLN + ADP; AMP, Rate Law: compartment*aamp*camp*Vgs*((-P_i*ADP*GLN/Keq)+NH4*ATP*GLU)/(Kgsatp*Kgsglu*Kgsnh*(1+P_i/Kgspi+ADP/Kgsadp+P_i*ADP/(Kgsadp*Kgspi)+ATP/Kgsatp)*(1+NH4/Kgsnh+GLN/Kgsgln+NH4*GLN/(Kgsgln*Kgsnh)+GLU/Kgsglu+NH4*GLU/(Kgsglu*Kgsnh))*(1+12^n1amp*(AMP/(bamp*GStot))^n1amp)*(1+12^n2amp*(AMP/(damp*GStot))^n2amp))
Keqgdh = 1290.0; Kgdhkg = 0.32; Kgdhnh = 1.1; Vgdh = 360.0; Kgdhglu = 10.0; Kgdhnadp = 0.042; Kgdhnadph = 0.04Reaction: NH4 + KG + NADPH => GLU + NADP, Rate Law: compartment*Vgdh*(KG*NADPH*NH4-NADP*GLU/Keqgdh)/(Kgdhkg*Kgdhnadph*Kgdhnh*(1+NADP/Kgdhnadp+NADPH/Kgdhnadph)*(1+NH4/Kgdhnh)*(1+KG/Kgdhkg+GLU/Kgdhglu))
Kazglndemazinter = 0.5; Kazglndemazgln = 1.0; Vazglndem = 20.0; Kazglndemeq = 1.0E10Reaction: AZGLN => AZgln, Rate Law: compartment*Vazglndem*((-AZgln/Kazglndemeq)+AZGLN)/(Kazglndemazgln*(1+AZgln/Kazglndemazinter+AZGLN/Kazglndemazgln))
Kazgludemazglu = 0.3; Vazgludem = 30.0; Kazgludemazinter = 0.5 dimensionless; Kazgludemeq = 1.0E10 dimensionlessReaction: AZGLU => AZglu, Rate Law: compartment*Vazgludem*((-AZglu/Kazgludemeq)+AZGLU)/(Kazgludemazglu*(1+AZglu/Kazgludemazinter+AZGLU/Kazgludemazglu))
Kglnut = 0.07; Kutpii = 0.003; UT = 6.0E-4; Kutippi = 0.1135; Kutpiiump = 0.0035; kcatut = 137.0; Kutipii = 0.0018; Kututp = 0.04Reaction: PIIUMP2 + UTP => PIIUMP3 + PPi; GLN, PII, PIIUMP, Rate Law: compartment*kcatut*UT*UTP*PIIUMP2/(Kutipii*Kututp*(1+GLN/Kglnut)*(1+UTP/Kututp+(PII+PIIUMP+PIIUMP2)/Kutipii+UTP*(PII+PIIUMP+PIIUMP2)/(Kutipii*Kututp)+PPi*UTP*(PII+PIIUMP+PIIUMP2)/(Kutipii*Kutippi*Kututp)+Kutpii*(PIIUMP+PIIUMP2+PIIUMP3)/(Kutipii*Kutpiiump)))
Kdeadpiiu = 1.805E-5; Kdeadpiikg = 2.274E-6; n1 = 8.491; Kd2 = 0.15; g1 = 3.323; m1 = 0.8821; Kd1piiump = 0.025; k1 = 1.0E-22; Vdead = 0.5; Kdeadgln = 0.04444; Kd3piiump = 0.15; Kdeadgsa = 2.015E-4; j1 = 1.0E-22; Kd3 = 0.15; i1 = 1.0E-22; f1 = 2.766; o1 = 0.8791; Kd1 = 0.005; e1 = 1.0E-22; h1 = 0.2148; l1 = 0.02316; Kd2piiump = 0.15Reaction: AMP => GS; GLN, PII, PIIUMP3, KG, Rate Law: compartment*Vdead*AMP*(f1*GLN/Kdeadgln+3*e1*KG*PII/(Kd1*Kdeadpiikg*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))+3*h1*KG*GLN*PII/(Kd1*Kdeadgln*Kdeadpiikg*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))+g1*KG^3*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiiu*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)))+j1*KG^3*GLN*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiiu*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)))+3*i1*KG^4*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiikg*Kdeadpiiu*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)))+3*k1*KG^4*GLN*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiikg*Kdeadpiiu*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))))/((Kdeadgsa+AMP)*(1+GLN/Kdeadgln+3*KG*PII/(Kd1*Kdeadpiikg*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))+3*KG*GLN*PII/(Kd1*Kdeadgln*Kdeadpiikg*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))*l1)+KG^3*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiiu*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)))+KG^3*GLN*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiiu*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*n1)+3*KG^4*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiikg*Kdeadpiiu*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*m1)+3*KG^4*GLN*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiikg*Kdeadpiiu*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))*(1+3*KG/Kd1piiump+3*KG^2/(Kd1piiump*Kd2piiump)+KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*o1)))
Kglnur = 0.07; Kurump = 8.4; kcatur = 5.5; Kurpiiump = 0.0023; UR = 6.0E-4Reaction: PIIUMP => PII + UMP; GLN, PIIUMP2, PIIUMP3, Rate Law: compartment*kcatur*UR*PIIUMP/(Kurpiiump*(1+Kglnur/GLN)*(1+(1+UMP/Kurump)*(PIIUMP+PIIUMP2+PIIUMP3)/Kurpiiump))
Kadgln = 0.9714; Kadgs = 0.001703; Kadpiikg = 1.052E-5; d1 = 0.0387; a1 = 1.0E-22; Vad = 0.5; Kd1 = 0.005; b1 = 0.5166; c1 = 0.5974; Kd3 = 0.15; Kd2 = 0.15Reaction: GS => AMP; GLN, PII, KG, Rate Law: compartment*Vad*GS*(b1*GLN/Kadgln+3*a1*KG*PII/(Kadpiikg*Kd1*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))+3*c1*KG*GLN*PII/(Kadgln*Kadpiikg*Kd1*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3))))/((Kadgs+GS)*(1+GLN/Kadgln+3*KG*PII/(Kadpiikg*Kd1*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))+3*KG*GLN*PII/(d1*Kadgln*Kadpiikg*Kd1*(1+3*KG/Kd1+3*KG^2/(Kd1*Kd2)+KG^3/(Kd1*Kd2*Kd3)))))

States:

NameDescription
GLN[L-glutamine residue; Glutamine]
ATP[ATP; ATP]
PIIUMPPIIUMP
AZglnAZgln
PIIUMP3PIIUMP3
AMP[AMP; AMP]
NADPH[NADPH; NADPH]
UTP[UTP; UTP]
PPi[diphosphate(4-); Diphosphate]
KG[Alpha-ketoglutarate permease]
AZGLUAZGLU
NADP[NADP(+); NADP+]
UMP[UMP; UMP]
P i[hydrogenphosphate]
GS[Glutamine synthetase]
AZGLNAZGLN
PIIUMP2PIIUMP2
NH4[ammonium; NH4+]
AZgluAZglu
PII[Nitrogen regulatory protein P-II 1]
ADP[ADP; ADP]
GLU[L-glutamic acid; L-Glutamate]

Brummel-Ziedins2012 - Contribution of the PC pathway to thrombin generation: MODEL1807180002v0.0.1

Mathematical model of the blood coagulation cascade including meizothrombin, protein C, thrombomodulin, factor VIIIa fra…

Details

The underlying cause of thrombosis in a large protein C (PC) deficient Vermont kindred appears to be multicausal and not explained by PC deficiency alone. We evaluated the contribution of coagulation factors to thrombin generation in this population utilizing a mathematical model that incorporates a mechanistic description of the PC pathway. Thrombin generation profiles for each individual were generated with and without the contribution of the PC pathway. Parameters that describe thrombin generation: maximum level (MaxL) and rate (MaxR), their respective times (TMaxL, TMaxR), area under the curve (AUC) and clotting time (CT) were examined in individuals ± PC mutation, ± prothrombin G20210A polymorphism and ± thrombosis history (DVT or PE). This family (n = 364) is shifted towards greater thrombin generation relative to the mean physiologic control. When this family was analyzed with the PC pathway, our results showed that: carriers of the PC mutation (n = 81) had higher MaxL and MaxR and greater AUC (all p<0.001) than non-carriers (n = 283); and individuals with a DVT and/or PE history (n = 13) had higher MaxL (p = 0.005) and greater AUC (p<0.001) than individuals without a thrombosis history (n = 351). These differences were further stratified by gender, with women in all categories generating more thrombin than males. These results show that all individuals within this family with or without PC deficiency have an increased baseline procoagulant potential reflective of increased thrombin generation. In addition, variations within the plasma composition of each individual can further segregate out increased procoagulant phenotypes, with gender-associated plasma compositional differences playing a large role. link: http://identifiers.org/pubmed/22984498

Brännmark2013 - Insulin signalling in human adipocytes (diabetic condition): BIOMD0000000449v0.0.1

Brännmark2013 - Insulin signalling in human adipocytes (diabetic condition)The paper describes insulin signalling in hum…

Details

Type 2 diabetes originates in an expanding adipose tissue that for unknown reasons becomes insulin resistant. Insulin resistance reflects impairments in insulin signaling, but mechanisms involved are unclear because current research is fragmented. We report a systems level mechanistic understanding of insulin resistance, using systems wide and internally consistent data from human adipocytes. Based on quantitative steady-state and dynamic time course data on signaling intermediaries, normally and in diabetes, we developed a dynamic mathematical model of insulin signaling. The model structure and parameters are identical in the normal and diabetic states of the model, except for three parameters that change in diabetes: (i) reduced concentration of insulin receptor, (ii) reduced concentration of insulin-regulated glucose transporter GLUT4, and (iii) changed feedback from mammalian target of rapamycin in complex with raptor (mTORC1). Modeling reveals that at the core of insulin resistance in human adipocytes is attenuation of a positive feedback from mTORC1 to the insulin receptor substrate-1, which explains reduced sensitivity and signal strength throughout the signaling network. Model simulations with inhibition of mTORC1 are comparable with experimental data on inhibition of mTORC1 using rapamycin in human adipocytes. We demonstrate the potential of the model for identification of drug targets, e.g. increasing the feedback restores insulin signaling, both at the cellular level and, using a multilevel model, at the whole body level. Our findings suggest that insulin resistance in an expanded adipose tissue results from cell growth restriction to prevent cell necrosis. link: http://identifiers.org/pubmed/23400783

Parameters:

NameDescription
n9 = 0.9855; km9 = 5873.0; k9f1 = 0.1298Reaction: S6K => S6Kp; mTORC1a, S6K, mTORC1a, Rate Law: S6K*k9f1*mTORC1a^n9/(km9^n9+mTORC1a^n9)
k5d = 1.06Reaction: mTORC2a => mTORC2; mTORC2a, Rate Law: k5d*mTORC2a
k2d = 280.8Reaction: IRS1p307 => IRS1p; IRS1p307, Rate Law: IRS1p307*k2d
k1c = 0.8768Reaction: IRins => IRp; IRins, Rate Law: IRins*k1c
k1f = 1840.0Reaction: IRip => IRi; Xp, IRip, Xp, Rate Law: IRip*k1f*Xp
k5a2 = 0.05506; k5a1 = 1.842Reaction: mTORC1 => mTORC1a; PKB308p, PKB308p473p, mTORC1, PKB308p473p, PKB308p, Rate Law: mTORC1*(k5a1*PKB308p473p+k5a2*PKB308p)
k4h = 0.5361Reaction: PKB473p => PKB; PKB473p, Rate Law: k4h*PKB473p
k3a = 0.001377Reaction: X => Xp; IRS1p, X, IRS1p, Rate Law: X*k3a*IRS1p
k9f2 = 3.329Reaction: S6 => S6p; S6Kp, S6, S6Kp, Rate Law: S6*k9f2*S6Kp
k7f = 50.98Reaction: GLUT4 => GLUT4m; AS160p, GLUT4, AS160p, Rate Law: GLUT4*k7f*AS160p
k4a = 5790.0Reaction: PKB => PKB308p; IRS1p, PKB, IRS1p, Rate Law: k4a*PKB*IRS1p
k2g = 0.2671Reaction: IRS1307 => IRS1; IRS1307, Rate Law: IRS1307*k2g
k1r = 0.5471Reaction: IRi => IR; IRi, Rate Law: IRi*k1r
k4e = 42.84Reaction: PKB473p => PKB308p473p; IRS1p307, PKB473p, IRS1p307, Rate Law: k4e*PKB473p*IRS1p307
k4c = 4.456Reaction: PKB308p => PKB308p473p; mTORC2a, PKB308p, mTORC2a, Rate Law: k4c*PKB308p*mTORC2a
k6f1 = 2.652; k6f2 = 36.93; km6 = 30.54; n6 = 2.137Reaction: AS160 => AS160p; PKB308p473p, PKB473p, AS160, PKB308p473p, PKB473p, Rate Law: AS160*(k6f1*PKB308p473p+k6f2*PKB473p^n6/(km6^n6+PKB473p^n6))
k2c = 5759.0; diabetes = 0.15Reaction: IRS1p => IRS1p307; mTORC1a, IRS1p, mTORC1a, Rate Law: IRS1p*k2c*mTORC1a*diabetes
k1a = 0.6331; insulin = 10.0Reaction: IR => IRins; IR, Rate Law: IR*k1a*insulin
k2a = 3.227Reaction: IRS1 => IRS1p; IRip, IRS1, IRip, Rate Law: IRS1*k2a*IRip
k5b = 24.83Reaction: mTORC1a => mTORC1; mTORC1a, Rate Law: mTORC1a*k5b
k5c = 0.08575Reaction: mTORC2 => mTORC2a; IRip, mTORC2, IRip, Rate Law: mTORC2*k5c*IRip
k6b = 65.18Reaction: AS160p => AS160; AS160p, Rate Law: AS160p*k6b
k1d = 31.01Reaction: IRp => IRip; IRp, Rate Law: IRp*k1d
k1basal = 0.03683Reaction: IR => IRp; IR, Rate Law: k1basal*IR
k2b = 3424.0Reaction: IRS1p => IRS1; IRS1p, Rate Law: IRS1p*k2b
k2f = 2.913Reaction: IRS1p307 => IRS1307; IRS1p307, Rate Law: IRS1p307*k2f
k4b = 34.8Reaction: PKB308p => PKB; PKB308p, Rate Law: k4b*PKB308p
k9b1 = 0.04441Reaction: S6Kp => S6K; S6Kp, Rate Law: S6Kp*k9b1
k7b = 2286.0Reaction: GLUT4m => GLUT4; GLUT4m, Rate Law: GLUT4m*k7b
k2basal = 0.04228Reaction: IRS1 => IRS1307; IRS1, Rate Law: IRS1*k2basal
k9b2 = 31.0Reaction: S6p => S6; S6p, Rate Law: S6p*k9b2
k4f = 143.6Reaction: PKB308p473p => PKB473p; PKB308p473p, Rate Law: k4f*PKB308p473p
k1g = 1944.0Reaction: IRp => IR; IRp, Rate Law: IRp*k1g
k3b = 0.09876Reaction: Xp => X; Xp, Rate Law: Xp*k3b

States:

NameDescription
GLUT4m[Solute carrier family 2, facilitated glucose transporter member 4; plasma membrane]
IRi[Insulin receptor]
PKB473p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
IRip[Insulin receptor; Phosphoprotein]
IR[Insulin receptor]
S6Kp[Ribosomal protein S6 kinase beta-1; Phosphoprotein]
S6K[Ribosomal protein S6 kinase beta-1]
S6p[40S ribosomal protein S6; Phosphoprotein]
PKB308p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
mTORC2[Serine/threonine-protein kinase mTOR; Rapamycin-insensitive companion of mTOR]
X[protein; Intermediate]
IRS1307[Insulin receptor substrate 1]
GLUT4[Solute carrier family 2, facilitated glucose transporter member 4]
AS160p[phosphorylated; TBC1 domain family member 4]
mTORC1[Serine/threonine-protein kinase mTOR; Regulatory-associated protein of mTOR]
PKB[RAC-beta serine/threonine-protein kinase]
AS160[TBC1 domain family member 4]
IRS1[Insulin receptor substrate 1]
IRp[Insulin receptor; Phosphoprotein]
IRins[Insulin receptor]
IRS1p[Insulin receptor substrate 1; Phosphoprotein]
mTORC1a[Serine/threonine-protein kinase mTOR; Regulatory-associated protein of mTOR]
IRS1p307[Insulin receptor substrate 1; Phosphoprotein; urn:miriam:mod:MOD%3A00046]
S6[40S ribosomal protein S6]
PKB308p473p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
mTORC2a[Serine/threonine-protein kinase mTOR; Rapamycin-insensitive companion of mTOR]
Xp[Phosphoprotein; Intermediate]

Brännmark2013 - Insulin signalling in human adipocytes (normal condition): BIOMD0000000448v0.0.1

Brännmark2013 - Insulin signalling in human adipocytes (normal condition)The paper describes insulin signalling in human…

Details

Type 2 diabetes originates in an expanding adipose tissue that for unknown reasons becomes insulin resistant. Insulin resistance reflects impairments in insulin signaling, but mechanisms involved are unclear because current research is fragmented. We report a systems level mechanistic understanding of insulin resistance, using systems wide and internally consistent data from human adipocytes. Based on quantitative steady-state and dynamic time course data on signaling intermediaries, normally and in diabetes, we developed a dynamic mathematical model of insulin signaling. The model structure and parameters are identical in the normal and diabetic states of the model, except for three parameters that change in diabetes: (i) reduced concentration of insulin receptor, (ii) reduced concentration of insulin-regulated glucose transporter GLUT4, and (iii) changed feedback from mammalian target of rapamycin in complex with raptor (mTORC1). Modeling reveals that at the core of insulin resistance in human adipocytes is attenuation of a positive feedback from mTORC1 to the insulin receptor substrate-1, which explains reduced sensitivity and signal strength throughout the signaling network. Model simulations with inhibition of mTORC1 are comparable with experimental data on inhibition of mTORC1 using rapamycin in human adipocytes. We demonstrate the potential of the model for identification of drug targets, e.g. increasing the feedback restores insulin signaling, both at the cellular level and, using a multilevel model, at the whole body level. Our findings suggest that insulin resistance in an expanded adipose tissue results from cell growth restriction to prevent cell necrosis. link: http://identifiers.org/pubmed/23400783

Parameters:

NameDescription
k5d = 1.06Reaction: mTORC2a => mTORC2; mTORC2a, Rate Law: k5d*mTORC2a
n9 = 0.9855; km9 = 5873.0; k9f1 = 0.1298Reaction: S6K => S6Kp; mTORC1a, S6K, mTORC1a, Rate Law: S6K*k9f1*mTORC1a^n9/(km9^n9+mTORC1a^n9)
k3b = 0.09876Reaction: Xp => X; Xp, Rate Law: Xp*k3b
k1c = 0.8768Reaction: IRins => IRp; IRins, Rate Law: IRins*k1c
k1f = 1840.0Reaction: IRip => IRi; Xp, IRip, Xp, Rate Law: IRip*k1f*Xp
k5a2 = 0.05506; k5a1 = 1.842Reaction: mTORC1 => mTORC1a; PKB308p, PKB308p473p, mTORC1, PKB308p473p, PKB308p, Rate Law: mTORC1*(k5a1*PKB308p473p+k5a2*PKB308p)
k3a = 0.001377Reaction: X => Xp; IRS1p, X, IRS1p, Rate Law: X*k3a*IRS1p
k4h = 0.5361Reaction: PKB473p => PKB; PKB473p, Rate Law: k4h*PKB473p
k9f2 = 3.329Reaction: S6 => S6p; S6Kp, S6, S6Kp, Rate Law: S6*k9f2*S6Kp
k7f = 50.98Reaction: GLUT4 => GLUT4m; AS160p, GLUT4, AS160p, Rate Law: GLUT4*k7f*AS160p
k4a = 5790.0Reaction: PKB => PKB308p; IRS1p, PKB, IRS1p, Rate Law: k4a*PKB*IRS1p
k2g = 0.2671Reaction: IRS1307 => IRS1; IRS1307, Rate Law: IRS1307*k2g
k1r = 0.5471Reaction: IRi => IR; IRi, Rate Law: IRi*k1r
k4e = 42.84Reaction: PKB473p => PKB308p473p; IRS1p307, PKB473p, IRS1p307, Rate Law: k4e*PKB473p*IRS1p307
k4c = 4.456Reaction: PKB308p => PKB308p473p; mTORC2a, PKB308p, mTORC2a, Rate Law: k4c*PKB308p*mTORC2a
k6f1 = 2.652; k6f2 = 36.93; km6 = 30.54; n6 = 2.137Reaction: AS160 => AS160p; PKB308p473p, PKB473p, AS160, PKB308p473p, PKB473p, Rate Law: AS160*(k6f1*PKB308p473p+k6f2*PKB473p^n6/(km6^n6+PKB473p^n6))
k2c = 5759.0; diabetes = 1.0Reaction: IRS1p => IRS1p307; mTORC1a, IRS1p, mTORC1a, Rate Law: IRS1p*k2c*mTORC1a*diabetes
k5b = 24.83Reaction: mTORC1a => mTORC1; mTORC1a, Rate Law: mTORC1a*k5b
k1a = 0.6331; insulin = 10.0Reaction: IR => IRins; IR, Rate Law: IR*k1a*insulin
k2a = 3.227Reaction: IRS1 => IRS1p; IRip, IRS1, IRip, Rate Law: IRS1*k2a*IRip
k5c = 0.08575Reaction: mTORC2 => mTORC2a; IRip, mTORC2, IRip, Rate Law: mTORC2*k5c*IRip
k6b = 65.18Reaction: AS160p => AS160; AS160p, Rate Law: AS160p*k6b
k1d = 31.01Reaction: IRp => IRip; IRp, Rate Law: IRp*k1d
k1basal = 0.03683Reaction: IR => IRp; IR, Rate Law: k1basal*IR
k4b = 34.8Reaction: PKB308p => PKB; PKB308p, Rate Law: k4b*PKB308p
k2b = 3424.0Reaction: IRS1p => IRS1; IRS1p, Rate Law: IRS1p*k2b
k9b1 = 0.04441Reaction: S6Kp => S6K; S6Kp, Rate Law: S6Kp*k9b1
k2f = 2.913Reaction: IRS1p307 => IRS1307; IRS1p307, Rate Law: IRS1p307*k2f
k7b = 2286.0Reaction: GLUT4m => GLUT4; GLUT4m, Rate Law: GLUT4m*k7b
k2basal = 0.04228Reaction: IRS1 => IRS1307; IRS1, Rate Law: IRS1*k2basal
k9b2 = 31.0Reaction: S6p => S6; S6p, Rate Law: S6p*k9b2
k4f = 143.6Reaction: PKB308p473p => PKB473p; PKB308p473p, Rate Law: k4f*PKB308p473p
k1g = 1944.0Reaction: IRp => IR; IRp, Rate Law: IRp*k1g
k2d = 280.8Reaction: IRS1p307 => IRS1p; IRS1p307, Rate Law: IRS1p307*k2d

States:

NameDescription
GLUT4m[Solute carrier family 2, facilitated glucose transporter member 4; plasma membrane]
IRi[Insulin receptor]
PKB473p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
IRip[Insulin receptor; Phosphoprotein]
IR[Insulin receptor]
S6Kp[Ribosomal protein S6 kinase beta-1; Phosphoprotein]
S6K[Ribosomal protein S6 kinase beta-1]
S6p[40S ribosomal protein S6; Phosphoprotein]
PKB308p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
mTORC2[Serine/threonine-protein kinase mTOR; Rapamycin-insensitive companion of mTOR]
X[protein; Intermediate]
GLUT4[Solute carrier family 2, facilitated glucose transporter member 4]
IRS1307[Insulin receptor substrate 1]
AS160p[TBC1 domain family member 4; phosphorylated]
mTORC1[Serine/threonine-protein kinase mTOR; Regulatory-associated protein of mTOR]
PKB[RAC-beta serine/threonine-protein kinase]
IRS1[Insulin receptor substrate 1]
AS160[TBC1 domain family member 4]
IRS1p[Insulin receptor substrate 1; Phosphoprotein]
IRins[Insulin receptor; Insulin]
IRp[Insulin receptor; Phosphoprotein]
mTORC1a[Serine/threonine-protein kinase mTOR; Regulatory-associated protein of mTOR]
IRS1p307[Insulin receptor substrate 1; Phosphoprotein; MOD:00046]
S6[40S ribosomal protein S6]
PKB308p473p[RAC-beta serine/threonine-protein kinase; Phosphoprotein]
mTORC2a[Serine/threonine-protein kinase mTOR; Rapamycin-insensitive companion of mTOR]
Xp[Phosphoprotein; Intermediate]

Bucher2011_Atorvastatin_Metabolism: BIOMD0000000328v0.0.1

This is the model of atorvastatin metabolism in hepaitc cells described in the article: A systems biology approach to d…

Details

BACKGROUND: The individual character of pharmacokinetics is of great importance in the risk assessment of new drug leads in pharmacological research. Amongst others, it is severely influenced by the properties and inter-individual variability of the enzymes and transporters of the drug detoxification system of the liver. Predicting individual drug biotransformation capacity requires quantitative and detailed models. RESULTS: In this contribution we present the de novo deterministic modeling of atorvastatin biotransformation based on comprehensive published knowledge on involved metabolic and transport pathways as well as physicochemical properties. The model was evaluated on primary human hepatocytes and parameter identifiability analysis was performed under multiple experimental constraints. Dynamic simulations of atorvastatin biotransformation considering the inter-individual variability of the two major involved enzymes CYP3A4 and UGT1A3 based on quantitative protein expression data in a large human liver bank (n = 150) highlighted the variability in the individual biotransformation profiles and therefore also points to the individuality of pharmacokinetics. CONCLUSIONS: A dynamic model for the biotransformation of atorvastatin has been developed using quantitative metabolite measurements in primary human hepatocytes. The model comprises kinetics for transport processes and metabolic enzymes as well as population liver expression data allowing us to assess the impact of inter-individual variability of concentrations of key proteins. Application of computational tools for parameter sensitivity analysis enabled us to considerably improve the validity of the model and to create a consistent framework for precise computer-aided simulations in toxicology. link: http://identifiers.org/pubmed/21548957

Parameters:

NameDescription
Export_ASL_k = 0.021822 ml per minuteReaction: ASL_c => ASL_m, Rate Law: Export_ASL_k*ASL_c
Export_ASpOH_k = 7.9526E-4 ml per minuteReaction: ASpOH_c => ASpOH_m, Rate Law: Export_ASpOH_k*ASpOH_c
Import_ASLpOH_k = 0.033729 ml per minuteReaction: ASLpOH_m => ASLpOH_c, Rate Law: Import_ASLpOH_k*ASLpOH_m
k_CR_ASL_c = 3.55E-5 ml per minute; k_PON_OH_c = 0.0039829 ml per minuteReaction: ASLoOH_c => ASoOH_c, Rate Law: (k_CR_ASL_c+k_PON_OH_c)*ASLoOH_c
Import_AS_k = 0.020335 ml per minuteReaction: AS_m => AS_c, Rate Law: Import_AS_k*AS_m
CYP3A4_ASpOH_Km1 = 25600.0 pmole per ml; CYP3A4_ASLoOH_Km1 = 3900.0 pmole per ml; CYP3A4_ASLpOH_Km1 = 1400.0 pmole per ml; CYP3A4_ASoOH_Km1 = 29700.0 pmole per ml; CYP3A4_ASLpOH_Vmax = 17.4446 pmole per minuteReaction: ASL_c => ASLpOH_c; AS_c, Rate Law: CYP3A4_ASLpOH_Vmax/CYP3A4_ASLpOH_Km1*ASL_c/(1+AS_c/CYP3A4_ASpOH_Km1+AS_c/CYP3A4_ASoOH_Km1+ASL_c/CYP3A4_ASLpOH_Km1+ASL_c/CYP3A4_ASLoOH_Km1)
Import_ASoOH_k = 3.8875E-4 ml per minuteReaction: ASoOH_m => ASoOH_c, Rate Law: Import_ASoOH_k*ASoOH_m
CYP3A4_ASpOH_Km1 = 25600.0 pmole per ml; CYP3A4_ASLoOH_Km1 = 3900.0 pmole per ml; CYP3A4_ASpOH_Vmax = 15.7336 pmole per minute; CYP3A4_ASLpOH_Km1 = 1400.0 pmole per ml; CYP3A4_ASoOH_Km1 = 29700.0 pmole per mlReaction: AS_c => ASpOH_c; ASL_c, Rate Law: CYP3A4_ASpOH_Vmax/CYP3A4_ASpOH_Km1*AS_c/(1+AS_c/CYP3A4_ASpOH_Km1+AS_c/CYP3A4_ASoOH_Km1+ASL_c/CYP3A4_ASLpOH_Km1+ASL_c/CYP3A4_ASLoOH_Km1)
CYP3A4_ASpOH_Km1 = 25600.0 pmole per ml; CYP3A4_ASLoOH_Km1 = 3900.0 pmole per ml; CYP3A4_ASLpOH_Km1 = 1400.0 pmole per ml; CYP3A4_ASLoOH_Vmax = 39.1342 pmole per minute; CYP3A4_ASoOH_Km1 = 29700.0 pmole per mlReaction: ASL_c => ASLoOH_c; AS_c, Rate Law: CYP3A4_ASLoOH_Vmax/CYP3A4_ASLoOH_Km1*ASL_c/(1+AS_c/CYP3A4_ASpOH_Km1+AS_c/CYP3A4_ASoOH_Km1+ASL_c/CYP3A4_ASLpOH_Km1+ASL_c/CYP3A4_ASLoOH_Km1)
k_PON_ASL_c = 0.0043734 ml per minute; k_CR_ASL_c = 3.55E-5 ml per minuteReaction: ASL_c => AS_c, Rate Law: (k_CR_ASL_c+k_PON_ASL_c)*ASL_c
Export_ASLoOH_k = 0.0026674 ml per minuteReaction: ASLoOH_c => ASLoOH_m, Rate Law: Export_ASLoOH_k*ASLoOH_c
fu_AS = 0.22 dimensionless; Prot_k1 = 8.52 ml per minuteReaction: AS_c => AS_b, Rate Law: Prot_k1*((1-fu_AS)/fu_AS*AS_c-AS_b)
Export_AS_k = 0.002166 ml per minuteReaction: AS_c => AS_m, Rate Law: Export_AS_k*AS_c
k_CR_ASL_m = 0.005 ml per minuteReaction: ASL_m => AS_m, Rate Law: k_CR_ASL_m*ASL_m
UGT1A3_AS_KI1 = 75000.0 pmole per ml; UGT1A3_AS_Vmax = 13.5862 pmole per minute; UGT1A3_AS_Km1 = 12000.0 pmole per mlReaction: AS_c => ASL_c, Rate Law: UGT1A3_AS_Vmax*AS_c/(UGT1A3_AS_Km1+AS_c+AS_c*AS_c/UGT1A3_AS_KI1)
Export_ASLpOH_k = 0.0011319 ml per minuteReaction: ASLpOH_c => ASLpOH_m, Rate Law: Export_ASLpOH_k*ASLpOH_c
Import_ASL_k = 0.2754 ml per minuteReaction: ASL_m => ASL_c, Rate Law: Import_ASL_k*ASL_m
Import_ASLoOH_k = 0.026122 ml per minuteReaction: ASLoOH_m => ASLoOH_c, Rate Law: Import_ASLoOH_k*ASLoOH_m
Import_ASpOH_k = 0.0039614 ml per minuteReaction: ASpOH_m => ASpOH_c, Rate Law: Import_ASpOH_k*ASpOH_m
Export_ASoOH_k = 0.0015983 ml per minuteReaction: ASoOH_c => ASoOH_m, Rate Law: Export_ASoOH_k*ASoOH_c
fu_ASL = 0.22 dimensionless; Prot_k1 = 8.52 ml per minuteReaction: ASL_c => ASL_b, Rate Law: Prot_k1*((1-fu_ASL)/fu_ASL*ASL_c-ASL_b)
CYP3A4_ASoOH_Vmax = 47.4985 pmole per minute; CYP3A4_ASpOH_Km1 = 25600.0 pmole per ml; CYP3A4_ASLoOH_Km1 = 3900.0 pmole per ml; CYP3A4_ASLpOH_Km1 = 1400.0 pmole per ml; CYP3A4_ASoOH_Km1 = 29700.0 pmole per mlReaction: AS_c => ASoOH_c; ASL_c, Rate Law: CYP3A4_ASoOH_Vmax/CYP3A4_ASoOH_Km1*AS_c/(1+AS_c/CYP3A4_ASpOH_Km1+AS_c/CYP3A4_ASoOH_Km1+ASL_c/CYP3A4_ASLpOH_Km1+ASL_c/CYP3A4_ASLoOH_Km1)

States:

NameDescription
ASL c[6483036]
AS m[atorvastatin; 60823]
ASL b[6483036]
AS b[atorvastatin]
ASpOH c[atorvastatin]
AS c[atorvastatin]
ASLpOH b[6483036]
ASLoOH c[6483036]
ASLoOH m[6483036]
ASoOH b[atorvastatin]
ASLoOH b[6483036]
ASL m[6483036]
ASoOH c[atorvastatin]
ASoOH m[atorvastatin]
ASLpOH m[6483036]
ASpOH m[atorvastatin]
ASpOH b[atorvastatin]
ASLpOH c[6483036]

Budding yeast size control by titration of nuclear sites: BIOMD0000000856v0.0.1

This model is decribed in the article: Dilution and titration of cell-cycle regulators may control cell size in budding…

Details

The size of a cell sets the scale for all biochemical processes within it, thereby affecting cellular fitness and survival. Hence, cell size needs to be kept within certain limits and relatively constant over multiple generations. However, how cells measure their size and use this information to regulate growth and division remains controversial. Here, we present two mechanistic mathematical models of the budding yeast (S. cerevisiae) cell cycle to investigate competing hypotheses on size control: inhibitor dilution and titration of nuclear sites. Our results suggest that an inhibitor-dilution mechanism, in which cell growth dilutes the transcriptional inhibitor Whi5 against the constant activator Cln3, can facilitate size homeostasis. This is achieved by utilising a positive feedback loop to establish a fixed size threshold for the START transition, which efficiently couples cell growth to cell cycle progression. Yet, we show that inhibitor dilution cannot reproduce the size of mutants that alter the cell’s overall ploidy and WHI5 gene copy number. By contrast, size control through titration of Cln3 against a constant number of genomic binding sites for the transcription factor SBF recapitulates both size homeostasis and the size of these mutant strains. Moreover, this model produces an imperfect ‘sizer’ behaviour in G1 and a ‘timer’ in S/G2/M, which combine to yield an ‘adder’ over the whole cell cycle; an observation recently made in experiments. Hence, our model connects these phenomenological data with the molecular details of the cell cycle, providing a systems-level perspective of budding yeast size control. link: http://identifiers.org/doi/10.1371/journal.pcbi.1006548

Parameters:

NameDescription
kDeCln = 1.0 1/minReaction: CLN =>, Rate Law: kDeCln*CLN
GCN = 1.0 #; GDt = 500.0 #; kSyCdc = 0.042 AU/(#*min)Reaction: => CDCi; GDTM, Rate Law: tV*kSyCdc*GDTM/tV*GCN/GDt
kDeClb = 0.01 1/min; kDeClbCdh = 2.0 AV/(AU*min)Reaction: CLB => ; CDHa, Rate Law: tV*(kDeClb+kDeClbCdh*CDHa/tV)*CLB/tV
kDpSbf = 0.2 1/minReaction: SBFp => SBFu, Rate Law: kDpSbf*SBFp
kInCdhCln = 0.125 1/min; jCdh = 0.001 AU/AV; kInCdhClb = 2.0 1/minReaction: CDHa => CDHi; CLN, CLB, Rate Law: tV*(kInCdhCln*CLN/tV+kInCdhClb*CLB/tV)*CDHa/tV/(jCdh+CDHa/tV)
GCN = 1.0 #; kSyCdh = 0.042 AU/(#*min); GDt = 500.0 #Reaction: => CDHi; GDTM, Rate Law: tV*kSyCdh*GDTM/tV*GCN/GDt
jCdh = 0.001 AU/AV; kAcCdh = 0.01 AU/(AV*min); kAcCdhCdc = 2.0 1/minReaction: CDHi => CDHa; CDCa, Rate Law: tV*(kAcCdh+kAcCdhCdc*CDCa/tV)*CDHi/tV/(jCdh+CDHi/tV)
kPhWhiCln3 = 1.0 1/minReaction: CLN3WHISBF => CLN3 + WHIpSBF, Rate Law: kPhWhiCln3*CLN3WHISBF
kPhWhiCln = 100.0 AV/(AU*min)Reaction: WHI => WHIp; CLN, Rate Law: tV*kPhWhiCln*CLN/tV*WHI/tV
kAsGdTm = 1.0 AV/(#*min); kDsGdTm = 1.0 1/minReaction: TM + GD => GDTM, Rate Law: tV*(kAsGdTm*TM/tV*GD/tV-kDsGdTm*GDTM/tV)
kDpWhi = 1.0 1/minReaction: WHIp => WHI, Rate Law: kDpWhi*WHIp
jCdc = 0.001 AU/AV; kInCdc = 0.25 AU/(AV*min)Reaction: CDCa => CDCi, Rate Law: tV*kInCdc*CDCa/tV/(jCdc+CDCa/tV)
GIt = 1.0 #; GRd = 0.0; kSyWhi = 0.02 AU/(#*min); GWt = 1.0 #Reaction: => WHIn; GITM, Rate Law: tV*GRd*kSyWhi*GITM/tV*GWt/GIt
GIt = 1.0 #Reaction: GI = GIt-GITM, Rate Law: missing
GCN = 1.0 #; GDt = 500.0 #; kSyCln = 8.0 AU/(#*min)Reaction: => CLN; GDTM, SBF, SBFt, SBFu, Rate Law: tV*kSyCln*GDTM/tV*GCN/GDt*SBF/tV/(SBFt/tV)*SBFu/tV/(SBFt/tV)
GDt = 500.0 #Reaction: GD = GDt-GDTM, Rate Law: missing
kDsGiTm = 0.1 1/min; kAsGiTm = 10.0 AV/(#*min)Reaction: TM + GI => GITM, Rate Law: tV*(kAsGiTm*TM/tV*GI/tV-kDsGiTm*GITM/tV)
kPhWhipCln3 = 1.0 AV/(AU*min); kPhWhipCln = 3.0 AV/(AU*min)Reaction: WHIpSBF => SBF + WHIp; CLN3, CLN, Rate Law: tV*(kPhWhipCln3*CLN3/tV+kPhWhipCln*CLN/tV)*WHIpSBF/tV
GCt = 1.0 #; GDt = 500.0 #; kSyCln3 = 1.5 AU/(#*min)Reaction: => CLN3; GDTM, Rate Law: tV*kSyCln3*GDTM/tV*GCt/GDt
kAsCln3Whi = 100.0 AV/(AU*min); kDsCln3Whi = 0.1 1/minReaction: CLN3 + WHISBF => CLN3WHISBF, Rate Law: tV*(kAsCln3Whi*CLN3/tV*WHISBF/tV-kDsCln3Whi*CLN3WHISBF/tV)
kPhSbfClb = 5.0 AV/(AU*min)Reaction: SBFu => SBFp; CLB, Rate Law: tV*kPhSbfClb*CLB/tV*SBFu/tV
kAsWhiSbf = 1.0 AV/(AU*min)Reaction: WHI + SBF => WHISBF, Rate Law: kAsWhiSbf*WHI*SBF/tV
kAcCdcClb = 0.5 1/min; jCdc = 0.001 AU/AVReaction: CDCi => CDCa; CLB, Rate Law: tV*kAcCdcClb*CLB/tV*CDCi/tV/(jCdc+CDCi/tV)
NSt = 1.0 AUReaction: SBF = ((((NSt/tV-WHISBF/tV)-CLN3WHISBF/tV)-WHIpSBF/tV)+1E-12)*tV, Rate Law: missing
kDeCln3 = 1.0 1/minReaction: CLN3 =>, Rate Law: kDeCln3*CLN3
GCN = 1.0 #; GDt = 500.0 #; kSyTm = 2.1 1/minReaction: => TM; GDTM, Rate Law: tV*kSyTm*GDTM/tV*GCN/GDt
GCN = 1.0 #; jSyClb = 0.3 AU/AV; GDt = 500.0 #; kSyClb = 0.01 AU/(#*min); kSyClbClb = 0.3 AU/(#*min)Reaction: => CLB; CLB, GDTM, Rate Law: tV*(kSyClb+kSyClbClb*CLB/tV/(jSyClb+CLB/tV))*GDTM/tV*GCN/GDt

States:

NameDescription
SBFuSBFu
WHIWHI
CDHiCDHi
WHIpSBFWHIpSBF
active SBFactive SBF
GITMGITM
TMTM
SBFpSBFp
CDCaCDCa
CLN3WHISBFCLN3WHISBF
CLN3tCLN3t
SBFSBF
WHISBFWHISBF
GDTMGDTM
CLNCLN
WHItWHIt
SBFtSBFt
GIGI
CLBCLB
TMtTMt
CDCiCDCi
CDHaCDHa
GDGD
WHInWHIn
CLN3CLN3
WHIpWHIp

Bulik2016 - Regulation of hepatic glucose metabolism: BIOMD0000000633v0.0.1

Bulik2016 - Regulation of hepatic glucose metabolismThis model is described in the article: [The relative importance of…

Details

Adaptation of the cellular metabolism to varying external conditions is brought about by regulated changes in the activity of enzymes and transporters. Hormone-dependent reversible enzyme phosphorylation and concentration changes of reactants and allosteric effectors are the major types of rapid kinetic enzyme regulation, whereas on longer time scales changes in protein abundance may also become operative. Here, we used a comprehensive mathematical model of the hepatic glucose metabolism of rat hepatocytes to decipher the relative importance of different regulatory modes and their mutual interdependencies in the hepatic control of plasma glucose homeostasis.Model simulations reveal significant differences in the capability of liver metabolism to counteract variations of plasma glucose in different physiological settings (starvation, ad libitum nutrient supply, diabetes). Changes in enzyme abundances adjust the metabolic output to the anticipated physiological demand but may turn into a regulatory disadvantage if sudden unexpected changes of the external conditions occur. Allosteric and hormonal control of enzyme activities allow the liver to assume a broad range of metabolic states and may even fully reverse flux changes resulting from changes of enzyme abundances alone. Metabolic control analysis reveals that control of the hepatic glucose metabolism is mainly exerted by enzymes alone, which are differently controlled by alterations in enzyme abundance, reversible phosphorylation, and allosteric effects.In hepatic glucose metabolism, regulation of enzyme activities by changes of reactants, allosteric effects, and reversible phosphorylation is equally important as changes in protein abundance of key regulatory enzymes. link: http://identifiers.org/pubmed/26935066

Parameters:

NameDescription
v_UGT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: utp + glc1p => udpglc, Rate Law: v_UGT
v_FBP1 = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: fru16bp => fru6p, Rate Law: v_FBP1
v_GPI = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glc6p => fru6p, Rate Law: v_GPI
v_GP = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glyglc => glc1p, Rate Law: v_GP
v_PC = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pyr_mito => oa_mito, Rate Law: v_PC
v_TPI = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: dhap => gap, Rate Law: v_TPI
v_LACT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: => lac, Rate Law: v_LACT
v_G6P_ER = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glc6p_er => glc_er, Rate Law: v_G6P_ER
v_GK = NaN dimensionlessReaction: glc => glc6p, Rate Law: v_GK
v_PK = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pep => pyr, Rate Law: v_PK
v_MDH = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: mal => oa, Rate Law: v_MDH
v_NDK_UTP = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: udp => utp, Rate Law: v_NDK_UTP
v_ALD = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: fru16bp => gap + dhap, Rate Law: v_ALD
v_EN = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pg2 => pep, Rate Law: v_EN
v_NDK_GTP_mito = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: gdp_mito => gtp_mito, Rate Law: v_NDK_GTP_mito
v_PyrT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pyr => pyr_mito, Rate Law: v_PyrT
v_NDK_GTP = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: gdp => gtp, Rate Law: v_NDK_GTP
v_GLCT_ER = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glc => glc_er, Rate Law: v_GLCT_ER
v_G6PT_ER = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glc6p => glc6p_er, Rate Law: v_G6PT_ER
v_MDH_mito = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: mal_mito => oa_mito, Rate Law: v_MDH_mito
v_PFK1 = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: fru6p => fru16bp, Rate Law: v_PFK1
v_FBP2 = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: fru26bp => fru6p, Rate Law: v_FBP2
v_PEPCK_mito = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: oa_mito + gtp_mito => pep_mito + gdp_mito, Rate Law: v_PEPCK_mito
v_MALT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: mal_mito => mal, Rate Law: v_MALT
v_PGK = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: bpg13 => pg3, Rate Law: v_PGK
v_PGM = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pg3 => pg2, Rate Law: v_PGM
v_PFK2 = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: fru6p => fru26bp, Rate Law: v_PFK2
v_GS = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: udpglc => glyglc + udp, Rate Law: v_GS
v_PEPCK = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: oa + gtp => pep + gdp, Rate Law: v_PEPCK
v_GLUT2 = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: => glc, Rate Law: v_GLUT2
v_LDH = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pyr => lac, Rate Law: v_LDH
v_PyrMalT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: mal_mito + pyr => pyr_mito + mal, Rate Law: v_PyrMalT
v_GAPDH = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: gap => bpg13, Rate Law: v_GAPDH
v_PEPT = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: pep_mito => pep, Rate Law: v_PEPT
v_G1PI = NaN m^(-3)*mol*(3600*s)^(-1)Reaction: glc1p => glc6p, Rate Law: v_G1PI

States:

NameDescription
gtp[GTP]
glc1p[D-Glucose 1-phosphate]
fru6p[D-Fructose 6-phosphate]
glc[glucose; urn:miriam:ChEBI:CHEBI:17234]
pep[Phosphoenolpyruvate]
fru16bp[D-Fructose 1,6-bisphosphate]
pyr[Pyruvate]
utp[UTP]
glyglc[Starch]
oa mito[Oxaloacetate]
udpglc[UDP-glucose]
pep mito[Phosphoenolpyruvate]
gdp[GDP]
fru26bp[beta-D-Fructose 2,6-bisphosphate]
gdp mito[GDP]
glc6p[D-Glucose 6-phosphate]
pg2[2-Phospho-D-glycerate]
dhap[Glycerone phosphate]
pg3[3-Phospho-D-glycerate]
bpg13[Glyceric acid 1,3-biphosphate; urn:miriam:ChEBI:CHEBI:89363]
oa[Oxaloacetate]
glc er[glucose; urn:miriam:ChEBI:CHEBI:17234]
glc6p er[D-Glucose 6-phosphate]
udp[UDP]
mal[(S)-Malate]
pyr mito[Pyruvate]
lac[lactate; urn:miriam:ChEBI:CHEBI:24996]
mal mito[(S)-Malate]
gap[D-Glyceraldehyde 3-phosphate]
gtp mito[GTP]

Bungay2003_Thrombin_Generation: BIOMD0000000334v0.0.1

This model is from the article: A mathematical model of lipid-mediated thrombin generation Bungay Sharene D., Gen…

Details

Thrombin is an enzyme that is generated in both vascular and non-vascular systems. In blood coagulation, a fundamental process in all species, thrombin induces the formation of a fibrin clot. A dynamical model of thrombin generation in the presence of lipid surfaces is presented. This model also includes the self-regulating thrombin feedback reactions, the thrombomodulin-protein C-protein S inhibitory system, tissue factor pathway inhibitor (TFPI), and the inhibitor, antithrombin (AT). The dynamics of this complex system were found to be highly lipid dependent, as would be expected from experimental studies. Simulations of this model indicate that a threshold lipid level is required to generate physiologically relevant amounts of thrombin. The dependence of the onset, the peak levels, and the duration of thrombin generation on lipid was saturable. The lipid concentration affects the way in which the inhibitors modulate thrombin production. A novel feature of this model is the inclusion of the dynamical protein C pathway, initiated by thrombin feedback. This inhibitory system exerts its effects on the lipid surface, where its substrates are formed. The maximum impact of TFPI occurs at intermediate vesicle concentrations. Inhibition by AT is only indirectly affected by the lipid since AT irreversibly binds only to solution phase proteins. In a system with normal plasma concentrations of the proteins involved in thrombin formation, the combination of these three inhibitors is sufficient both to effectively stop thrombin generation prior to the exhaustion of its precursor, prothrombin, and to inhibit all thrombin formed. This model can be used to predict thrombin generation under extreme lipid conditions that are difficult to implement experimentally and to examine thrombin generation in non-vascular systems. link: http://identifiers.org/pubmed/12974500

Parameters:

NameDescription
koffV = 0.145; nva = 100.0; konV = 0.05Reaction: V_f + LIPID => V_l, Rate Law: compartment*(konV*V_f*LIPID/nva-koffV*V_l)
k13 = 15.2Reaction: TF_VII_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k13*TF_VII_Xa_l
k39 = 0.05; k40 = 44.8Reaction: Xa_l + VII_l => VII_Xa_l, Rate Law: compartment*(k39*VII_l*Xa_l-k40*VII_Xa_l)
k31 = 13.8; k30 = 0.1Reaction: IIa_f + VIII_l => VIII_IIa_l, Rate Law: compartment*(k30*VIII_l*IIa_f-k31*VIII_IIa_l)
k33 = 0.1; k34 = 100.0Reaction: II_l + Xa_Va_l => Xa_Va_II_l, Rate Law: compartment*(k33*Xa_Va_l*II_l-k34*Xa_Va_II_l)
k67 = 6.4; k66 = 0.1Reaction: PC_l + IIa_TM_l => IIa_TM_PC_l, Rate Law: compartment*(k66*IIa_TM_l*PC_l-k67*IIa_TM_PC_l)
k41 = 15.2Reaction: VII_Xa_l => Xa_l + VIIa_l, Rate Law: compartment*k41*VII_Xa_l
k44 = 1.43Reaction: XI_IIa_l => IIa_f + XIa_l, Rate Law: compartment*k44*XI_IIa_l
k27 = 0.1; k28 = 6.94Reaction: IIa_f + V_l => V_IIa_l, Rate Law: compartment*(k27*V_l*IIa_f-k28*V_IIa_l)
konVIIIa = 0.05; nva = 100.0; koffVIIIa = 0.335Reaction: VIIIa_f + LIPID => VIIIa_l, Rate Law: compartment*(konVIIIa*VIIIa_f*LIPID/nva-koffVIIIa*VIIIa_l)
k17 = 1.0; k16 = 1.0Reaction: Va_l + Xa_l => Xa_Va_l, Rate Law: compartment*(k16*Xa_l*Va_l-k17*Xa_Va_l)
koffIXa = 0.115; nva = 100.0; konIXa = 0.05Reaction: IXa_f + LIPID => IXa_l, Rate Law: compartment*(konIXa*IXa_f*LIPID/nva-koffIXa*IXa_l)
k57 = 6.83E-5Reaction: AT_f + IIa_f => IIa_AT_f, Rate Law: compartment*k57*IIa_f*AT_f
k23 = 0.043Reaction: V_Xa_l => Xa_l + Va_l, Rate Law: compartment*k23*V_Xa_l
k74 = 0.183Reaction: XIa_IX_l => IXa_l + XIa_l, Rate Law: compartment*k74*XIa_IX_l
k73 = 1.417; k72 = 0.01Reaction: IX_l + XIa_l => XIa_IX_l, Rate Law: compartment*(k72*XIa_l*IX_l-k73*XIa_IX_l)
k58 = 0.1; k59 = 6.94Reaction: mIIa_l + V_l => V_mIIa_l, Rate Law: compartment*(k58*V_l*mIIa_l-k59*V_mIIa_l)
k75 = 1.0Reaction: TF_VIIa_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k75*TF_VIIa_Xa_l
k61 = 0.1; k62 = 13.8Reaction: mIIa_l + VIII_l => VIII_mIIa_l, Rate Law: compartment*(k61*VIII_l*mIIa_l-k62*VIII_mIIa_l)
k26 = 0.023Reaction: VIII_Xa_l => Xa_l + VIIIa_l, Rate Law: compartment*k26*VIII_Xa_l
k10 = 1.5Reaction: TF_VIIa_X_l => TF_VIIa_Xa_l, Rate Law: compartment*k10*TF_VIIa_X_l
k60 = 1.035Reaction: V_mIIa_l => mIIa_l + Va_l, Rate Law: compartment*k60*V_mIIa_l
koffVai = 0.17; nva = 100.0; konVai = 0.057Reaction: Vai_f + LIPID => Vai_l, Rate Law: compartment*(konVai*Vai_f*LIPID/nva-koffVai*Vai_l)
k55 = 4.9E-7Reaction: AT_f + IXa_f => IXa_AT_f, Rate Law: compartment*k55*IXa_f*AT_f
konX = 0.01; koffX = 1.9; nva = 100.0Reaction: X_f + LIPID => X_l, Rate Law: compartment*(konX*X_f*LIPID/nva-koffX*X_l)
k48 = 0.1; k49 = 1.6Reaction: Va_l + APC_PS_l => APC_PS_Va_l, Rate Law: compartment*(k48*APC_PS_l*Va_l-k49*APC_PS_Va_l)
k56 = 2.3E-6Reaction: AT_f + Xa_f => Xa_AT_f, Rate Law: compartment*k56*Xa_f*AT_f
konAPC = 0.05; koffAPC = 3.5; nva = 100.0Reaction: APC_f + LIPID => APC_l, Rate Law: compartment*(konAPC*APC_f*LIPID/nva-koffAPC*APC_l)
koffPC = 11.5; konPC = 0.05; nva = 100.0Reaction: PC_f + LIPID => PC_l, Rate Law: compartment*(konPC*PC_f*LIPID/nva-koffPC*PC_l)
k70 = 0.1; k71 = 0.5Reaction: PS_l + APC_l => APC_PS_l, Rate Law: compartment*(k70*APC_l*PS_l-k71*APC_PS_l)
k69 = 6.83E-6Reaction: AT_f + mIIa_f => mIIa_AT_l, Rate Law: compartment*k69*mIIa_f*AT_f
k51 = 0.016; k52 = 3.3E-4Reaction: Xa_f + TFPI_f => TFPI_Xa_l, Rate Law: compartment*(k51*TFPI_f*Xa_f-k52*TFPI_Xa_l)
koffVIIIai = 0.335; nva = 100.0; konVIIIai = 0.05Reaction: VIIIai_f + LIPID => VIIIai_l, Rate Law: compartment*(konVIIIai*VIIIai_f*LIPID/nva-koffVIIIai*VIIIai_l)
k43 = 10.0; k42 = 0.1Reaction: IIa_f + XI_f => XI_IIa_l, Rate Law: compartment*(k42*XI_f*IIa_f-k43*XI_IIa_l)
k50 = 0.4Reaction: APC_PS_Va_l => Vai_l + APC_PS_l, Rate Law: compartment*k50*APC_PS_Va_l
k53 = 0.01; k54 = 0.0011Reaction: TF_VIIa_l + TFPI_Xa_l => TFPI_Xa_TF_VIIa_l, Rate Law: compartment*(k53*TFPI_Xa_l*TF_VIIa_l-k54*TFPI_Xa_TF_VIIa_l)
k65 = 0.5; k64 = 1.0Reaction: TM_l + IIa_f => IIa_TM_l, Rate Law: compartment*(k64*IIa_f*TM_l-k65*IIa_TM_l)
koffPS = 0.2; nva = 100.0; konPS = 0.05Reaction: PS_f + LIPID => PS_l, Rate Law: compartment*(konPS*PS_f*LIPID/nva-koffPS*PS_l)
k24 = 0.1; k25 = 2.1Reaction: Xa_l + VIII_l => VIII_Xa_l, Rate Law: k24*VIII_l*Xa_l-k25*VIII_Xa_l
konVIIa = 0.05; nva = 100.0; koffVIIa = 0.227Reaction: VIIa_f + LIPID => VIIa_l, Rate Law: compartment*(konVIIa*VIIa_f*LIPID/nva-koffVIIa*VIIa_l)
k36 = 66.0; k35 = 0.1Reaction: mIIa_l + Xa_Va_l => Xa_Va_mIIa_l, Rate Law: compartment*(k35*Xa_Va_l*mIIa_l-k36*Xa_Va_mIIa_l)
k12 = 44.8; k11 = 0.05Reaction: Xa_l + TF_VII_l => TF_VII_Xa_l, Rate Law: compartment*(k11*TF_VII_l*Xa_l-k12*TF_VII_Xa_l)
konII = 0.0043; koffII = 1.0; nva = 100.0Reaction: II_f + LIPID => II_l, Rate Law: compartment*(konII*II_f*LIPID/nva-koffII*II_l)
konVa = 0.057; nva = 100.0; koffVa = 0.17Reaction: Va_f + LIPID => Va_l, Rate Law: compartment*(konVa*Va_f*LIPID/nva-koffVa*Va_l)
k63 = 0.9Reaction: VIII_mIIa_l => mIIa_l + VIIIa_l, Rate Law: compartment*k63*VIII_mIIa_l
k68 = 3.6Reaction: IIa_TM_PC_l => APC_l + IIa_TM_l, Rate Law: compartment*k68*IIa_TM_PC_l
koffmIIa = 0.475; nva = 100.0; konmIIa = 0.05Reaction: mIIa_f + LIPID => mIIa_l, Rate Law: compartment*(konmIIa*mIIa_f*LIPID/nva-koffmIIa*mIIa_l)
konIX = 0.05; nva = 100.0; koffIX = 0.115Reaction: IX_f + LIPID => IX_l, Rate Law: compartment*(konIX*IX_f*LIPID/nva-koffIX*IX_l)
koffXa = 3.3; konXa = 0.029; nva = 100.0Reaction: Xa_f + LIPID => Xa_l, Rate Law: konXa*Xa_f*LIPID/nva-koffXa*Xa_l
k47 = 0.4Reaction: APC_PS_VIIIa_l => VIIIai_l + APC_PS_l, Rate Law: compartment*k47*APC_PS_VIIIa_l
konVIII = 0.05; nva = 100.0; koffVIII = 0.1Reaction: VIII_f + LIPID => VIII_l, Rate Law: compartment*(konVIII*VIII_f*LIPID/nva-koffVIII*VIII_l)
konVII = 0.05; koffVII = 0.66; nva = 100.0Reaction: VII_f + LIPID => VII_l, Rate Law: compartment*(konVII*VII_f*LIPID/nva-koffVII*VII_l)
k20 = 8.3Reaction: IXa_VIIIa_X_l => Xa_l + IXa_VIIIa_l, Rate Law: compartment*k20*IXa_VIIIa_X_l

States:

NameDescription
XIa IX l[coagulation factor XI; coagulation factor IX; non-covalently-bound molecular entity]
TF VIIa Xa l[coagulation factor VII; coagulation factor X; tissue factor; non-covalently-bound molecular entity]
APC l[vitamin K-dependent protein C; non-covalently-bound molecular entity]
IXa AT f[coagulation factor IX; antithrombin-III; follicular fluid]
PC l[vitamin K-dependent protein C; non-covalently-bound molecular entity]
LIPID[lipid]
PS l[vitamin K-dependent protein S; non-covalently-bound molecular entity]
mIIa l[prothrombin; non-covalently-bound molecular entity]
IIa TM l[prothrombin; thrombomodulin; non-covalently-bound molecular entity]
VIIIai l[coagulation factor VIII; non-covalently-bound molecular entity]
II f[prothrombin; follicular fluid]
IIa TM PC l[prothrombin; vitamin K-dependent protein C; thrombomodulin; non-covalently-bound molecular entity]
Xa Va mIIa l[prothrombin; coagulation factor V; coagulation factor X; non-covalently-bound molecular entity]
Vai l[coagulation factor V; non-covalently-bound molecular entity]
Xa l[coagulation factor X; non-covalently-bound molecular entity]
mIIa f[prothrombin; follicular fluid]
mIIa AT l[prothrombin; non-covalently-bound molecular entity]
VIII f[coagulation factor VIII; follicular fluid]
V l[coagulation factor V; non-covalently-bound molecular entity]
AT f[antithrombin-III; follicular fluid]
TFPI Xa l[coagulation factor X; tissue factor pathway inhibitor; non-covalently-bound molecular entity]
TFPI f[tissue factor pathway inhibitor; follicular fluid]
VII Xa l[coagulation factor VII; coagulation factor X; non-covalently-bound molecular entity]
Va f[coagulation factor V; follicular fluid]
VIII mIIa l[prothrombin; coagulation factor VIII; non-covalently-bound molecular entity]
IXa f[coagulation factor IX; follicular fluid]
IIa AT f[prothrombin; antithrombin-III; follicular fluid]
IXa VIIIa l[coagulation factor VIII; coagulation factor IX; non-covalently-bound molecular entity]
APC PS Va l[coagulation factor V; vitamin K-dependent protein C; vitamin K-dependent protein S; non-covalently-bound molecular entity]
Va l[coagulation factor V; non-covalently-bound molecular entity]
VIIIa l[coagulation factor VIII; non-covalently-bound molecular entity]
V mIIa l[prothrombin; coagulation factor V; non-covalently-bound molecular entity]
APC PS l[vitamin K-dependent protein C; vitamin K-dependent protein S; non-covalently-bound molecular entity]
VIII l[coagulation factor VIII; non-covalently-bound molecular entity]
X f[coagulation factor X; follicular fluid]
TM l[thrombomodulin; non-covalently-bound molecular entity]
IXa l[coagulation factor IX; non-covalently-bound molecular entity]
II l[prothrombin; non-covalently-bound molecular entity]
XIa l[coagulation factor XI; non-covalently-bound molecular entity]
PS f[vitamin K-dependent protein S; follicular fluid]
TFPI Xa TF VIIa l[coagulation factor VII; coagulation factor X; tissue factor; tissue factor pathway inhibitor; non-covalently-bound molecular entity]
Xa AT f[coagulation factor X; antithrombin-III; follicular fluid]
Xa f[coagulation factor X; follicular fluid]
XI IIa l[prothrombin; coagulation factor XI; non-covalently-bound molecular entity]
APC PS VIIIa l[coagulation factor VIII; vitamin K-dependent protein C; vitamin K-dependent protein S; non-covalently-bound molecular entity]

Bungay2006_FollicularFluid: BIOMD0000000333v0.0.1

This model is from the article: Modelling thrombin generation in human ovarian follicular fluid Bungay Sharene D.…

Details

A mathematical model is constructed to study thrombin production in human ovarian follicular fluid. The model results show that the amount of thrombin that can be produced in ovarian follicular fluid is much lower than that in blood plasma, failing to reach the level required for fibrin formation, and thereby supporting the hypothesis that in follicular fluid thrombin functions to initiate cellular activities via intracellular signalling receptors. It is also concluded that the absence of the amplification pathway to thrombin production in follicular fluid is a major factor in restricting the amount of thrombin that can be produced. Titration of the initial concentrations of the various reactants in the model lead to predictions for the amount of tissue factor and phospholipid that is required to maintain thrombin production in the follicle, as well as to the conclusion that tissue factor pathway inhibitor has little effect on the time that thrombin generation is sustained. Numerical experiments to determine the effect of factor V, which is at a much reduced level in follicular fluid compared to plasma, and thrombomodulin, illustrate the importance for further experimental work to determine values for several parameters that have yet to be reported in the literature. link: http://identifiers.org/pubmed/16838084

Parameters:

NameDescription
koffV = 0.145; nva = 100.0; konV = 0.05Reaction: V_f + LIPID => V_l, Rate Law: compartment*(konV*V_f*LIPID/nva-koffV*V_l)
k13 = 15.2Reaction: TF_VII_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k13*TF_VII_Xa_l
k39 = 0.05; k40 = 44.8Reaction: Xa_l + VII_l => VII_Xa_l, Rate Law: compartment*(k39*VII_l*Xa_l-k40*VII_Xa_l)
k33 = 0.1; k34 = 100.0Reaction: II_l + Xa_Va_l => Xa_Va_II_l, Rate Law: compartment*(k33*Xa_Va_l*II_l-k34*Xa_Va_II_l)
k67 = 6.4; k66 = 0.1Reaction: PC_l + IIa_TM_l => IIa_TM_PC_l, Rate Law: compartment*(k66*IIa_TM_l*PC_l-k67*IIa_TM_PC_l)
k57 = 6.83E-6Reaction: AT_f + IIa_f => IIa_AT_f, Rate Law: compartment*k57*IIa_f*AT_f
k41 = 15.2Reaction: VII_Xa_l => Xa_l + VIIa_l, Rate Law: compartment*k41*VII_Xa_l
k2 = 0.005; k1 = 0.5Reaction: VIIa_l + TF_l => TF_VIIa_l, Rate Law: compartment*(k1*TF_l*VIIa_l-k2*TF_VIIa_l)
k27 = 0.1; k28 = 6.94Reaction: IIa_f + V_l => V_IIa_l, Rate Law: compartment*(k27*V_l*IIa_f-k28*V_IIa_l)
k17 = 1.0; k16 = 1.0Reaction: Va_l + Xa_l => Xa_Va_l, Rate Law: compartment*(k16*Xa_l*Va_l-k17*Xa_Va_l)
k58 = 0.1; k59 = 6.94Reaction: mIIa_l + V_l => V_mIIa_l, Rate Law: compartment*(k58*V_l*mIIa_l-k59*V_mIIa_l)
k23 = 0.043Reaction: V_Xa_l => Xa_l + Va_l, Rate Law: compartment*k23*V_Xa_l
k75 = 1.0Reaction: TF_VIIa_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k75*TF_VIIa_Xa_l
k10 = 1.5Reaction: TF_VIIa_X_l => TF_VIIa_Xa_l, Rate Law: compartment*k10*TF_VIIa_X_l
k60 = 1.035Reaction: V_mIIa_l => mIIa_l + Va_l, Rate Law: compartment*k60*V_mIIa_l
koffVai = 0.17; nva = 100.0; konVai = 0.057Reaction: Vai_f + LIPID => Vai_l, Rate Law: compartment*(konVai*Vai_f*LIPID/nva-koffVai*Vai_l)
k4 = 0.005; k3 = 0.005Reaction: VII_l + TF_l => TF_VII_l, Rate Law: compartment*(k3*TF_l*VII_l-k4*TF_VII_l)
k77 = 2.5E-6Reaction: alpha2M_l + IIa_f => alpha2M_IIa_l, Rate Law: compartment*k77*alpha2M_l*IIa_f
konX = 0.01; koffX = 1.9; nva = 100.0Reaction: X_f + LIPID => X_l, Rate Law: compartment*(konX*X_f*LIPID/nva-koffX*X_l)
k48 = 0.1; k49 = 1.6Reaction: Va_l + APC_PS_l => APC_PS_Va_l, Rate Law: compartment*(k48*APC_PS_l*Va_l-k49*APC_PS_Va_l)
k56 = 2.3E-6Reaction: AT_f + Xa_f => Xa_AT_f, Rate Law: compartment*k56*Xa_f*AT_f
konAPC = 0.05; koffAPC = 3.5; nva = 100.0Reaction: APC_f + LIPID => APC_l, Rate Law: compartment*(konAPC*APC_f*LIPID/nva-koffAPC*APC_l)
koffPC = 11.5; konPC = 0.05; nva = 100.0Reaction: PC_f + LIPID => PC_l, Rate Law: compartment*(konPC*PC_f*LIPID/nva-koffPC*PC_l)
k70 = 0.1; k71 = 0.5Reaction: PS_l + APC_l => APC_PS_l, Rate Law: compartment*(k70*APC_l*PS_l-k71*APC_PS_l)
k69 = 6.83E-6Reaction: AT_f + mIIa_f => mIIa_AT_l, Rate Law: compartment*k69*mIIa_f*AT_f
k37 = 13.0Reaction: Xa_Va_II_l => Xa_Va_mIIa_l, Rate Law: compartment*k37*Xa_Va_II_l
k38 = 15.0Reaction: Xa_Va_mIIa_l => IIa_f + Xa_Va_l + LIPID, Rate Law: compartment*k38*Xa_Va_mIIa_l
k29 = 0.23Reaction: V_IIa_l => IIa_f + Va_l, Rate Law: compartment*k29*V_IIa_l
k50 = 0.4Reaction: APC_PS_Va_l => Vai_l + APC_PS_l, Rate Law: compartment*k50*APC_PS_Va_l
k53 = 0.01; k54 = 0.0011Reaction: TF_VIIa_l + TFPI_Xa_l => TFPI_Xa_TF_VIIa_l, Rate Law: compartment*(k53*TFPI_Xa_l*TF_VIIa_l-k54*TFPI_Xa_TF_VIIa_l)
k65 = 0.5; k64 = 1.0Reaction: TM_l + IIa_f => IIa_TM_l, Rate Law: compartment*(k64*IIa_f*TM_l-k65*IIa_TM_l)
koffPS = 0.2; nva = 100.0; konPS = 0.05Reaction: PS_f + LIPID => PS_l, Rate Law: compartment*(konPS*PS_f*LIPID/nva-koffPS*PS_l)
k21 = 0.1; k22 = 1.0Reaction: Xa_l + V_l => V_Xa_l, Rate Law: compartment*(k21*V_l*Xa_l-k22*V_Xa_l)
konVIIa = 0.05; nva = 100.0; koffVIIa = 0.227Reaction: VIIa_f + LIPID => VIIa_l, Rate Law: compartment*(konVIIa*VIIa_f*LIPID/nva-koffVIIa*VIIa_l)
k36 = 66.0; k35 = 0.1Reaction: mIIa_l + Xa_Va_l => Xa_Va_mIIa_l, Rate Law: compartment*(k35*Xa_Va_l*mIIa_l-k36*Xa_Va_mIIa_l)
k12 = 44.8; k11 = 0.05Reaction: Xa_l + TF_VII_l => TF_VII_Xa_l, Rate Law: compartment*(k11*TF_VII_l*Xa_l-k12*TF_VII_Xa_l)
k9 = 32.5; k8 = 0.1Reaction: X_l + TF_VIIa_l => TF_VIIa_X_l, Rate Law: compartment*(k8*TF_VIIa_l*X_l-k9*TF_VIIa_X_l)
konII = 0.0043; koffII = 1.0; nva = 100.0Reaction: II_f + LIPID => II_l, Rate Law: compartment*(konII*II_f*LIPID/nva-koffII*II_l)
k78 = 1.4E-6Reaction: alpha2M_l + Xa_f => alpha2M_Xa_l, Rate Law: compartment*k78*alpha2M_l*Xa_f
konVa = 0.057; nva = 100.0; koffVa = 0.17Reaction: Va_f + LIPID => Va_l, Rate Law: compartment*(konVa*Va_f*LIPID/nva-koffVa*Va_l)
k68 = 3.6Reaction: IIa_TM_PC_l => APC_l + IIa_TM_l, Rate Law: compartment*k68*IIa_TM_PC_l
koffmIIa = 0.475; nva = 100.0; konmIIa = 0.05Reaction: mIIa_f + LIPID => mIIa_l, Rate Law: compartment*(konmIIa*mIIa_f*LIPID/nva-koffmIIa*mIIa_l)
koffXa = 3.3; konXa = 0.029; nva = 100.0Reaction: Xa_f + LIPID => Xa_l, Rate Law: konXa*Xa_f*LIPID/nva-koffXa*Xa_l
konVII = 0.05; koffVII = 0.66; nva = 100.0Reaction: VII_f + LIPID => VII_l, Rate Law: compartment*(konVII*VII_f*LIPID/nva-koffVII*VII_l)

States:

NameDescription
TF VIIa Xa l[coagulation factor VII; coagulation factor X; tissue factor; non-covalently-bound molecular entity]
VII l[coagulation factor VII; non-covalently-bound molecular entity]
PC l[vitamin K-dependent protein C; non-covalently-bound molecular entity]
VII f[coagulation factor VII; follicular fluid]
IIa f[prothrombin; follicular fluid]
LIPID[lipid]
PS l[vitamin K-dependent protein S; non-covalently-bound molecular entity]
mIIa l[prothrombin; non-covalently-bound molecular entity]
V IIa l[prothrombin; coagulation factor V; non-covalently-bound molecular entity]
IIa TM l[prothrombin; thrombomodulin; non-covalently-bound molecular entity]
II f[prothrombin; follicular fluid]
IIa TM PC l[prothrombin; vitamin K-dependent protein C; thrombomodulin; non-covalently-bound molecular entity]
alpha2M l[alpha-2-macroglobulin; non-covalently-bound molecular entity]
Xa Va mIIa l[prothrombin; coagulation factor V; coagulation factor X; non-covalently-bound molecular entity]
VIIa l[coagulation factor VII; non-covalently-bound molecular entity]
V Xa l[coagulation factor V; coagulation factor X; non-covalently-bound molecular entity]
Vai l[coagulation factor V; non-covalently-bound molecular entity]
Xa l[coagulation factor X; non-covalently-bound molecular entity]
mIIa f[follicular fluid; prothrombin]
mIIa AT l[prothrombin; antithrombin-III; non-covalently-bound molecular entity]
V l[coagulation factor V; non-covalently-bound molecular entity]
alpha2M IIa l[prothrombin; alpha-2-macroglobulin; non-covalently-bound molecular entity]
TF VII l[coagulation factor VII; tissue factor; non-covalently-bound molecular entity]
TF VIIa X l[coagulation factor VII; coagulation factor X; tissue factor; non-covalently-bound molecular entity]
VII Xa l[coagulation factor VII; coagulation factor X; non-covalently-bound molecular entity]
TF l[tissue factor; non-covalently-bound molecular entity]
Va f[coagulation factor V; follicular fluid]
APC PS Va l[coagulation factor V; vitamin K-dependent protein C; vitamin K-dependent protein S; non-covalently-bound molecular entity]
TF VII Xa l[coagulation factor VII; coagulation factor X; tissue factor; non-covalently-bound molecular entity]
Vai f[coagulation factor V; follicular fluid]
Va l[coagulation factor V; non-covalently-bound molecular entity]
V f[coagulation factor V; follicular fluid]
V mIIa l[prothrombin; coagulation factor V; non-covalently-bound molecular entity]
APC PS l[vitamin K-dependent protein C; vitamin K-dependent protein S; non-covalently-bound molecular entity]
TM l[thrombomodulin; non-covalently-bound molecular entity]
TF VIIa l[coagulation factor VII; tissue factor; non-covalently-bound molecular entity]
II l[non-covalently-bound molecular entity; prothrombin]
Xa Va l[coagulation factor V; coagulation factor X; non-covalently-bound molecular entity]
PS f[vitamin K-dependent protein S; follicular fluid]
TFPI Xa TF VIIa l[coagulation factor VII; coagulation factor X; tissue factor pathway inhibitor; tissue factor; non-covalently-bound molecular entity]
Xa Va II l[prothrombin; coagulation factor V; coagulation factor X; non-covalently-bound molecular entity]
alpha2M Xa l[alpha-2-macroglobulin; coagulation factor X; non-covalently-bound molecular entity]
Xa AT f[coagulation factor X; antithrombin-III; follicular fluid]
PC f[vitamin K-dependent protein C; follicular fluid]
VIIa f[coagulation factor VII; follicular fluid]

Bungay2006_Plasma: BIOMD0000000332v0.0.1

This model is from the article: Modelling thrombin generation in human ovarian follicular fluid Bungay Sharene D.…

Details

A mathematical model is constructed to study thrombin production in human ovarian follicular fluid. The model results show that the amount of thrombin that can be produced in ovarian follicular fluid is much lower than that in blood plasma, failing to reach the level required for fibrin formation, and thereby supporting the hypothesis that in follicular fluid thrombin functions to initiate cellular activities via intracellular signalling receptors. It is also concluded that the absence of the amplification pathway to thrombin production in follicular fluid is a major factor in restricting the amount of thrombin that can be produced. Titration of the initial concentrations of the various reactants in the model lead to predictions for the amount of tissue factor and phospholipid that is required to maintain thrombin production in the follicle, as well as to the conclusion that tissue factor pathway inhibitor has little effect on the time that thrombin generation is sustained. Numerical experiments to determine the effect of factor V, which is at a much reduced level in follicular fluid compared to plasma, and thrombomodulin, illustrate the importance for further experimental work to determine values for several parameters that have yet to be reported in the literature. link: http://identifiers.org/pubmed/16838084

Parameters:

NameDescription
koffV = 0.145; nva = 100.0; konV = 0.05Reaction: V_f + LIPID => V_l, Rate Law: compartment*(konV*V_f*LIPID/nva-koffV*V_l)
k5 = 0.01; k6 = 2.09Reaction: IX_l + TF_VIIa_l => TF_VIIa_IX_l, Rate Law: compartment*(k5*TF_VIIa_l*IX_l-k6*TF_VIIa_IX_l)
k13 = 15.2Reaction: TF_VII_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k13*TF_VII_Xa_l
k39 = 0.05; k40 = 44.8Reaction: Xa_l + VII_l => VII_Xa_l, Rate Law: compartment*(k39*VII_l*Xa_l-k40*VII_Xa_l)
k31 = 13.8; k30 = 0.1Reaction: IIa_f + VIII_l => VIII_IIa_l, Rate Law: compartment*(k30*VIII_l*IIa_f-k31*VIII_IIa_l)
k33 = 0.1; k34 = 100.0Reaction: II_l + Xa_Va_l => Xa_Va_II_l, Rate Law: compartment*(k33*Xa_Va_l*II_l-k34*Xa_Va_II_l)
k67 = 6.4; k66 = 0.1Reaction: PC_l + IIa_TM_l => IIa_TM_PC_l, Rate Law: compartment*(k66*IIa_TM_l*PC_l-k67*IIa_TM_PC_l)
k57 = 6.83E-6Reaction: AT_f + IIa_f => IIa_AT_f, Rate Law: compartment*k57*IIa_f*AT_f
k41 = 15.2Reaction: VII_Xa_l => Xa_l + VIIa_l, Rate Law: compartment*k41*VII_Xa_l
k2 = 0.005; k1 = 0.5Reaction: VIIa_l + TF_l => TF_VIIa_l, Rate Law: compartment*(k1*TF_l*VIIa_l-k2*TF_VIIa_l)
k27 = 0.1; k28 = 6.94Reaction: IIa_f + V_l => V_IIa_l, Rate Law: compartment*(k27*V_l*IIa_f-k28*V_IIa_l)
konVIIIa = 0.05; nva = 100.0; koffVIIIa = 0.335Reaction: VIIIa_f + LIPID => VIIIa_l, Rate Law: compartment*(konVIIIa*VIIIa_f*LIPID/nva-koffVIIIa*VIIIa_l)
koffIXa = 0.115; nva = 100.0; konIXa = 0.05Reaction: IXa_f + LIPID => IXa_l, Rate Law: compartment*(konIXa*IXa_f*LIPID/nva-koffIXa*IXa_l)
k17 = 1.0; k16 = 1.0Reaction: Va_l + Xa_l => Xa_Va_l, Rate Law: compartment*(k16*Xa_l*Va_l-k17*Xa_Va_l)
k58 = 0.1; k59 = 6.94Reaction: mIIa_l + V_l => V_mIIa_l, Rate Law: compartment*(k58*V_l*mIIa_l-k59*V_mIIa_l)
k74 = 0.183Reaction: XIa_IX_l => IXa_l + XIa_l, Rate Law: compartment*k74*XIa_IX_l
k73 = 1.417; k72 = 0.01Reaction: IX_l + XIa_l => XIa_IX_l, Rate Law: compartment*(k72*XIa_l*IX_l-k73*XIa_IX_l)
k23 = 0.043Reaction: V_Xa_l => Xa_l + Va_l, Rate Law: compartment*k23*V_Xa_l
k7 = 0.34Reaction: TF_VIIa_IX_l => TF_VIIa_l + IXa_l, Rate Law: compartment*k7*TF_VIIa_IX_l
k75 = 1.0Reaction: TF_VIIa_Xa_l => Xa_l + TF_VIIa_l, Rate Law: compartment*k75*TF_VIIa_Xa_l
k61 = 0.1; k62 = 13.8Reaction: mIIa_l + VIII_l => VIII_mIIa_l, Rate Law: compartment*(k61*VIII_l*mIIa_l-k62*VIII_mIIa_l)
k26 = 0.023Reaction: VIII_Xa_l => Xa_l + VIIIa_l, Rate Law: compartment*k26*VIII_Xa_l
k60 = 1.035Reaction: V_mIIa_l => mIIa_l + Va_l, Rate Law: compartment*k60*V_mIIa_l
koffVai = 0.17; nva = 100.0; konVai = 0.057Reaction: Vai_f + LIPID => Vai_l, Rate Law: compartment*(konVai*Vai_f*LIPID/nva-koffVai*Vai_l)
k55 = 4.9E-7Reaction: AT_f + IXa_f => IXa_AT_f, Rate Law: compartment*k55*IXa_f*AT_f
k4 = 0.005; k3 = 0.005Reaction: VII_l + TF_l => TF_VII_l, Rate Law: compartment*(k3*TF_l*VII_l-k4*TF_VII_l)
konX = 0.01; koffX = 1.9; nva = 100.0Reaction: X_f + LIPID => X_l, Rate Law: compartment*(konX*X_f*LIPID/nva-koffX*X_l)
k48 = 0.1; k49 = 1.6Reaction: Va_l + APC_PS_l => APC_PS_Va_l, Rate Law: compartment*(k48*APC_PS_l*Va_l-k49*APC_PS_Va_l)
k18 = 0.1; k19 = 10.7Reaction: X_l + IXa_VIIIa_l => IXa_VIIIa_X_l, Rate Law: compartment*(k18*IXa_VIIIa_l*X_l-k19*IXa_VIIIa_X_l)
k14 = 0.1; k15 = 0.2Reaction: VIIIa_l + IXa_l => IXa_VIIIa_l, Rate Law: compartment*(k14*IXa_l*VIIIa_l-k15*IXa_VIIIa_l)
k56 = 2.3E-6Reaction: AT_f + Xa_f => Xa_AT_f, Rate Law: compartment*k56*Xa_f*AT_f
k76 = 2.3E-6Reaction: AT_f + XIa_l => AT_XIa_l, Rate Law: compartment*k76*AT_f*XIa_l
konAPC = 0.05; koffAPC = 3.5; nva = 100.0Reaction: APC_f + LIPID => APC_l, Rate Law: compartment*(konAPC*APC_f*LIPID/nva-koffAPC*APC_l)
k69 = 6.83E-6Reaction: AT_f + mIIa_f => mIIa_AT_l, Rate Law: compartment*k69*mIIa_f*AT_f
koffVIIIai = 0.335; nva = 100.0; konVIIIai = 0.05Reaction: VIIIai_f + LIPID => VIIIai_l, Rate Law: compartment*(konVIIIai*VIIIai_f*LIPID/nva-koffVIIIai*VIIIai_l)
k51 = 0.016; k52 = 3.3E-4Reaction: Xa_f + TFPI_f => TFPI_Xa_l, Rate Law: compartment*(k51*TFPI_f*Xa_f-k52*TFPI_Xa_l)
k29 = 0.23Reaction: V_IIa_l => IIa_f + Va_l, Rate Law: compartment*k29*V_IIa_l
k50 = 0.4Reaction: APC_PS_Va_l => Vai_l + APC_PS_l, Rate Law: compartment*k50*APC_PS_Va_l
k21 = 0.1; k22 = 1.0Reaction: Xa_l + V_l => V_Xa_l, Rate Law: compartment*(k21*V_l*Xa_l-k22*V_Xa_l)
koffPS = 0.2; nva = 100.0; konPS = 0.05Reaction: PS_f + LIPID => PS_l, Rate Law: compartment*(konPS*PS_f*LIPID/nva-koffPS*PS_l)
k65 = 0.5; k64 = 1.0Reaction: TM_l + IIa_f => IIa_TM_l, Rate Law: compartment*(k64*IIa_f*TM_l-k65*IIa_TM_l)
k53 = 0.01; k54 = 0.0011Reaction: TF_VIIa_l + TFPI_Xa_l => TFPI_Xa_TF_VIIa_l, Rate Law: compartment*(k53*TFPI_Xa_l*TF_VIIa_l-k54*TFPI_Xa_TF_VIIa_l)
k24 = 0.1; k25 = 2.1Reaction: Xa_l + VIII_l => VIII_Xa_l, Rate Law: k24*VIII_l*Xa_l-k25*VIII_Xa_l
konVIIa = 0.05; nva = 100.0; koffVIIa = 0.227Reaction: VIIa_f + LIPID => VIIa_l, Rate Law: compartment*(konVIIa*VIIa_f*LIPID/nva-koffVIIa*VIIa_l)
k36 = 66.0; k35 = 0.1Reaction: mIIa_l + Xa_Va_l => Xa_Va_mIIa_l, Rate Law: compartment*(k35*Xa_Va_l*mIIa_l-k36*Xa_Va_mIIa_l)
k12 = 44.8; k11 = 0.05Reaction: Xa_l + TF_VII_l => TF_VII_Xa_l, Rate Law: compartment*(k11*TF_VII_l*Xa_l-k12*TF_VII_Xa_l)
k9 = 32.5; k8 = 0.1Reaction: X_l + TF_VIIa_l => TF_VIIa_X_l, Rate Law: compartment*(k8*TF_VIIa_l*X_l-k9*TF_VIIa_X_l)
konII = 0.0043; koffII = 1.0; nva = 100.0Reaction: II_f + LIPID => II_l, Rate Law: compartment*(konII*II_f*LIPID/nva-koffII*II_l)
k78 = 1.4E-6Reaction: alpha2M_l + Xa_f => alpha2M_Xa_l, Rate Law: compartment*k78*alpha2M_l*Xa_f
konVa = 0.057; nva = 100.0; koffVa = 0.17Reaction: Va_f + LIPID => Va_l, Rate Law: compartment*(konVa*Va_f*LIPID/nva-koffVa*Va_l)
k63 = 0.9Reaction: VIII_mIIa_l => mIIa_l + VIIIa_l, Rate Law: compartment*k63*VIII_mIIa_l
k68 = 3.6Reaction: IIa_TM_PC_l => APC_l + IIa_TM_l, Rate Law: compartment*k68*IIa_TM_PC_l
koffmIIa = 0.475; nva = 100.0; konmIIa = 0.05Reaction: mIIa_f + LIPID => mIIa_l, Rate Law: compartment*(konmIIa*mIIa_f*LIPID/nva-koffmIIa*mIIa_l)
konIX = 0.05; nva = 100.0; koffIX = 0.115Reaction: IX_f + LIPID => IX_l, Rate Law: compartment*(konIX*IX_f*LIPID/nva-koffIX*IX_l)
k45 = 0.1; k46 = 1.6Reaction: VIIIa_l + APC_PS_l => APC_PS_VIIIa_l, Rate Law: compartment*(k45*APC_PS_l*VIIIa_l-k46*APC_PS_VIIIa_l)
k32 = 0.9Reaction: VIII_IIa_l => IIa_f + VIIIa_l, Rate Law: compartment*k32*VIII_IIa_l
koffXa = 3.3; konXa = 0.029; nva = 100.0Reaction: Xa_f + LIPID => Xa_l, Rate Law: konXa*Xa_f*LIPID/nva-koffXa*Xa_l
konVIII = 0.05; nva = 100.0; koffVIII = 0.1Reaction: VIII_f + LIPID => VIII_l, Rate Law: compartment*(konVIII*VIII_f*LIPID/nva-koffVIII*VIII_l)
konVII = 0.05; koffVII = 0.66; nva = 100.0Reaction: VII_f + LIPID => VII_l, Rate Law: compartment*(konVII*VII_f*LIPID/nva-koffVII*VII_l)
k20 = 8.3Reaction: IXa_VIIIa_X_l => Xa_l + IXa_VIIIa_l, Rate Law: compartment*k20*IXa_VIIIa_X_l

States:

NameDescription
V l[non-covalently-bound molecular entity; coagulation factor V]
VIIa f[follicular fluid; coagulation factor VII]
VII l[non-covalently-bound molecular entity; coagulation factor VII]
AT f[follicular fluid; antithrombin-III]
IXa AT f[follicular fluid; coagulation factor IX; antithrombin-III]
IX l[non-covalently-bound molecular entity; coagulation factor IX]
IX f[follicular fluid; coagulation factor IX]
VII f[follicular fluid; coagulation factor VII]
TFPI Xa l[non-covalently-bound molecular entity; tissue factor pathway inhibitor; coagulation factor X]
VII Xa l[non-covalently-bound molecular entity; coagulation factor X; coagulation factor VII]
Va f[follicular fluid; coagulation factor V]
LIPID[lipid]
VIII mIIa l[non-covalently-bound molecular entity; coagulation factor VIII; prothrombin]
IIa AT f[follicular fluid; prothrombin; antithrombin-III]
APC PS Va l[non-covalently-bound molecular entity; vitamin K-dependent protein C; vitamin K-dependent protein S; coagulation factor V]
IXa f[follicular fluid; coagulation factor IX]
X l[non-covalently-bound molecular entity; coagulation factor X]
mIIa l[non-covalently-bound molecular entity; prothrombin]
Va l[non-covalently-bound molecular entity; coagulation factor V]
VIIIa f[follicular fluid; coagulation factor VIII]
VIIIa l[non-covalently-bound molecular entity; coagulation factor VIII]
IIa TM l[non-covalently-bound molecular entity; thrombomodulin; prothrombin]
V f[follicular fluid; coagulation factor V]
VIII l[non-covalently-bound molecular entity; coagulation factor VIII]
V mIIa l[non-covalently-bound molecular entity; coagulation factor V; prothrombin]
II f[follicular fluid; prothrombin]
X f[follicular fluid; coagulation factor X]
TM l[non-covalently-bound molecular entity; thrombomodulin]
IXa l[non-covalently-bound molecular entity; coagulation factor IX]
II l[non-covalently-bound molecular entity; prothrombin]
IIa TM PC l[non-covalently-bound molecular entity; thrombomodulin; prothrombin; vitamin K-dependent protein C]
TFPI Xa TF VIIa l[non-covalently-bound molecular entity; tissue factor pathway inhibitor; coagulation factor X; tissue factor; coagulation factor VII]
VIIa l[non-covalently-bound molecular entity; coagulation factor VII]
alpha2M Xa l[non-covalently-bound molecular entity; coagulation factor X; alpha-2-macroglobulin]
Xa AT f[follicular fluid; coagulation factor X; antithrombin-III]
Xa l[non-covalently-bound molecular entity; coagulation factor X]
mIIa f[follicular fluid; prothrombin]
Xa f[follicular fluid; coagulation factor X]
mIIa AT l[non-covalently-bound molecular entity; prothrombin; antithrombin-III]
VIII f[follicular fluid; coagulation factor VIII]

Burghaus2011 - Simulating Rivaroxaban effects on blood coagulation: MODEL1805140001v0.0.1

Another mathematical model of blood coagulation.

Details

Rivaroxaban is an oral, direct Factor Xa inhibitor approved in the European Union and several other countries for the prevention of venous thromboembolism in adult patients undergoing elective hip or knee replacement surgery and is in advanced clinical development for the treatment of thromboembolic disorders. Its mechanism of action is antithrombin independent and differs from that of other anticoagulants, such as warfarin (a vitamin K antagonist), enoxaparin (an indirect thrombin/Factor Xa inhibitor) and dabigatran (a direct thrombin inhibitor). A blood coagulation computer model has been developed, based on several published models and preclinical and clinical data. Unlike previous models, the current model takes into account both the intrinsic and extrinsic pathways of the coagulation cascade, and possesses some unique features, including a blood flow component and a portfolio of drug action mechanisms. This study aimed to use the model to compare the mechanism of action of rivaroxaban with that of warfarin, and to evaluate the efficacy and safety of different rivaroxaban doses with other anticoagulants included in the model. Rather than reproducing known standard clinical measurements, such as the prothrombin time and activated partial thromboplastin time clotting tests, the anticoagulant benchmarking was based on a simulation of physiologically plausible clotting scenarios. Compared with warfarin, rivaroxaban showed a favourable sensitivity for tissue factor concentration inducing clotting, and a steep concentration-effect relationship, rapidly flattening towards higher inhibitor concentrations, both suggesting a broad therapeutic window. The predicted dosing window is highly accordant with the final dose recommendation based upon extensive clinical studies. link: http://identifiers.org/pubmed/21526168

Burghaus2014 - Simulating blood coagulation factor Xa inhibitors: MODEL1807180005v0.0.1

Mathematical model of blood coagulation factors II, VII, IX and X as well as protein C and protein S and the effect of w…

Details

The long-lasting anticoagulant effect of vitamin K antagonists can be problematic in cases of adverse drug reactions or when patients are switched to another anticoagulant therapy. The objective of this study was to examine in silico the anticoagulant effect of rivaroxaban, an oral, direct Factor Xa inhibitor, combined with the residual effect of discontinued warfarin. Our simulations were based on the recommended anticoagulant dosing regimen for stroke prevention in patients with atrial fibrillation. The effects of the combination of discontinued warfarin plus rivaroxaban were simulated using an extended version of a previously validated blood coagulation computer model. A strong synergistic effect of the two distinct mechanisms of action was observed in the first 2-3 days after warfarin discontinuation; thereafter, the effect was close to additive. Nomograms for the introduction of rivaroxaban therapy after warfarin discontinuation were derived for Caucasian and Japanese patients using safety and efficacy criteria described previously, together with the coagulation model. The findings of our study provide a mechanistic pharmacologic rationale for dosing schedules during the therapy switch from warfarin to rivaroxaban and support the switching strategies as outlined in the Summary of Product Characteristics and Prescribing Information for rivaroxaban. link: http://identifiers.org/pubmed/25426077

Bush2016 - Extended Carrousel model of GPCR-RGS: BIOMD0000000638v0.0.1

Bush2016 - Extended Carrousel model of GPCR-RGSThis model is described in the article: [Yeast GPCR signaling reflects t…

Details

According to receptor theory, the effect of a ligand depends on the amount of agonist-receptor complex. Therefore, changes in receptor abundance should have quantitative effects. However, the response to pheromone in Saccharomyces cerevisiae is robust (unaltered) to increases or reductions in the abundance of the G-protein-coupled receptor (GPCR), Ste2, responding instead to the fraction of occupied receptor. We found experimentally that this robustness originates during G-protein activation. We developed a complete mathematical model of this step, which suggested the ability to compute fractional occupancy depends on the physical interaction between the inhibitory regulator of G-protein signaling (RGS), Sst2, and the receptor. Accordingly, replacing Sst2 by the heterologous hsRGS4, incapable of interacting with the receptor, abolished robustness. Conversely, forcing hsRGS4:Ste2 interaction restored robustness. Taken together with other results of our work, we conclude that this GPCR pathway computes fractional occupancy because ligand-bound GPCR-RGS complexes stimulate signaling while unoccupied complexes actively inhibit it. In eukaryotes, many RGSs bind to specific GPCRs, suggesting these complexes with opposing activities also detect fraction occupancy by a ratiometric measurement. Such complexes operate as push-pull devices, which we have recently described. link: http://identifiers.org/pubmed/28034910

Parameters:

NameDescription
k_off_L_RG = 0.001; k_on_L_RG = 0.0Reaction: RG => LRG, Rate Law: PM*(k_on_L_RG*RG-k_off_L_RG*LRG)
k_Ef_G = 6.2E-4Reaction: G => Gt + Gbg, Rate Law: PM*k_Ef_G*G
k_off_R_Gd = 0.09; k_on_R_Gd = 0.00415Reaction: LRrgs + Gd => LRrgsGd, Rate Law: PM*(k_on_R_Gd*LRrgs*Gd-k_off_R_Gd*LRrgsGd)
k_off_LR_G = 0.09; k_on_LR_G = 0.00415Reaction: LR + G => LRG, Rate Law: PM*(k_on_LR_G*LR*G-k_off_LR_G*LRG)
k_off_L_R = 0.001; k_on_L_R = 0.0Reaction: R => LR, Rate Law: PM*(k_on_L_R*R-k_off_L_R*LR)
k_Ef_Gd = 6.2E-4Reaction: Gd => Gt, Rate Law: PM*k_Ef_Gd*Gd
k_Hf_LRGt = 0.002Reaction: LRGt => LRGd, Rate Law: PM*k_Hf_LRGt*LRGt
k_Hf_Gt = 0.002Reaction: Gt => Gd, Rate Law: PM*k_Hf_Gt*Gt
k_Hf_RrgsGt = 0.28Reaction: RrgsGt => RrgsGd, Rate Law: PM*k_Hf_RrgsGt*RrgsGt
k_Ar_LRGd = 0.0013; k_Af_LRGd = 0.2158Reaction: LRGd + Gbg => LRG, Rate Law: PM*(k_Af_LRGd*LRGd*Gbg-k_Ar_LRGd*LRG)
k_off_L_RGd = 0.001; k_on_L_RGd = 0.0Reaction: RGd => LRGd, Rate Law: PM*(k_on_L_RGd*RGd-k_off_L_RGd*LRGd)
k_off_LR_Gd = 0.09; k_on_LR_Gd = 0.00415Reaction: LR + Gd => LRGd, Rate Law: PM*(k_on_LR_Gd*LR*Gd-k_off_LR_Gd*LRGd)
k_Ar_Gd = 0.0013; k_Af_Gd = 0.2158Reaction: Gd + Gbg => G, Rate Law: PM*(k_Af_Gd*Gd*Gbg-k_Ar_Gd*G)
k_on_R_rgs = 0.0151829268292683; k_off_R_rgs = 3.0Reaction: RGd + rgs => RrgsGd, Rate Law: k_on_R_rgs*RGd*rgs-k_off_R_rgs*RrgsGd
k_Hf_LRrgsGt = 0.28Reaction: LRrgsGt => LRrgsGd, Rate Law: PM*k_Hf_LRrgsGt*LRrgsGt
k_Ef_LRG = 1.5Reaction: LRrgsG => LRrgsGt + Gbg, Rate Law: PM*k_Ef_LRG*LRrgsG
k_on_R_Gt = 0.00415; k_off_R_Gt = 0.09Reaction: R + Gt => RGt, Rate Law: PM*(k_on_R_Gt*R*Gt-k_off_R_Gt*RGt)
k_on_L_RGt = 0.0; k_off_L_RGt = 0.001Reaction: RrgsGt => LRrgsGt, Rate Law: PM*(k_on_L_RGt*RrgsGt-k_off_L_RGt*LRrgsGt)
k_Af_RGd = 0.2158; k_Ar_RGd = 0.0013Reaction: RrgsGd + Gbg => RrgsG, Rate Law: PM*(k_Af_RGd*RrgsGd*Gbg-k_Ar_RGd*RrgsG)
k_Ef_LRGd = 1.5Reaction: LRGd => LRGt, Rate Law: PM*k_Ef_LRGd*LRGd
k_on_LR_Gt = 0.00415; k_off_LR_Gt = 0.09Reaction: LR + Gt => LRGt, Rate Law: PM*(k_on_LR_Gt*LR*Gt-k_off_LR_Gt*LRGt)
k_Ef_RG = 6.2E-4Reaction: RG => RGt + Gbg, Rate Law: PM*k_Ef_RG*RG
k_Ef_RGd = 6.2E-4Reaction: RGd => RGt, Rate Law: PM*k_Ef_RGd*RGd
k_off_R_G = 0.09; k_on_R_G = 0.00415Reaction: R + G => RG, Rate Law: PM*(k_on_R_G*R*G-k_off_R_G*RG)

States:

NameDescription
LR[Pheromone alpha factor receptor; Mating factor alpha-1]
RGd[GDP; Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit gamma]
Rrgs[Pheromone alpha factor receptor]
RGt[GDP; Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit gamma]
Gd[GDP; Guanine nucleotide-binding protein subunit gamma]
LRGt[GTP; Pheromone alpha factor receptor; Mating factor alpha-1]
G[Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
LRrgs[Pheromone alpha factor receptor; Mating factor alpha-1]
rgsrgs
LRrgsGd[Pheromone alpha factor receptor; Mating factor alpha-1]
Gt[GDP; Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
Gbg[Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
RrgsGd[GDP; Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit gamma]
LRrgsG[Pheromone alpha factor receptor; Mating factor alpha-1]
RG[Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
LRGd[GDP; Pheromone alpha factor receptor; Mating factor alpha-1; Guanine nucleotide-binding protein subunit gamma]
RrgsG[Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
R[Pheromone alpha factor receptor]
RrgsGt[Pheromone alpha factor receptor; Mating factor alpha-1; Guanine nucleotide-binding protein subunit gamma]
LRG[Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma; Pheromone alpha factor receptor; Mating factor alpha-1]
LRrgsGt[GTP; Pheromone alpha factor receptor; Mating factor alpha-1; Guanine nucleotide-binding protein subunit gamma]

Bush2016 - Simplified Carrousel model of GPCR: BIOMD0000000637v0.0.1

Bush2016 - Simplified Carrousel model of GPCRThis model is described in the article: [Yeast GPCR signaling reflects the…

Details

According to receptor theory, the effect of a ligand depends on the amount of agonist-receptor complex. Therefore, changes in receptor abundance should have quantitative effects. However, the response to pheromone in Saccharomyces cerevisiae is robust (unaltered) to increases or reductions in the abundance of the G-protein-coupled receptor (GPCR), Ste2, responding instead to the fraction of occupied receptor. We found experimentally that this robustness originates during G-protein activation. We developed a complete mathematical model of this step, which suggested the ability to compute fractional occupancy depends on the physical interaction between the inhibitory regulator of G-protein signaling (RGS), Sst2, and the receptor. Accordingly, replacing Sst2 by the heterologous hsRGS4, incapable of interacting with the receptor, abolished robustness. Conversely, forcing hsRGS4:Ste2 interaction restored robustness. Taken together with other results of our work, we conclude that this GPCR pathway computes fractional occupancy because ligand-bound GPCR-RGS complexes stimulate signaling while unoccupied complexes actively inhibit it. In eukaryotes, many RGSs bind to specific GPCRs, suggesting these complexes with opposing activities also detect fraction occupancy by a ratiometric measurement. Such complexes operate as push-pull devices, which we have recently described. link: http://identifiers.org/pubmed/28034910

Parameters:

NameDescription
k_off_L_RG = 0.001; k_on_L_RG = 0.0Reaction: RG => LRG, Rate Law: PM*(k_on_L_RG*RG-k_off_L_RG*LRG)
k_Hf_RGt = 0.11Reaction: RGt => RGd, Rate Law: PM*k_Hf_RGt*RGt
k_Ef_G = 6.2E-4Reaction: G => Gt + Gbg, Rate Law: PM*k_Ef_G*G
k_off_R_Gd = 0.1; k_on_R_Gd = 0.00461111111111111Reaction: R + Gd => RGd, Rate Law: PM*(k_on_R_Gd*R*Gd-k_off_R_Gd*RGd)
k_off_L_R = 0.001; k_on_L_R = 0.0Reaction: R => LR, Rate Law: PM*(k_on_L_R*R-k_off_L_R*LR)
k_Ef_Gd = 6.2E-4Reaction: Gd => Gt, Rate Law: PM*k_Ef_Gd*Gd
k_on_R_Gt = 0.00461111111111111; k_off_R_Gt = 0.1Reaction: R + Gt => RGt, Rate Law: PM*(k_on_R_Gt*R*Gt-k_off_R_Gt*RGt)
k_Hf_Gt = 0.002Reaction: Gt => Gd, Rate Law: PM*k_Hf_Gt*Gt
k_Ar_LRGd = 0.0013; k_Af_LRGd = 0.2158Reaction: LRGd + Gbg => LRG, Rate Law: PM*(k_Af_LRGd*LRGd*Gbg-k_Ar_LRGd*LRG)
k_off_L_RGd = 0.001; k_on_L_RGd = 0.0Reaction: RGd => LRGd, Rate Law: PM*(k_on_L_RGd*RGd-k_off_L_RGd*LRGd)
k_Ar_Gd = 0.0013; k_Af_Gd = 0.2158Reaction: Gd + Gbg => G, Rate Law: PM*(k_Af_Gd*Gd*Gbg-k_Ar_Gd*G)
k_Hf_LRGt = 0.11Reaction: LRGt => LRGd, Rate Law: PM*k_Hf_LRGt*LRGt
k_off_LR_Gt = 0.1; k_on_LR_Gt = 0.00461111111111111Reaction: LR + Gt => LRGt, Rate Law: PM*(k_on_LR_Gt*LR*Gt-k_off_LR_Gt*LRGt)
k_Ef_LRG = 1.5Reaction: LRG => LRGt + Gbg, Rate Law: PM*k_Ef_LRG*LRG
k_on_L_RGt = 0.0; k_off_L_RGt = 0.001Reaction: RGt => LRGt, Rate Law: PM*(k_on_L_RGt*RGt-k_off_L_RGt*LRGt)
k_on_R_G = 0.00461111111111111; k_off_R_G = 0.1Reaction: R + G => RG, Rate Law: PM*(k_on_R_G*R*G-k_off_R_G*RG)
k_Af_RGd = 0.2158; k_Ar_RGd = 0.0013Reaction: RGd + Gbg => RG, Rate Law: PM*(k_Af_RGd*RGd*Gbg-k_Ar_RGd*RG)
k_Ef_LRGd = 1.5Reaction: LRGd => LRGt, Rate Law: PM*k_Ef_LRGd*LRGd
k_on_LR_Gd = 0.00461111111111111; k_off_LR_Gd = 0.1Reaction: LR + Gd => LRGd, Rate Law: PM*(k_on_LR_Gd*LR*Gd-k_off_LR_Gd*LRGd)
k_Ef_RG = 6.2E-4Reaction: RG => RGt + Gbg, Rate Law: PM*k_Ef_RG*RG
k_off_LR_G = 0.1; k_on_LR_G = 0.00461111111111111Reaction: LR + G => LRG, Rate Law: PM*(k_on_LR_G*LR*G-k_off_LR_G*LRG)
k_Ef_RGd = 6.2E-4Reaction: RGd => RGt, Rate Law: PM*k_Ef_RGd*RGd

States:

NameDescription
LR[Pheromone alpha factor receptor; Mating factor alpha-1]
RGd[GDP; Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit gamma]
RGt[GTP; Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit gamma]
Gd[GDP; Guanine nucleotide-binding protein subunit gamma]
LRGt[GTP; Pheromone alpha factor receptor; Mating factor alpha-1]
G[Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
Gt[GTP; Guanine nucleotide-binding protein subunit gamma; Guanine nucleotide-binding protein subunit beta]
Gbg[Guanine nucleotide-binding protein subunit gamma; Guanine nucleotide-binding protein subunit beta]
RG[Pheromone alpha factor receptor; Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]
LRGd[GDP; Pheromone alpha factor receptor; Mating factor alpha-1; Guanine nucleotide-binding protein subunit gamma]
R[Pheromone alpha factor receptor]
LRG[Pheromone alpha factor receptor; Mating factor alpha-1; Guanine nucleotide-binding protein subunit beta; Guanine nucleotide-binding protein subunit gamma]

Butenas2004_BloodCoagulation: BIOMD0000000362v0.0.1

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/…

Details

The presence of activation peptides (AP) of the vitamin K-dependent proteins in the phlebotomy blood of human subjects suggests that active serine proteases may circulate in blood as well. The goal of the current study was to evaluate the influence of trace amounts of key coagulation proteases on tissue factor-independent thrombin generation using three models of coagulation. With procoagulants and select coagulation inhibitors at mean physiological concentrations, concentrations of factor IXa, factor Xa, and thrombin were set either equal to those of their AP or to values that would result based upon the rates of AP/enzyme generation and steady state enzyme inhibition. In the latter case, numerical simulation predicts that sufficient thrombin to produce a solid clot would be generated in approximately 2 min. Empirical data from the synthetic plasma suggest clotting times of 3-5 min, which are similar to that observed in contact pathway-inhibited whole blood (4.3 min) initiated with the same concentrations of factors IXa and Xa and thrombin. Numerical simulations performed with the concentrations of two of the enzymes held constant and one varied suggest that the presence of any pair of enzymes is sufficient to yield rapid clot formation. Modeling of states (numerical simulation and whole blood) where only one circulating protease is present at steady state concentration shows significant thrombin generation only for factor IXa. The addition of factor Xa and thrombin has little effect (if any) on thrombin generation induced by factor IXa alone. These data indicate that 1) concentrations of active coagulation enzymes circulating in vivo are significantly lower than can be predicted from the concentrations of their AP, and 2) expected trace amounts of factor IXa can trigger thrombin generation in the absence of tissue factor. link: http://identifiers.org/pubmed/15039440

Parameters:

NameDescription
k15 = 1.8Reaction: TF_VIIa_IX => TF_VIIa + IXa, Rate Law: compartment_1*k15*TF_VIIa_IX
k29 = 103.0; k30 = 1.0E8Reaction: Xa_Va + II => Xa_Va_II, Rate Law: compartment_1*(k30*Xa_Va*II-k29*Xa_Va_II)
k27 = 0.2; k28 = 4.0E8Reaction: Xa + Va => Xa_Va, Rate Law: compartment_1*(k28*Xa*Va-k27*Xa_Va)
k21 = 1.0E8; k20 = 0.001Reaction: IXa_VIIIa + X => IXa_VIIIa_X, Rate Law: compartment_1*(k21*IXa_VIIIa*X-k20*IXa_VIIIa_X)
k6 = 1.3E7Reaction: Xa + VII => Xa + VIIa, Rate Law: compartment_1*k6*Xa*VII
k40 = 490.0Reaction: IXa + ATIII => IXa_ATIII, Rate Law: compartment_1*k40*IXa*ATIII
k37 = 5.0E7Reaction: TF_VIIa + Xa_TFPI => TF_VIIa_Xa_TFPI, Rate Law: compartment_1*k37*TF_VIIa*Xa_TFPI
k41 = 7100.0Reaction: IIa + ATIII => IIa_ATIII, Rate Law: compartment_1*k41*IIa*ATIII
k9 = 2.5E7; k8 = 1.05Reaction: TF_VIIa + X => TF_VIIa_X, Rate Law: compartment_1*(k9*TF_VIIa*X-k8*TF_VIIa_X)
k17 = 2.0E7Reaction: IIa + VIII => IIa + VIIIa, Rate Law: compartment_1*k17*IIa*VIII
k23 = 22000.0; k24 = 0.006Reaction: VIIIa => VIIIa1_L + VIIIa2, Rate Law: compartment_1*(k24*VIIIa-k23*VIIIa1_L*VIIIa2)
k25 = 0.001Reaction: IXa_VIIIa_X => VIIIa1_L + VIIIa2 + X + IXa, Rate Law: compartment_1*k25*IXa_VIIIa_X
k35 = 1.1E-4; k36 = 3.2E8Reaction: TF_VIIa_Xa + TFPI => TF_VIIa_Xa_TFPI, Rate Law: compartment_1*(k36*TF_VIIa_Xa*TFPI-k35*TF_VIIa_Xa_TFPI)
k32 = 1.5E7Reaction: mIIa + Xa_Va => IIa + Xa_Va, Rate Law: compartment_1*k32*mIIa*Xa_Va
k16 = 7500.0Reaction: Xa + II => Xa + IIa, Rate Law: compartment_1*k16*Xa*II
k5 = 440000.0Reaction: TF_VIIa + VII => TF_VIIa + VIIa, Rate Law: compartment_1*k5*TF_VIIa*VII
k10 = 6.0Reaction: TF_VIIa_X => TF_VIIa_Xa, Rate Law: compartment_1*k10*TF_VIIa_X
k4 = 2.3E7; k3 = 0.0031Reaction: TF + VIIa => TF_VIIa, Rate Law: compartment_1*(k4*TF*VIIa-k3*TF_VIIa)
k39 = 7100.0Reaction: mIIa + ATIII => mIIa_ATIII, Rate Law: compartment_1*k39*mIIa*ATIII
k7 = 23000.0Reaction: IIa + VII => IIa + VIIa, Rate Law: compartment_1*k7*IIa*VII
k26 = 2.0E7Reaction: IIa + V => IIa + Va, Rate Law: compartment_1*k26*IIa*V
k44 = 3000000.0Reaction: mIIa + V => mIIa + Va, Rate Law: compartment_1*k44*mIIa*V
k31 = 63.5Reaction: Xa_Va_II => Xa_Va + mIIa, Rate Law: compartment_1*k31*Xa_Va_II
k38 = 1500.0Reaction: Xa + ATIII => Xa_ATIII, Rate Law: compartment_1*k38*Xa*ATIII
k34 = 900000.0; k33 = 3.6E-4Reaction: Xa + TFPI => Xa_TFPI, Rate Law: compartment_1*(k34*Xa*TFPI-k33*Xa_TFPI)
k2 = 3200000.0; k1 = 0.0031Reaction: TF + VII => TF_VII, Rate Law: compartment_1*(k2*TF*VII-k1*TF_VII)
k22 = 8.2Reaction: IXa_VIIIa_X => IXa_VIIIa + Xa, Rate Law: compartment_1*k22*IXa_VIIIa_X
k43 = 5700.0Reaction: IXa + X => IXa + Xa, Rate Law: compartment_1*k43*IXa*X
k12 = 2.2E7; k11 = 19.0Reaction: TF_VIIa + Xa => TF_VIIa_Xa, Rate Law: compartment_1*(k12*TF_VIIa*Xa-k11*TF_VIIa_Xa)
k42 = 230.0Reaction: TF_VIIa + ATIII => TF_VIIa_ATIII, Rate Law: compartment_1*k42*TF_VIIa*ATIII
k19 = 1.0E7; k18 = 0.005Reaction: IXa + VIIIa => IXa_VIIIa, Rate Law: compartment_1*(k19*IXa*VIIIa-k18*IXa_VIIIa)
k14 = 1.0E7; k13 = 2.4Reaction: TF_VIIa + IX => TF_VIIa_IX, Rate Law: compartment_1*(k14*TF_VIIa*IX-k13*TF_VIIa_IX)

States:

NameDescription
IIa ATIII[Prothrombin; Antithrombin-III]
TFPI[Tissue factor pathway inhibitor]
Xa ATIII[Antithrombin-III; Coagulation factor X]
VIII[Coagulation factor VIII]
V[Coagulation factor V]
Xa Va II[Prothrombin; Coagulation factor V; Coagulation factor X]
ATIII[Antithrombin-III]
Xa[Coagulation factor X]
VIIIa1 L[Coagulation factor VIII]
TF VIIa ATIII[Tissue factor; Coagulation factor VII; Antithrombin-III]
IXa ATIII[Coagulation factor IX; Antithrombin-III]
TF VIIa X[Coagulation factor X; Coagulation factor VII; Tissue factor]
TF[Tissue factor]
TF VIIa Xa[Coagulation factor X; Coagulation factor VII; Tissue factor]
TF VIIa Xa TFPI[Tissue factor pathway inhibitor; Coagulation factor X; Coagulation factor VII; Tissue factor]
mIIa ATIII[Prothrombin; Antithrombin-III]
TF VII[Coagulation factor VII; Tissue factor]
Xa Va[Coagulation factor V; Coagulation factor X]
X[Coagulation factor X]
VIIIa2[Coagulation factor VIII]
TF VIIa[Coagulation factor VII; Tissue factor]
VIIIa[Coagulation factor VIII]
Va[Coagulation factor V]
mIIa[Prothrombin]
Xa TFPI[Tissue factor pathway inhibitor; Coagulation factor X]
VIIa[Coagulation factor VII]
IXa VIIIa X[Coagulation factor X; Coagulation factor VIII; Coagulation factor IX]
IIa[Prothrombin]
TF VIIa IX[Coagulation factor IX; Coagulation factor VII; Tissue factor]
IXa[Coagulation factor IX]
VII[Coagulation factor VII]
II[Prothrombin]
IX[Coagulation factor IX]
IXa VIIIa[Coagulation factor VIII; Coagulation factor IX]

Butera1999_Bursting_Pacemaker_Neuron_Model_1: MODEL7891585309v0.0.1

This is the model without the slow potassium current, model 1, described in the article: Models of respiratory rhythm…

Details

A network of oscillatory bursting neurons with excitatory coupling is hypothesized to define the primary kernel for respiratory rhythm generation in the pre-Bötzinger complex (pre-BötC) in mammals. Two minimal models of these neurons are proposed. In model 1, bursting arises via fast activation and slow inactivation of a persistent Na+ current INaP-h. In model 2, bursting arises via a fast-activating persistent Na+ current INaP and slow activation of a K+ current IKS. In both models, action potentials are generated via fast Na+ and K+ currents. The two models have few differences in parameters to facilitate a rigorous comparison of the two different burst-generating mechanisms. Both models are consistent with many of the dynamic features of electrophysiological recordings from pre-BötC oscillatory bursting neurons in vitro, including voltage-dependent activity modes (silence, bursting, and beating), a voltage-dependent burst frequency that can vary from 0.05 to >1 Hz, and a decaying spike frequency during bursting. These results are robust and persist across a wide range of parameter values for both models. However, the dynamics of model 1 are more consistent with experimental data in that the burst duration decreases as the baseline membrane potential is depolarized and the model has a relatively flat membrane potential trajectory during the interburst interval. We propose several experimental tests to demonstrate the validity of either model and to differentiate between the two mechanisms. link: http://identifiers.org/pubmed/10400966

C


Cacace2020 - Logical model of the regulatory network controlling T cell commitment: MODEL2002170001v0.0.1

Boolean approaches and extensions thereof are becoming increasingly popular to model signaling and regulatory networks,…

Details

Boolean approaches and extensions thereof are becoming increasingly popular to model signaling and regulatory networks, including those controlling cell differentiation, pattern formation and embryonic development. Here, we describe a logical modeling framework relying on three steps: the delineation of a regulatory graph, the specification of multilevel components, and the encoding of Boolean rules specifying the behavior of model components depending on the levels or activities of their regulators. Referring to a non-deterministic, asynchronous updating scheme, we present several complementary methods and tools enabling the computation of stable activity patterns, the verification of the reachability of such patterns, as well as the generation of mean temporal evolution curves and the computation of the probabilities to reach distinct activity patterns. We apply this logical framework to the regulatory network controlling T lymphocyte specification. This process involves cross-regulations between specific T cell regulatory factors and factors driving alternative differentiation pathways, which remain accessible during the early steps of thymocyte development. Many transcription factors needed for T cell specification are required in other hematopoietic differentiation pathways and are combined in a fine-tuned, time-dependent fashion to achieve T cell commitment. Using the software GINsim, we integrated current knowledge into a dynamical model, which recapitulates the main developmental steps from early progenitors entering the thymus up to T cell commitment, as well as the impact of various documented environmental and genetic perturbations. Our model analysis further enabled the identification of several knowledge gaps. The model, software and whole analysis workflow are provided in computer-readable and executable form to ensure reproducibility and ease extensions. link: http://identifiers.org/pubmed/32450961

Caldwell2019 - The Vicodin abuse problem: BIOMD0000000840v0.0.1

This is a mathematical model of Vicodin use and abuse used to investigate methods of combating Vicodin abuse in a popula…

Details

The prescription drug epidemic in the United States has gained attention in recent years. Vicodin, along with its generic version, is the country's mostly widely prescribed pain reliever, and it contains a narcotic component that can lead to physical and chemical dependency. The majority of Vicodin abusers were first introduced via prescription, unlike other drugs which are often experienced for the first time due to experimentation. Most abusers report obtaining their supply from a prescription, either their own or someone else's. Although the problem with prescription drug abuse is well known, there is no standard method of addressing the problem. To better understand how to do this, we develop and analyze a mathematical model of Vicodin use and abuse, considering only those patients who were initially prescribed the drug. Through global sensitivity analysis, we show that focusing efforts on abuse prevention rather than treatment has greater success at reducing the population of Vicodin abusers. Our results demonstrate that relying solely on rehabilitation and other treatment programs is not enough to combat the prescription drug problem in the United States. We anticipate that implementing preventative measures in both prescribers and patients will reduce the number of Vicodin abusers. link: http://identifiers.org/pubmed/31513802

Parameters:

NameDescription
delta = 0.05Reaction: C2 => A, Rate Law: compartment*delta*C2
gamma_1 = 0.24Reaction: T => A, Rate Law: compartment*gamma_1*T
gamma_2 = 0.293Reaction: T =>, Rate Law: compartment*gamma_2*T
rho = 1.0E-6; lambda = 3000000.0Reaction: => M; A, Rate Law: compartment*lambda/(1+rho*A)
alpha_2 = 0.45Reaction: M =>, Rate Law: compartment*alpha_2*M
alpha_1 = 0.22Reaction: M => C1, Rate Law: compartment*alpha_1*M
gamma_3 = 8.0E-10Reaction: T => A, Rate Law: compartment*gamma_3*A*T
beta = 0.14Reaction: C2 =>, Rate Law: compartment*beta*C2
epsilon = 0.03Reaction: A => T, Rate Law: compartment*epsilon*A

States:

NameDescription
C2[C14141]
A[C16522]
C1[C14141]
T[treatment]
M[C14140]

Calzone2007_CellCycle: BIOMD0000000144v0.0.1

This is the Dynamical model of nuclear division cycles during early embryogenesis of Drosophila, without StringT regulat…

Details

Immediately following fertilization, the fruit fly embryo undergoes 13 rapid, synchronous, syncytial nuclear division cycles driven by maternal genes and proteins. During these mitotic cycles, there are barely detectable oscillations in the total level of B-type cyclins. In this paper, we propose a dynamical model for the molecular events underlying these early nuclear division cycles in Drosophila. The model distinguishes nuclear and cytoplasmic compartments of the embryo and permits exploration of a variety of rules for protein transport between the compartments. Numerical simulations reproduce the main features of wild-type mitotic cycles: patterns of protein accumulation and degradation, lengthening of later cycles, and arrest in interphase 14. The model is consistent with mutations that introduce subtle changes in the number of mitotic cycles before interphase arrest. Bifurcation analysis of the differential equations reveals the dependence of mitotic oscillations on cycle number, and how this dependence is altered by mutations. The model can be used to predict the phenotypes of novel mutations and effective ranges of the unmeasured rate constants and transport coefficients in the proposed mechanism. link: http://identifiers.org/pubmed/17667953

Parameters:

NameDescription
kins_1 = 0.08Reaction: => StgPn; StgPc, Rate Law: cytoplasm*kins_1*StgPc
ksxp_1 = 0.001Reaction: => Xp; Xm, Rate Law: cytoplasm*ksxp_1*Xm
E_1 = 7.0E-5; Wee1T = 0.8Reaction: Wee1Pc = (Wee1T-N*E_1*(Wee1n+Wee1Pn))/(1-N*E_1)-Wee1c, Rate Law: missing
Jm = 0.05; kdm = 0.2; kdmp = 0.002Reaction: Stgm => ; Xp, Rate Law: nuclei*(kdmp*Stgm/(Jm+Stgm)+kdm*Xp*Stgm)
E_1 = 7.0E-5; kinw_1 = 0.04Reaction: Wee1c => ; N, Rate Law: cytoplasm*kinw_1*Wee1c*E_1*N/(1-N*E_1)
kinw_1 = 0.04Reaction: => Wee1Pn; Wee1Pc, Rate Law: cytoplasm*kinw_1*Wee1Pc
ksxm_1 = 5.0E-4Reaction: => Xm; N, Rate Law: nuclei*ksxm_1*N
kt = 0.15Reaction: => MPFn; MPFc, Rate Law: cytoplasm*kt*MPFc
kouts_1 = 0.02Reaction: StgPn =>, Rate Law: nuclei*kouts_1*StgPn
kout_1 = 0.0Reaction: MPFn =>, Rate Law: nuclei*kout_1*MPFn
Jawee = 0.05; kawee = 0.3Reaction: Wee1Pn => Wee1n, Rate Law: nuclei*kawee*Wee1Pn/(Jawee+Wee1Pn)
E_1 = 7.0E-5; kouts_1 = 0.02Reaction: => StgPc; StgPn, N, Rate Law: nuclei*kouts_1*StgPn*E_1*N/(1-N*E_1)
E_1 = 7.0E-5; kt = 0.15Reaction: MPFc => ; N, Rate Law: cytoplasm*kt*MPFc*E_1*N/(1-N*E_1)
ksc = 0.01Reaction: => MPFc, Rate Law: ksc*cytoplasm
kdstg = 0.0Reaction: StgPc =>, Rate Law: cytoplasm*kdstg*StgPc
koutw_1 = 0.01Reaction: Wee1n =>, Rate Law: nuclei*koutw_1*Wee1n
kdn = 1.5; kdnp = 0.01Reaction: MPFn => ; FZYa, Rate Law: nuclei*(kdnp+kdn*FZYa)*MPFn
E_1 = 7.0E-5; kins_1 = 0.08Reaction: StgPc => ; N, Rate Law: cytoplasm*kins_1*StgPc*E_1*N/(1-N*E_1)
kstgp = 0.2; kstg = 2.0Reaction: preMPFc => MPFc; StgPc, Rate Law: cytoplasm*(kstgp+kstg*StgPc)*preMPFc
Jastg = 0.05; kastg = 1.0; kastgp = 0.0Reaction: Stgn => StgPn; MPFn, Rate Law: nuclei*(kastgp+kastg*MPFn)*Stgn/(Jastg+Stgn)
kaie = 1.0; Jaie = 0.01Reaction: => IEa_1; MPFn, Rate Law: nuclei*kaie*(1-IEa_1)*MPFn/((Jaie+1)-IEa_1)
E_1 = 7.0E-5; kout_1 = 0.0Reaction: => MPFc; N, MPFn, Rate Law: nuclei*kout_1*MPFn*E_1*N/(1-N*E_1)
Jistg = 0.05; kistg = 0.3Reaction: StgPn => Stgn, Rate Law: nuclei*kistg*StgPn/(Jistg+StgPn)
kafzy = 1.0; Jafzy = 0.01Reaction: => FZYa; IEa_1, Rate Law: nuclei*kafzy*IEa_1*(1-FZYa)/((Jafzy+1)-FZYa)
kweep = 0.005; kwee = 1.0Reaction: MPFc => preMPFc; Wee1c, Rate Law: cytoplasm*(kweep+kwee*Wee1c)*MPFc
Jiwee = 0.05; kiweep = 0.01; kiwee = 1.0Reaction: Wee1n => Wee1Pn; MPFn, Rate Law: nuclei*(kiweep+kiwee*MPFn)*Wee1n/(Jiwee+Wee1n)
Jifzy = 0.01; kifzy = 0.2Reaction: FZYa =>, Rate Law: nuclei*kifzy*FZYa/(Jifzy+FZYa)
kdc = 0.01Reaction: MPFc =>, Rate Law: cytoplasm*kdc*MPFc
kiie = 0.4; Jiie = 0.01Reaction: IEa_1 =>, Rate Law: nuclei*kiie*IEa_1/(Jiie+IEa_1)
ksstg = 0.0Reaction: => Stgc; Stgm, Rate Law: cytoplasm*ksstg*Stgm
koutw_1 = 0.01; E_1 = 7.0E-5Reaction: => Wee1Pc; Wee1Pn, N, Rate Law: nuclei*koutw_1*Wee1Pn*N*E_1/(1-N*E_1)

States:

NameDescription
Xm[messenger RNA]
Wee1Pc[Wee1-like protein kinase; Wee1-like protein kinase]
StgPc[M-phase inducer phosphatase]
preMPFc[MPF complex]
Wee1c[Wee1-like protein kinase; Wee1-like protein kinase]
StgPn[M-phase inducer phosphatase; IPR000751]
IEa 1FZYa
MPFn[G2/mitotic-specific cyclin-B; Cyclin-dependent kinase 1; MPF complex]
Stgc[M-phase inducer phosphatase]
Stgn[M-phase inducer phosphatase; IPR000751]
FZYa[FI02843pFizzyLD44795p; IPR000002]
NN
Stgm[messenger RNA]
Wee1Pn[Wee1-like protein kinase; Wee1-like protein kinase]
Wee1n[Wee1-like protein kinase; Wee1-like protein kinase]
MPFc[Cyclin-dependent kinase 1; G2/mitotic-specific cyclin-B; MPF complex]
XpXp
preMPFn[MPF complex]

Calzone2008_Rb: MODEL4132046015v0.0.1

Protein names are HUGO names or usual names. In the latter case, they are identified with a star (*) and the HUGO name i…

Details

We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large-scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway. link: http://identifiers.org/pubmed/18319725

Calzone2010_Cellfate_Master_Model: MODEL0912180000v0.0.1

**Attention:** As this model cannot be encoded in SBML at this time, the SBML file contains the whole model in [GINML](…

Details

Cytokines such as TNF and FASL can trigger death or survival depending on cell lines and cellular conditions. The mechanistic details of how a cell chooses among these cell fates are still unclear. The understanding of these processes is important since they are altered in many diseases, including cancer and AIDS. Using a discrete modelling formalism, we present a mathematical model of cell fate decision recapitulating and integrating the most consistent facts extracted from the literature. This model provides a generic high-level view of the interplays between NFkappaB pro-survival pathway, RIP1-dependent necrosis, and the apoptosis pathway in response to death receptor-mediated signals. Wild type simulations demonstrate robust segregation of cellular responses to receptor engagement. Model simulations recapitulate documented phenotypes of protein knockdowns and enable the prediction of the effects of novel knockdowns. In silico experiments simulate the outcomes following ligand removal at different stages, and suggest experimental approaches to further validate and specialise the model for particular cell types. We also propose a reduced conceptual model implementing the logic of the decision process. This analysis gives specific predictions regarding cross-talks between the three pathways, as well as the transient role of RIP1 protein in necrosis, and confirms the phenotypes of novel perturbations. Our wild type and mutant simulations provide novel insights to restore apoptosis in defective cells. The model analysis expands our understanding of how cell fate decision is made. Moreover, our current model can be used to assess contradictory or controversial data from the literature. Ultimately, it constitutes a valuable reasoning tool to delineate novel experiments. link: http://identifiers.org/pubmed/20221256

Cao2010 - Epigenetic state of lysogeny in phage lambda: MODEL1308080003v0.0.1

References: 1. Xiaomei Zhu, Lan Yin, Leroy Hood, David Galas and Ping Ao, Efficiency, Robustness and Stochasticity of Ge…

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Computational studies of biological networks can help to identify components and wirings responsible for observed phenotypes. However, studying stochastic networks controlling many biological processes is challenging. Similar to Schrödinger's equation in quantum mechanics, the chemical master equation (CME) provides a basic framework for understanding stochastic networks. However, except for simple problems, the CME cannot be solved analytically. Here we use a method called discrete chemical master equation (dCME) to compute directly the full steady-state probability landscape of the lysogeny maintenance network in phage lambda from its CME. Results show that wild-type phage lambda can maintain a constant level of repressor over a wide range of repressor degradation rate and is stable against UV irradiation, ensuring heritability of the lysogenic state. Furthermore, it can switch efficiently to the lytic state once repressor degradation increases past a high threshold by a small amount. We find that beyond bistability and nonlinear dimerization, cooperativity between repressors bound to O(R)1 and O(R)2 is required for stable and heritable epigenetic state of lysogeny that can switch efficiently. Mutants of phage lambda lack stability and do not possess a high threshold. Instead, they are leaky and respond to gradual changes in degradation rate. Our computation faithfully reproduces the hair triggers for UV-induced lysis observed in mutants and the limitation in robustness against mutations. The landscape approach computed from dCME is general and can be applied to study broad issues in systems biology. link: http://identifiers.org/pubmed/20937911

Cappuccio2006 - Cancer immunotherapy by interleukin-21: BIOMD0000000761v0.0.1

This model describes the effects of Il-21 on tumor eradication via natural killer cell-mediated and CD8+ T-cell-mediated…

Details

The newly characterized interleukin (IL)-21 plays a central role in the transition from innate immunity to adaptive immunity and shows substantial tumor regression in mice. IL-21 is now developed as a cancer immunotherapeutic drug, but conditions for efficacious therapy, and the conflicting immunostimulatory and immunoinhibitory influence of the cytokine, are yet to be defined. We studied the effects of IL-21 on tumor eradication in a mathematical model focusing on natural killer (NK) cell-mediated and CD8+ T-cell-mediated lysis of tumor cells. Model parameters were estimated using results in tumor-bearing mice treated with IL-21 via cytokine gene therapy (CGT), hydrodynamics-based gene delivery (HGD), or standard interval dosing (SID). Our model accurately retrieved experimental growth dynamics in the nonimmunogenic B16 melanoma and the immunogenic MethA and MCA205 fibrosarcomas, showing a strong dependence of the NK-cell/CD8+ T-cell balance on tumor immunogenicity. Moreover, in melanoma, simulations of CGT-like dosing regimens, dynamically determined according to tumor mass changes, resulted in efficient disease elimination. In contrast, in fibrosarcoma, such a strategy was not superior to that of fixed dosing regimens, HGD or SID. Our model supports clinical use of IL-21 as a potent stimulator of cellular immunity against cancer, and suggests selecting the immunotherapy strategy according to tumor immunogenicity. Nonimmunogenic tumors, but not highly immunogenic tumors, should be controlled by IL-21 dosing, which depends on tumor mass at the time of administration. This method imitates, yet amplifies, the natural anticancer immune response rather than accelerates only one of the response arms in an unbalanced manner. link: http://identifiers.org/pubmed/16849579

Parameters:

NameDescription
sigma = 0.003; h2zero = 0.066; r2 = 0.26 1/d; D = 1418.4Reaction: Y => ; M, Rate Law: compartment*r2*Y^2/(h2zero+sigma*M/(1+M/D))
h = 634.0 nmol/(mm*ml*d)Reaction: => U; Z, Rate Law: compartment*h*Z^(3/2)
mu2 = 0.014 1/dReaction: M =>, Rate Law: compartment*mu2*M
p1 = 0.01; p2 = 1.054; q1 = 0.54; r1 = 0.095 1/dReaction: X => ; X, U, Rate Law: compartment*r1*X^2/((p1*U+p2)/(U+q1))
mu3 = 0.08 1/dReaction: P =>, Rate Law: compartment*mu3*P
r2 = 0.26 1/dReaction: => Y, Rate Law: compartment*r2*Y
c = 5.1 (mm^2)/dReaction: => Z, Rate Law: compartment*c
mu1 = 10.0 1/dReaction: U =>, Rate Law: compartment*mu1*U
k1 = 0.05 ml/(d*nmol)Reaction: Z => ; P, X, Rate Law: compartment*k1*P*X*Z
r1 = 0.095 1/dReaction: => X, Rate Law: compartment*r1*X
a = 0.58 ml/(nmol*d)Reaction: => M; U, Rate Law: compartment*a*U
b2 = 0.1 nmol/ml; b1 = 1.0 nmol/(d*ml)Reaction: => P; U, Rate Law: compartment*b1*U/(b2+U)
k2 = 0.0485 ml/(d*nmol)Reaction: Z => ; P, Y, Rate Law: compartment*k2*P*Y*Z

States:

NameDescription
Y[CD8-Positive T-Lymphocyte; CD8-positive, alpha-beta thymocyte; lymph node]
Z[Surface; Tumor Mass]
U[Interleukin-21]
M[Regulator]
X[natural killer cell; spleen]
P[Perforin 1 (Pore forming protein)Perforin 1 (Pore forming protein), isoform CRA_a; Interferon gamma]

Capuani2015 - Human Core Catabolic Network: MODEL1506170000v0.0.1

Capuani2015 - Human Core Catabolic NetworkThis model is described in the article: [Quantitative constraint-based comput…

Details

Cancer cells utilize large amounts of ATP to sustain growth, relying primarily on non-oxidative, fermentative pathways for its production. In many types of cancers this leads, even in the presence of oxygen, to the secretion of carbon equivalents (usually in the form of lactate) in the cell’s surroundings, a feature known as the Warburg effect. While the molecular basis of this phenomenon are still to be elucidated, it is clear that the spilling of energy resources contributes to creating a peculiar microenvironment for tumors, possibly characterized by a degree of toxicity. This suggests that mechanisms for recycling the fermentation products (e.g. a lactate shuttle) may be active, effectively inducing a mutually beneficial metabolic coupling between aberrant and non-aberrant cells. Here we analyze this scenario through a large-scale in silico metabolic model of interacting human cells. By going beyond the cell-autonomous description, we show that elementary physico-chemical constraints indeed favor the establishment of such a coupling under very broad conditions. The characterization we obtained by tuning the aberrant cell’s demand for ATP, amino-acids and fatty acids and/or the imbalance in nutrient partitioning provides quantitative support to the idea that synergistic multi-cell effects play a central role in cancer sustainment. link: http://identifiers.org/doi/10.1038/srep11880

Caravagna2010 - Tumour suppression by immune system: BIOMD0000000912v0.0.1

Tumour suppression by immune system through stochastic oscillations GiulioCaravagnaa Albertod’Onofriob PaoloMilazzoa R…

Details

The well-known Kirschner-Panetta model for tumour-immune System interplay [Kirschner, D., Panetta, J.C., 1998. Modelling immunotherapy of the tumour-immune interaction. J. Math. Biol. 37 (3), 235-252] reproduces a number of features of this essential interaction, but it excludes the possibility of tumour suppression by the immune system in the absence of therapy. Here we present a hybrid-stochastic version of that model. In this new framework, we show that in reality the model is also able to reproduce the suppression, through stochastic extinction after the first spike of an oscillation. link: http://identifiers.org/pubmed/20580640

Parameters:

NameDescription
g3 = 1000.0; p2 = 5.0; V = 3.2; s2 = 0.0Reaction: => I; T, E, Rate Law: compartment*(p2/V*T*E/(g3*V+T)+s2)
p1 = 0.1245; s1 = 0.0; g1 = 2.0E7; V = 3.2; c = 0.02Reaction: => E; I, T, Rate Law: compartment*(p1*I/(g1*I)*E+c*T+V*s1)
a = 1.0; V = 3.2; g2 = 100000.0Reaction: T => ; E, Rate Law: compartment*a*T/(g2*V+T)*E
mu3 = 10.0Reaction: I =>, Rate Law: compartment*mu3*I
mu2 = 0.03Reaction: E =>, Rate Law: compartment*mu2*E
r2 = 0.18; V = 3.2; b = 1.0E-9Reaction: => T, Rate Law: compartment*r2*T*(1-b/V*T)

States:

NameDescription
I[Interleukin-2]
T[neoplasm]
E[Immune Cell]

Carbo2013 - Cytokine driven CD4+ T Cell differentiation and phenotype plasticity: BIOMD0000000451v0.0.1

Carbo2013 - Cytokine driven CD4+ T Cell differentiation and phenotype plasticityCD4+ T cells can differentiate into diff…

Details

Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu, complex intracellular signaling networks and numerous transcriptional regulators. We combined experimental approaches and computational modeling to investigate the mechanisms controlling differentiation and plasticity of CD4+ T cells in the gut of mice. Our computational model encompasses the major intracellular pathways involved in CD4+ T cell differentiation into T helper 1 (Th1), Th2, Th17 and induced regulatory T cells (iTreg). Our modeling efforts predicted a critical role for peroxisome proliferator-activated receptor gamma (PPARγ) in modulating plasticity between Th17 and iTreg cells. PPARγ regulates differentiation, activation and cytokine production, thereby controlling the induction of effector and regulatory responses, and is a promising therapeutic target for dysregulated immune responses and inflammation. Our modeling efforts predict that following PPARγ activation, Th17 cells undergo phenotype switch and become iTreg cells. This prediction was validated by results of adoptive transfer studies showing an increase of colonic iTreg and a decrease of Th17 cells in the gut mucosa of mice with colitis following pharmacological activation of PPARγ. Deletion of PPARγ in CD4+ T cells impaired mucosal iTreg and enhanced colitogenic Th17 responses in mice with CD4+ T cell-induced colitis. Thus, for the first time we provide novel molecular evidence in vivo demonstrating that PPARγ in addition to regulating CD4+ T cell differentiation also plays a major role controlling Th17 and iTreg plasticity in the gut mucosa. link: http://identifiers.org/pubmed/23592971

Parameters:

NameDescription
parameter_1 = 2.0; K3=98.0373; K5=4.32731; K2=56.3452; Vr=0.1; K4=0.855534; K1=0.210399; Vf=0.1Reaction: species_15 => s31; s26, species_13, s31, s35, s39, species_15, s26, species_13, s31, s35, s39, Rate Law: Vf*species_15*K1^parameter_1/(s26^parameter_1+K1^parameter_1)*K2^parameter_1/(species_13^parameter_1+K2^parameter_1)*(s31^parameter_1/(s31^parameter_1+K3^parameter_1)+s35^parameter_1/(s35^parameter_1+K4^parameter_1)+s39^parameter_1/(s39^parameter_1+K5^parameter_1))-Vr*s31
K4=0.321065; K5=0.1; parameter_1 = 2.0; K3=0.214012; Vr=0.1; K2=9.61521; Vf=0.1; K1=0.199351Reaction: s81 => s35; s27, s49, s45, s34, s83, s81, s27, s49, s45, s34, s83, s35, Rate Law: c1*(Vf*s81*K1^parameter_1/(s27^parameter_1+K1^parameter_1)*K2^parameter_1/(s49^parameter_1+K2^parameter_1)*K3^parameter_1/(s45^parameter_1+K3^parameter_1)*(s34^parameter_1/(s34^parameter_1+K4^parameter_1)+s83^parameter_1/(s83^parameter_1+K5^parameter_1))-Vr*s35)
Vr=0.1; parameter_1 = 2.0; Vf=0.1; K=0.1; K1=25.5354Reaction: species_9 + species_8 => s57; s83, s48, species_9, species_8, s83, s48, s57, Rate Law: c1*(Vf*species_9*species_8*K^parameter_1/(s83^parameter_1+K^parameter_1)*(1+s48^parameter_1/(s48^parameter_1+K1^parameter_1))-Vr*s57)
K6=100.0; K5=2.07945; Vr=0.1; K2=0.354892; K7=1.93254E-7; Vf=0.1; K4=6.79025E-4; parameter_1 = 2.0; K1=100.0; K3=1.31281Reaction: s78 => s40; s34, s49, s48, s45, s26, s39, s83, s78, s34, s49, s48, s45, s26, s39, s83, s40, Rate Law: c1*(Vf*s78*K1^parameter_1/(s34^parameter_1+K1^parameter_1)*K2^parameter_1/(s49^parameter_1+K2^parameter_1)*K3^parameter_1/(s48^parameter_1+K3^parameter_1)*(s45^parameter_1/(s45^parameter_1+K4^parameter_1)+s26^parameter_1/(s26^parameter_1+K5^parameter_1)+s39^parameter_1/(s39^parameter_1+K6^parameter_1)+s83^parameter_1/(s83^parameter_1+K7^parameter_1))-Vr*s40)
k1=0.1; k2=0.1Reaction: s87 + s44 => s45; s87, s44, s45, Rate Law: k1*s87*s44-k2*s45
parameter_1 = 2.0; K3=5.47889; K1=1.62893; Vf=0.225095; Vr=0.1; K2=0.526832; K=0.1Reaction: species_7 => s73; s83, s59, s50, s21, species_7, s83, s59, s50, s21, s73, Rate Law: c1*(Vf*species_7*K^parameter_1/(s83^parameter_1+K^parameter_1)*(s59^parameter_1/(s59^parameter_1+K1^parameter_1)+s50^parameter_1/(s50^parameter_1+K2^parameter_1)+s21^parameter_1/(s21^parameter_1+K3^parameter_1))-Vr*s73)
Vr=0.1; parameter_1 = 2.0; Vf=0.1; K=0.374591Reaction: s77 => s39; s38, s77, s38, s39, Rate Law: c1*(Vf*s77*(1+s38^parameter_1/(s38^parameter_1+K^parameter_1))-Vr*s39)
parameter_1 = 2.0; V=0.1; k=0.5Reaction: species_17 => s11; species_17, s11, Rate Law: default*V*(species_17^parameter_1/(species_17^parameter_1+s11^parameter_1+0.001)-k*s11)
parameter_1 = 2.0; K4=0.137545; K2=39.018; Vr=0.1; K1=0.636796; Vf=0.1; K=0.1; K3=2.26986Reaction: s76 => s49; s83, s54, s59, s63, s48, s76, s83, s54, s59, s63, s48, s49, Rate Law: c1*(Vf*s76*K^parameter_1/(s83^parameter_1+K^parameter_1)*(s54^parameter_1/(s54^parameter_1+K1^parameter_1)+s59^parameter_1/(s59^parameter_1+K2^parameter_1)+s63^parameter_1/(s63^parameter_1+K3^parameter_1)+s48^parameter_1/(s48^parameter_1+K4^parameter_1))-Vr*s49)
k2=0.1896; k1=0.184881Reaction: species_1 + species_4 => species_3; species_1, species_4, species_3, Rate Law: k1*species_1*species_4-k2*species_3
K=2.01676; Vr=0.1; parameter_1 = 2.0; Vf=0.1Reaction: s65 => s10; s3, s65, s3, s10, Rate Law: c1*(Vf*s65*(1+s3^parameter_1/(s3^parameter_1+K^parameter_1))-Vr*s10)
Vr=0.1; parameter_1 = 2.0; n1=0.004304; K1=0.1; Vf=0.1; K=0.1Reaction: s82 => s34; s25, s33, s82, s25, s33, s34, Rate Law: c1*(Vf*s82*K^parameter_1/(s25^parameter_1+K^parameter_1)*s33^n1/(s33^n1+K1^n1)-Vr*s34)
Vr=0.1; parameter_1 = 2.0; K=4.66107; Vf=0.1Reaction: s57 + s58 => s59; s27, s57, s58, s27, s59, Rate Law: c1*(Vf*s57*s58*K^parameter_1/(s27^parameter_1+K^parameter_1)-Vr*s59)
Vr=0.1; parameter_1 = 2.0; K1=0.1; Vf=0.1; K=0.1Reaction: s85 + s86 => s83; s25, s33, s85, s86, s25, s33, s83, Rate Law: c1*(Vf*s85*s86*K^parameter_1/(s25^parameter_1+K^parameter_1)*(1+s33^parameter_1/(s33^parameter_1+K1^parameter_1))-Vr*s83)
Vr=0.1; parameter_1 = 2.0; K2=0.667462; Vf=0.1; K1=7.83763Reaction: s79 => s29; s26, s27, s79, s26, s27, s29, Rate Law: c1*(Vf*s79*s26^parameter_1/(s26^parameter_1+K1^parameter_1)*s27^parameter_1/(s27^parameter_1+K2^parameter_1)-Vr*s29)
parameter_1 = 2.0; K3=3.58849; K2=1.33537; K1=0.916783; K4=0.727962; Vr=0.1; K5=6.97805; Vf=0.1Reaction: s80 => s27; s45, s49, s21, s26, s27, s80, s45, s49, s21, s26, s27, Rate Law: c1*(Vf*s80*K1^parameter_1/(s45^parameter_1+K1^parameter_1)*K2^parameter_1/(s49^parameter_1+K2^parameter_1)*(s21^parameter_1/(s21^parameter_1+K3^parameter_1)+s26^parameter_1/(s26^parameter_1+K4^parameter_1)+s27^parameter_1/(s27^parameter_1+K5^parameter_1))-Vr*s27)
parameter_1 = 2.0; K2=0.703778; Vf=0.2249; K3=1.24123; Vr=0.1; K4=997.263; K1=9722.09Reaction: s75 => s50; s40, s83, s49, s45, s75, s40, s83, s49, s45, s50, Rate Law: c1*(Vf*s75*K1^parameter_1/(s40^parameter_1+K1^parameter_1)*K2^parameter_1/(s83^parameter_1+K2^parameter_1)*(s49^parameter_1/(s49^parameter_1+K3^parameter_1)+s45^parameter_1/(s45^parameter_1+K4^parameter_1))-Vr*s50)
Vr=0.1; parameter_1 = 2.0; K=0.118892; Vf=0.1Reaction: species_6 => s52; s49, species_6, s49, s52, Rate Law: c1*(Vf*species_6*(1+s49^parameter_1/(s49^parameter_1+K^parameter_1))-Vr*s52)
parameter_1 = 2.0; K1=0.125481; K3=0.031433; Vr=0.1; Vf=0.1; K4=66.6168; K2=0.896854Reaction: s67 => s21; s54, s35, s14, s59, s67, s54, s35, s14, s59, s21, Rate Law: c1*(Vf*s67*K1^parameter_1/(s54^parameter_1+K1^parameter_1)*K2^parameter_1/(s35^parameter_1+K2^parameter_1)*(s14^parameter_1/(s14^parameter_1+K3^parameter_1)+s59^parameter_1/(s59^parameter_1+K4^parameter_1))-Vr*s21)
parameter_1 = 2.0; K3=14.9778; Vr=0.1; K1=5.04432; K2=0.0705365; Vf=0.1; K=0.1Reaction: s70 => s26; s83, s54, s25, s28, s70, s83, s54, s25, s28, s26, Rate Law: c1*(Vf*s70*K^parameter_1/(s83^parameter_1+K^parameter_1)*(s54^parameter_1/(s54^parameter_1+K1^parameter_1)+s25^parameter_1/(s25^parameter_1+K2^parameter_1)+s28^parameter_1/(s28^parameter_1+K3^parameter_1))-Vr*s26)
k=0.1; parameter_1 = 2.0; V=0.1Reaction: species_19 => s51; species_19, s51, Rate Law: default*V*(species_19^parameter_1/(species_19^parameter_1+s51^parameter_1+0.001)-k*s51)
Vr=0.1; parameter_1 = 2.0; K=0.138094; Vf=0.1Reaction: species_12 + s2 => s3; s34, species_12, s2, s34, s3, Rate Law: Vf*species_12*s2*K^parameter_1/(s34^parameter_1+K^parameter_1)-Vr*s3
k1=0.1Reaction: s12 => s11; s12, Rate Law: k1*s12
K=0.240705; Vr=0.1; parameter_1 = 2.0; K1=8.14189; Vf=0.1Reaction: s51 + s53 => s54; s39, species_3, s51, s53, s39, species_3, s54, Rate Law: Vf*s51*s53*K^parameter_1/(s39^parameter_1+K^parameter_1)*(1+species_3^parameter_1/(species_3^parameter_1+K1^parameter_1))-Vr*s54
Vr=0.1; parameter_1 = 2.0; K=0.263953; Vf=0.1Reaction: s22 + s24 => s25; s29, s22, s24, s29, s25, Rate Law: Vf*s22*s24*K^parameter_1/(s29^parameter_1+K^parameter_1)-Vr*s25
Vr=0.1; parameter_1 = 2.0; K2=0.743847; Vf=0.1; K1=2.94611Reaction: s11 + s13 => s14; s34, s83, s11, s13, s34, s83, s14, Rate Law: Vf*s11*s13*K1^parameter_1/(s34^parameter_1+K1^parameter_1)*K2^parameter_1/(s83^parameter_1+K2^parameter_1)-Vr*s14
parameter_1 = 2.0; Vr=0.1; K1=0.1; K2=0.004433; Vf=0.1; K3=99.987Reaction: s69 => s28; s83, s29, s25, s69, s83, s29, s25, s28, Rate Law: c1*(Vf*s69*K1^parameter_1/(s83^parameter_1+K1^parameter_1)*K2^parameter_1/(s29^parameter_1+K2^parameter_1)*(1+s25^parameter_1/(s25^parameter_1+K3^parameter_1))-Vr*s28)
K4=100.0; parameter_1 = 2.0; K3=0.645162; K2=0.00125893; K=0.508159; Vr=0.1; K1=0.1; Vf=0.1Reaction: species_27 => s74; s59, s83, s54, s35, s39, species_27, s59, s83, s54, s35, s39, s74, Rate Law: Vf*species_27*K^parameter_1/(s59^parameter_1+K^parameter_1)*(s83^parameter_1/(s83^parameter_1+K1^parameter_1)+s54^parameter_1/(s54^parameter_1+K2^parameter_1)+s35^parameter_1/(s35^parameter_1+K3^parameter_1)+s39^parameter_1/(s39^parameter_1+K4^parameter_1))-Vr*s74
Vr=0.1; parameter_1 = 2.0; K=13.0657; Vf=0.1Reaction: s30 + s32 => s33; s29, s30, s32, s29, s33, Rate Law: Vf*s30*s32*K^parameter_1/(s29^parameter_1+K^parameter_1)-Vr*s33

States:

NameDescription
species 26[Interleukin-4]
s27[Transcription factor T-bet; phosphorylated]
s14[Interleukin-12 subunit beta; Interleukin-12 subunit alpha; Interleukin-12 receptor subunit beta-1; Interleukin-12 receptor subunit beta-2]
s37[Interleukin-2 receptor subunit alpha]
s40[Forkhead box protein P3; acetylation]
species 1[IPR010345]
species 20[Interleukin-23 subunit alpha]
s44[TGF-beta receptor type-1]
species 18[Interferon gamma]
species 16[Interleukin-18]
s36[Interleukin-2]
s34[Signal transducer and transcription activator 6; phosphorylated]
s31[Interleukin-4]
s52[Interleukin-21]
s10[Interleukin-1 receptor-associated kinase 1; phosphorylated]
s38[Interleukin-2; Interleukin-2 receptor subunit alpha]
s46[Interleukin-6]
s11[Interleukin-12 subunit alpha; Interleukin-12 subunit beta]
s70[Signal transducer and activator of transcription 1]
species 21[IPR010345]
species 8[Interleukin-23 subunit alpha]
s77[Signal transducer and activator of transcription 5A]
species 12[Interleukin-18]
species 25[Transforming growth factor beta-1]
species 17[Interleukin-12 subunit beta; Interleukin-12 subunit alpha]
s69[Tyrosine-protein kinase JAK1]
s45[Transforming growth factor beta-1; TGF-beta receptor type-1]
species 15[Interleukin-4]
species 2[Interleukin-10]
s55[Interleukin-23 subunit alpha]
s25[Interferon gamma; Interferon gamma receptor 1]
s75[Nuclear receptor ROR-gamma]
s33[Interleukin-4; Interleukin-4 receptor subunit alpha]
s49[Signal transducer and activator of transcription 3; phosphorylated]
species 24[Interleukin-2]
s82[Signal transducer and transcription activator 6]
s59[Interleukin-23 subunit alpha; Interleukin-23 receptor]
species 22[Interleukin-10]
s21[Signal transducer and activator of transcription 4; phosphorylated]
s90[Interleukin-6]
s74[Interleukin-10]
s28[Tyrosine-protein kinase JAK1; phosphorylated]
species 23[Interleukin-6]
s85[Peroxisome proliferator activated receptor gammaPeroxisome proliferator-activated receptor gammaPeroxisome proliferator-activated receptor gamma isoform 2Peroxisome proliferator-activated receptor gamma transcript 2]
s78[Forkhead box protein P3]
s76[Signal transducer and activator of transcription 3]
s86[SBO:0000280]
species 27[Interleukin-10]
s24[Interferon gamma receptor 1]
s35[Trans-acting T-cell-specific transcription factor GATA-3; phosphorylated]
s57[Interleukin-23 subunit alpha; Interleukin-12 subunit beta]
s43[Transforming growth factor beta-1]
s47[Interleukin-6 receptor subunit alpha; Interleukin-6 receptor subunit beta]
s81[Trans-acting T-cell-specific transcription factor GATA-3]
s87[Transforming growth factor beta-1]
s32[Interleukin-4 receptor subunit alpha]
s22[Interferon gamma]
s89[Interleukin-2]
s51[Interleukin-21]
s3[Interleukin-18; Interleukin-18 receptor 1]
s48[Interleukin-6; Interleukin-6 receptor subunit alpha; Interleukin-6 receptor subunit beta]
species 19[Interleukin-21]
s68[Interferon gamma]
s13[Interleukin-12 receptor subunit beta-1; Interleukin-12 receptor subunit beta-2]
s12[Interleukin-12 subunit alpha; Interleukin-12 subunit beta]
s73[IPR010345]
s30[Interleukin-4]
s79[Suppressor of cytokine signaling 1]
s62[Interleukin-10 receptor subunit alpha; Interleukin-10 receptor subunit beta]
s26[Signal transducer and activator of transcription 1; phosphorylated]
s39[Signal transducer and activator of transcription 5A; phosphorylated]
s65[Interleukin-1 receptor-associated kinase 1]
s29[Suppressor of cytokine signaling 1; Tyrosine-protein kinase JAK1]
s83[Peroxisome proliferator activated receptor gammaPeroxisome proliferator-activated receptor gammaPeroxisome proliferator-activated receptor gamma isoform 2Peroxisome proliferator-activated receptor gamma transcript 2; SBO:0000280]

Carbo2013 - Mucosal Immune Response during H.pylori Infection: BIOMD0000000480v0.0.1
Details

T helper (Th) cells play a major role in the immune response and pathology at the gastric mucosa during Helicobacter pylori infection. There is a limited mechanistic understanding regarding the contributions of CD4+ T cell subsets to gastritis development during H. pylori colonization. We used two computational approaches: ordinary differential equation (ODE)-based and agent-based modeling (ABM) to study the mechanisms underlying cellular immune responses to H. pylori and how CD4+ T cell subsets influenced initiation, progression and outcome of disease. To calibrate the model, in vivo experimentation was performed by infecting C57BL/6 mice intragastrically with H. pylori and assaying immune cell subsets in the stomach and gastric lymph nodes (GLN) on days 0, 7, 14, 30 and 60 post-infection. Our computational model reproduced the dynamics of effector and regulatory pathways in the gastric lamina propria (LP) in silico. Simulation results show the induction of a Th17 response and a dominant Th1 response, together with a regulatory response characterized by high levels of mucosal Treg) cells. We also investigated the potential role of peroxisome proliferator-activated receptor γ (PPARγ) activation on the modulation of host responses to H. pylori by using loss-of-function approaches. Specifically, in silico results showed a predominance of Th1 and Th17 cells in the stomach of the cell-specific PPARγ knockout system when compared to the wild-type simulation. Spatio-temporal, object-oriented ABM approaches suggested similar dynamics in induction of host responses showing analogous T cell distributions to ODE modeling and facilitated tracking lesion formation. In addition, sensitivity analysis predicted a crucial contribution of Th1 and Th17 effector responses as mediators of histopathological changes in the gastric mucosa during chronic stages of infection, which were experimentally validated in mice. These integrated immunoinformatics approaches characterized the induction of mucosal effector and regulatory pathways controlled by PPARγ during H. pylori infection affecting disease outcomes. link: http://identifiers.org/doi/10.1371/journal.pone.0073365

Parameters:

NameDescription
parameter_81 = 6416.67253955392Reaction: => s30, Rate Law: c3*parameter_81
parameter_19 = 1.0Reaction: s6 => ; s6, Rate Law: c2*parameter_19*s6
parameter_24 = 1.0E-6Reaction: s17 => s15; s21, s25, s17, s21, s25, Rate Law: c2*s17*(parameter_24*s21+parameter_24*s25)
parameter_58 = 5.0E-7Reaction: species_1 + s6 => s25; species_1, s6, Rate Law: c2*parameter_58*species_1*s6
parameter_92 = 100000.0; parameter_61 = 1.0; parameter_63 = 2.0Reaction: s22 => s21; s21, s15, s25, s22, s21, s15, s25, Rate Law: c2*parameter_61*s22*(s21^parameter_63/(s21^parameter_63+parameter_92^parameter_63)+s15^parameter_63/(s15^parameter_63+parameter_92^parameter_63)+s25^parameter_63/(s25^parameter_63+parameter_92^parameter_63))
parameter_16 = 0.00858Reaction: s13 => s29; s13, Rate Law: parameter_16*s13
k1=0.00214783Reaction: s28 => species_14; s28, Rate Law: k1*s28
parameter_48 = 1.0E-6; parameter_32 = 1.0E-4; parameter_38 = 1.0E-4Reaction: s2 => species_5; s13, s16, s19, s2, s13, s16, s19, Rate Law: c4*parameter_48*s2*(parameter_32*s13+parameter_32*s16+parameter_38*s19)
parameter_20 = 2.0; parameter_93 = 0.001Reaction: s6 => s6; s6, Rate Law: c2*parameter_20*s6/(parameter_93+s6)
parameter_55 = 0.313385Reaction: s4 + s1 => s9; s4, s1, Rate Law: parameter_55*s4*s1
parameter_37 = 1.0E-6Reaction: s1 => s6; s3, s1, s3, Rate Law: s1*s3*parameter_37
parameter_26 = 3.0E-7; parameter_102 = 3.0E-7Reaction: s29 => s30; s26, species_20, s29, s26, species_20, Rate Law: c3*s29*(parameter_26*s26+parameter_102*species_20)
parameter_9 = 1.0Reaction: s9 => s26; s9, Rate Law: parameter_9*s9
parameter_104 = 3.0E-13; parameter_29 = 3.0E-13Reaction: s28 => s30; s26, species_20, s28, s26, species_20, Rate Law: c3*s28*(parameter_29*s26+parameter_104*species_20)
parameter_15 = 0.00572Reaction: s15 => s17; s15, Rate Law: c2*parameter_15*s15
parameter_8 = 0.5Reaction: s31 => s13; s31, Rate Law: parameter_8*s31
parameter_88 = 2.5; parameter_92 = 100000.0; parameter_63 = 2.0Reaction: s16 => s15; s15, s25, s21, s16, s15, s25, s21, Rate Law: c2*parameter_88*s16*(s15^parameter_63/(s15^parameter_63+parameter_92^parameter_63)+s25^parameter_63/(s25^parameter_63+parameter_92^parameter_63)+s21^parameter_63/(s21^parameter_63+parameter_92^parameter_63))
parameter_84 = 92.0216844836741Reaction: => s16, Rate Law: c2*parameter_84
parameter_27 = 1.0E-6Reaction: s29 => s33; s27, s29, s27, Rate Law: c3*s29*s27*parameter_27
parameter_77 = 0.5Reaction: s4 => s25; species_10, s4, species_10, Rate Law: s4*species_10*parameter_77
parameter_31 = 1000.0; parameter_63 = 2.0; parameter_87 = 1.0; parameter_91 = 100000.0Reaction: s15 => s16; s16, s9, s19, s13, s3, s15, s16, s9, s19, s13, s3, Rate Law: c2*parameter_87*s15*(s16^parameter_63/(s16^parameter_63+parameter_91^parameter_63)+s9^parameter_63/(s9^parameter_63+parameter_91^parameter_63)+s19^parameter_63/(s19^parameter_63+parameter_91^parameter_63)+s13^parameter_63/(s13^parameter_63+parameter_91^parameter_63)+s3^parameter_63/(s3^parameter_63+parameter_31^parameter_63))
parameter_66 = 1000000.0; parameter_85 = 10000.0; parameter_40 = 1000.0; parameter_63 = 2.0; parameter_41 = 1000.0Reaction: => species_1; s3, s19, s9, s3, s19, s9, Rate Law: c2*(parameter_66+parameter_41*(s3^parameter_63/(s3^parameter_63+parameter_40^parameter_63)+s19^parameter_63/(s19^parameter_63+parameter_85^parameter_63)+s9^parameter_63/(s9^parameter_63+parameter_85^parameter_63)))
parameter_21 = 1.0Reaction: species_5 => s2; species_5, Rate Law: c4*parameter_21*species_5
parameter_57 = 0.313385Reaction: species_1 + s6 => s9; species_1, s6, Rate Law: c2*parameter_57*species_1*s6
parameter_80 = 14972.2359256258Reaction: => s31, Rate Law: c3*parameter_80
parameter_60 = 5.0E-7Reaction: s22 + s6 => s21; s22, s6, Rate Law: c2*parameter_60*s22*s6
parameter_79 = 0.0Reaction: => s33, Rate Law: c3*parameter_79
parameter_48 = 1.0E-6; parameter_39 = 1.0; parameter_38 = 1.0E-4Reaction: s6 => ; s3, s19, s6, s3, s19, Rate Law: c2*s6*parameter_48*(parameter_39*s3+parameter_38*s19)
parameter_101 = 7.0E-7; parameter_25 = 7.0E-7Reaction: s29 => s31; s26, species_20, s29, s26, species_20, Rate Law: c3*s29*(parameter_25*s26+parameter_101*species_20)
parameter_44 = 1.0Reaction: species_1 => ; species_1, Rate Law: c2*parameter_44*species_1
parameter_82 = 0.0Reaction: => s15, Rate Law: c2*parameter_82
parameter_7 = 1.0E-6Reaction: s2 => s3; s1, s2, s1, Rate Law: c4*s2*s1*parameter_7
k1=0.00260615Reaction: s28 => species_12; s28, Rate Law: k1*s28
parameter_78 = 0.313385Reaction: s4 => s9; species_10, s4, species_10, Rate Law: s4*species_10*parameter_78
parameter_59 = 5.0E-7Reaction: s22 + s6 => s19; s22, s6, Rate Law: c2*parameter_59*s22*s6
parameter_70 = 10.0Reaction: species_9 = 0.01*(s31+s30+s33+(s28+s29)/parameter_70), Rate Law: missing
parameter_63 = 2.0; parameter_88 = 2.5; parameter_92 = 100000.0Reaction: s30 => s33; s33, s27, s30, s33, s27, Rate Law: c3*parameter_88*s30*(s33^parameter_63/(s33^parameter_63+parameter_92^parameter_63)+s27^parameter_63/(s27^parameter_63+parameter_92^parameter_63))
parameter_83 = 214.717263795239Reaction: => s13, Rate Law: c2*parameter_83
parameter_92 = 100000.0; parameter_90 = 1.0; parameter_63 = 2.0Reaction: s19 => s21; s15, s21, s25, s19, s15, s21, s25, Rate Law: c2*parameter_90*s19*(s15^parameter_63/(s15^parameter_63+parameter_92^parameter_63)+s21^parameter_63/(s21^parameter_63+parameter_92^parameter_63)+s25^parameter_63/(s25^parameter_63+parameter_92^parameter_63))
k1=0.00346737Reaction: s28 => species_16; s28, Rate Law: k1*s28
k1=0.167494Reaction: species_15 => species_17; species_15, Rate Law: c1*k1*species_15
parameter_64 = 0.1287Reaction: s13 => ; s13, Rate Law: c2*parameter_64*s13
parameter_46 = 0.5Reaction: s26 => ; s26, Rate Law: c3*parameter_46*s26
parameter_103 = 7.0E-13; parameter_28 = 7.0E-13Reaction: s28 => s31; s26, s28, s26, Rate Law: c3*s28*(parameter_28*s26+parameter_103*s26)
parameter_89 = 2.0; parameter_31 = 1000.0; parameter_63 = 2.0; parameter_91 = 100000.0Reaction: s21 => s19; s13, s19, s9, s16, s3, s21, s13, s19, s9, s16, s3, Rate Law: c2*parameter_89*s21*(s13^parameter_63/(s13^parameter_63+parameter_91^parameter_63)+s19^parameter_63/(s19^parameter_63+parameter_91^parameter_63)+s9^parameter_63/(s9^parameter_63+parameter_91^parameter_63)+s16^parameter_63/(s16^parameter_63+parameter_91^parameter_63)+s3^parameter_63/(s3^parameter_63+parameter_31^parameter_63))
parameter_62 = 0.0218776162394955Reaction: s21 => ; s21, Rate Law: c2*parameter_62*s21
parameter_30 = 1.0E-12Reaction: s28 => s33; s27, s28, s27, Rate Law: c3*s28*s27*parameter_30
parameter_23 = 7.0E-7; parameter_100 = 7.0E-7Reaction: s17 => s13; s19, s9, species_18, s17, s19, s9, species_18, Rate Law: c2*s17*(parameter_23*s19+parameter_23*s9+parameter_100*species_18)
parameter_106 = 1.0; parameter_61 = 1.0; parameter_63 = 2.0; parameter_91 = 100000.0Reaction: s22 => s19; s19, s9, s13, s16, s3, s22, s19, s9, s13, s16, s3, Rate Law: c2*parameter_61*s22*(s19^parameter_63/(s19^parameter_63+parameter_91^parameter_63)+s9^parameter_63/(s9^parameter_63+parameter_91^parameter_63)+s13^parameter_63/(s13^parameter_63+parameter_91^parameter_63)+s16^parameter_63/(s16^parameter_63+parameter_91^parameter_63)+s3^parameter_63/(s3^parameter_63+parameter_106^parameter_63))
parameter_63 = 2.0; parameter_87 = 1.0; parameter_91 = 100000.0Reaction: s33 => s30; s31, s26, s30, s33, s31, s26, s30, Rate Law: c3*parameter_87*s33*(s31^parameter_63/(s31^parameter_63+parameter_91^parameter_63)+s26^parameter_63/(s26^parameter_63+parameter_91^parameter_63)+s30^parameter_63/(s30^parameter_63+parameter_91^parameter_63))
parameter_45 = 1.0Reaction: s22 => ; s22, Rate Law: c2*parameter_45*s22
parameter_56 = 5.0E-7Reaction: s4 + s1 => s25; s4, s1, Rate Law: parameter_56*s4*s1
parameter_99 = 3.0E-7; parameter_22 = 3.0E-7Reaction: s17 => s16; s19, s9, species_18, s17, s19, s9, species_18, Rate Law: c2*s17*(parameter_22*s19+parameter_22*s9+parameter_99*species_18)
parameter_106 = 1.0; parameter_105 = 0.0; parameter_63 = 2.0; parameter_91 = 100000.0Reaction: s2 => s3; s13, s16, s9, s19, s3, s2, s13, s16, s9, s19, s3, Rate Law: c4*parameter_105*s2*(s13^parameter_63/(s13^parameter_63+parameter_91^parameter_63)+s16^parameter_63/(s16^parameter_63+parameter_91^parameter_63)+s9^parameter_63/(s9^parameter_63+parameter_91^parameter_63)+s19^parameter_63/(s19^parameter_63+parameter_91^parameter_63)+s3^parameter_63/(s3^parameter_63+parameter_106^parameter_63))
k=1.35871; V=94.3761Reaction: species_1 => s4; species_1, s4, Rate Law: V*(species_1-k*s4)

States:

NameDescription
species 9[Region of mucosa]
species 1[dendritic cell; inactive]
species 20[tolerogen; Bacteria; dendritic cell]
species 4[Region of mucosa]
species 18[tolerogen; Bacteria; dendritic cell]
s9[dendritic cell]
s19[inflammatory macrophage]
s31[T-helper 1 cell]
s6[Helicobacter pylori]
s22[macrophage; undifferentiated]
s15[CD4-positive, CD25-positive, alpha-beta regulatory T cell; inactive]
species 8[Region of mucosa]
species 17[CD4-positive, CD25-positive, alpha-beta regulatory T cell; lamina propria]
species 5[epithelial cell; damaged]
s3[epithelial cell]
species 2[dendritic cell]
species 6[dendritic cell]
s17[Region of mucosa]
s13[T-helper 1 cell]
s25[dendritic cell]
s33[inactive]
s4[dendritic cell; inactive]
s2[epithelial cell]
s16[T-helper 17 cell]
s30[T-helper 17 cell]
s26[dendritic cell]
s21[alternatively activated macrophage]
species 3[macrophage]
s28[Region of mucosa]
s29[Region of mucosa]

Carcione2020 - Deterministic SEIR simulation of a COVID-19 outbreak: BIOMD0000000974v0.0.1

An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement…

Details

An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and the number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 24, but by no means attempts to perform a rigorous case study in view of the lack of suitable data and the uncertainty of the different parameters, namely, the variation of the degree of home isolation and social distancing as a function of time, the initial number of exposed individuals and infected people, the incubation and infectious periods, and the fatality rate. First, we perform an analysis of the results of the model by varying the parameters and initial conditions (in order for the epidemic to start, there should be at least one exposed or one infectious human). Then, we consider the Lombardy case and calibrate the model with the number of dead individuals to date (May 5, 2020) and constrain the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, with a reproduction ratio R 0 of 3 initially, 1.36 at day 22, and 0.8 after day 35, indicating different degrees of lockdown. The predicted death toll is approximately 15,600 casualties, with 2.7 million infected individuals at the end of the epidemic. The incubation period providing a better fit to the dead individuals is 4.25 days, and the infectious period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57%, and it is 2.37% if twice the reported number of casualties is assumed. However, these rates depend on the initial number of exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47%. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infectious periods, we observe that a higher incubation period (13 vs. 4.25 days) gives the same IFR (0.6 vs. 0.57%), but nine times more exposed individuals in the first case. Other choices of the set of parameters also provide a good fit to the data, but some of the results may not be realistic. Therefore, an accurate determination of the fatality rate and characteristics of the epidemic is subject to knowledge of the precise bounds of the parameters. Besides the specific example, the analysis proposed in this work shows how isolation measures, social distancing, and knowledge of the diffusion conditions help us to understand the dynamics of the epidemic. Hence, it is important to quantify the process to verify the effectiveness of the lockdown. link: http://identifiers.org/pubmed/32574303

Caron2010_mTOR_SignalingNetwork: MODEL1012220002v0.0.1

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/…

Details

The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation. mTOR signaling is frequently dysregulated in oncogenic cells, and thus an attractive target for anticancer therapy. Using CellDesigner, a modeling support software for graphical notation, we present herein a comprehensive map of the mTOR signaling network, which includes 964 species connected by 777 reactions. The map complies with both the systems biology markup language (SBML) and graphical notation (SBGN) for computational analysis and graphical representation, respectively. As captured in the mTOR map, we review and discuss our current understanding of the mTOR signaling network and highlight the impact of mTOR feedback and crosstalk regulations on drug-based cancer therapy. This map is available on the Payao platform, a Web 2.0 based community-wide interactive process for creating more accurate and information-rich databases. Thus, this comprehensive map of the mTOR network will serve as a tool to facilitate systems-level study of up-to-date mTOR network components and signaling events toward the discovery of novel regulatory processes and therapeutic strategies for cancer. link: http://identifiers.org/pubmed/21179025

Caron2010_mTORC1_UpstreamRegulators: MODEL1012220003v0.0.1

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/…

Details

The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation. mTOR signaling is frequently dysregulated in oncogenic cells, and thus an attractive target for anticancer therapy. Using CellDesigner, a modeling support software for graphical notation, we present herein a comprehensive map of the mTOR signaling network, which includes 964 species connected by 777 reactions. The map complies with both the systems biology markup language (SBML) and graphical notation (SBGN) for computational analysis and graphical representation, respectively. As captured in the mTOR map, we review and discuss our current understanding of the mTOR signaling network and highlight the impact of mTOR feedback and crosstalk regulations on drug-based cancer therapy. This map is available on the Payao platform, a Web 2.0 based community-wide interactive process for creating more accurate and information-rich databases. Thus, this comprehensive map of the mTOR network will serve as a tool to facilitate systems-level study of up-to-date mTOR network components and signaling events toward the discovery of novel regulatory processes and therapeutic strategies for cancer. link: http://identifiers.org/pubmed/21179025

Caron2010_mTORsignalingNetwork_ActivityFlow: MODEL1012220004v0.0.1

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/…

Details

The mammalian target of rapamycin (mTOR) is a central regulator of cell growth and proliferation. mTOR signaling is frequently dysregulated in oncogenic cells, and thus an attractive target for anticancer therapy. Using CellDesigner, a modeling support software for graphical notation, we present herein a comprehensive map of the mTOR signaling network, which includes 964 species connected by 777 reactions. The map complies with both the systems biology markup language (SBML) and graphical notation (SBGN) for computational analysis and graphical representation, respectively. As captured in the mTOR map, we review and discuss our current understanding of the mTOR signaling network and highlight the impact of mTOR feedback and crosstalk regulations on drug-based cancer therapy. This map is available on the Payao platform, a Web 2.0 based community-wide interactive process for creating more accurate and information-rich databases. Thus, this comprehensive map of the mTOR network will serve as a tool to facilitate systems-level study of up-to-date mTOR network components and signaling events toward the discovery of novel regulatory processes and therapeutic strategies for cancer. link: http://identifiers.org/pubmed/21179025

Caspeta2012 - Genome-scale metabolic network of Pichia pastoris (iLC915): MODEL1507180065v0.0.1

Caspeta2012 - Genome-scale metabolic network of Pichia pastoris (iLC915)This model is described in the article: [Genome…

Details

BACKGROUND: Pichia stipitis and Pichia pastoris have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been driving the production of several recombinant proteins. As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research. RESULTS: In this work, genome-scale metabolic models (GEMs) of P. stipitis (iSS884) and P. pastoris (iLC915) were reconstructed. iSS884 includes 1332 reactions, 922 metabolites, and 4 compartments. iLC915 contains 1423 reactions, 899 metabolites, and 7 compartments. Compared with the previous GEMs of P. pastoris, PpaMBEL1254 and iPP668, iLC915 contains more genes and metabolic functions, as well as improved predictive capabilities. Simulations of physiological responses for the growth of both yeasts on selected carbon sources using iSS884 and iLC915 closely reproduced the experimental data. Additionally, the iSS884 model was used to predict ethanol production from xylose at different oxygen uptake rates. Simulations with iLC915 closely reproduced the effect of oxygen uptake rate on physiological states of P. pastoris expressing a recombinant protein. The potential of P. stipitis for the conversion of xylose and glucose into ethanol using reactors in series, and of P. pastoris to produce recombinant proteins using mixtures of methanol and glycerol or sorbitol are also discussed. CONCLUSIONS: In conclusion the first GEM of P. stipitis (iSS884) was reconstructed and validated. The expanded version of the P. pastoris GEM, iLC915, is more complete and has improved capabilities over the existing models. Both GEMs are useful frameworks to explore the versatility of these yeasts and to capitalize on their biotechnological potentials. link: http://identifiers.org/pubmed/22472172

Caspeta2012 - Genome-scale metabolic network of Pichia stipitis (iSS884): MODEL1507180022v0.0.1

Caspeta2012 - Genome-scale metabolic network of Pichia stipitis (iSS884)This model is described in the article: [Genome…

Details

BACKGROUND: Pichia stipitis and Pichia pastoris have long been investigated due to their native abilities to metabolize every sugar from lignocellulose and to modulate methanol consumption, respectively. The latter has been driving the production of several recombinant proteins. As a result, significant advances in their biochemical knowledge, as well as in genetic engineering and fermentation methods have been generated. The release of their genome sequences has allowed systems level research. RESULTS: In this work, genome-scale metabolic models (GEMs) of P. stipitis (iSS884) and P. pastoris (iLC915) were reconstructed. iSS884 includes 1332 reactions, 922 metabolites, and 4 compartments. iLC915 contains 1423 reactions, 899 metabolites, and 7 compartments. Compared with the previous GEMs of P. pastoris, PpaMBEL1254 and iPP668, iLC915 contains more genes and metabolic functions, as well as improved predictive capabilities. Simulations of physiological responses for the growth of both yeasts on selected carbon sources using iSS884 and iLC915 closely reproduced the experimental data. Additionally, the iSS884 model was used to predict ethanol production from xylose at different oxygen uptake rates. Simulations with iLC915 closely reproduced the effect of oxygen uptake rate on physiological states of P. pastoris expressing a recombinant protein. The potential of P. stipitis for the conversion of xylose and glucose into ethanol using reactors in series, and of P. pastoris to produce recombinant proteins using mixtures of methanol and glycerol or sorbitol are also discussed. CONCLUSIONS: In conclusion the first GEM of P. stipitis (iSS884) was reconstructed and validated. The expanded version of the P. pastoris GEM, iLC915, is more complete and has improved capabilities over the existing models. Both GEMs are useful frameworks to explore the versatility of these yeasts and to capitalize on their biotechnological potentials. link: http://identifiers.org/pubmed/22472172

Castillo2016 - Whole-genome metabolic model of A.clavatus using CoReCo: MODEL1604280016v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.fumigatus using CoReCo: MODEL1604280029v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.gossypii using CoReCo: MODEL1604280044v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.nidulans using CoReCo: MODEL1604280008v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.niger using CoReCo: MODEL1604280021v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.oryzae using CoReCo: MODEL1604280012v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of A.terreus using CoReCo: MODEL1604280019v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of B.cinerea using CoReCo: MODEL1604280032v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of B.dendrobatidis using CoReCo: MODEL1604280048v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.albicans using CoReCo: MODEL1604280052v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.cinereus using CoReCo: MODEL1604280009v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.glabrata using CoReCo: MODEL1604280033v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.globosum using CoReCo: MODEL1604280005v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.immitis using CoReCo: MODEL1604280011v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.lusitaniae using CoReCo: MODEL1604280043v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.neoformans using CoReCo: MODEL1604280045v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of C.tropicalis using CoReCo: MODEL1604280006v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of D.hansenii using CoReCo: MODEL1604280028v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of E.cuniculi using CoReCo: MODEL1604280035v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of F.graminearum using CoReCo: MODEL1604280031v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of F.oxysporum using CoReCo: MODEL1604280018v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of F.verticillioides using CoReCo: MODEL1604280003v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of H.capsulatum using CoReCo: MODEL1604280027v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of K.lactis using CoReCo: MODEL1604280015v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of L.bicolor using CoReCo: MODEL1604280047v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of L.elongisporus using CoReCo: MODEL1604280039v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of M.graminicola using CoReCo: MODEL1604280036v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of M.grisea using CoReCo: MODEL1604280013v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of N.crassa using CoReCo: MODEL1604280046v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of N.fischeri using CoReCo: MODEL1604280053v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of N.haematococca using CoReCo: MODEL1604280025v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.blakesleeanus using CoReCo: MODEL1604280014v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.chrysogenum using CoReCo: MODEL1604280001v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.chrysosporium using CoReCo: MODEL1604280030v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.graminis using CoReCo: MODEL1604280051v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.guilliermondii using CoReCo: MODEL1604280007v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.nodorum using CoReCo: MODEL1604280002v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.pastoris using CoReCo: MODEL1604280055v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.placenta using CoReCo: MODEL1604280037v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of P.stipitis using CoReCo: MODEL1604280049v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of R.oryzae using CoReCo: MODEL1604280023v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of S.cerevisiae using CoReCo: MODEL1604280034v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of S.japonicus using CoReCo: MODEL1604280026v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of S.pombe using CoReCo: MODEL1604280041v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of S.roseus using CoReCo: MODEL1604280042v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706

Castillo2016 - Whole-genome metabolic model of S.sclerotiorum using CoReCo: MODEL1604280040v0.0.1

This model was reconstructed with CoReCo method from protein sequence and phylogeny data. CoReCo is described in Pitkane…

Details

Trichoderma reesei is one of the main sources of biomass-hydrolyzing enzymes for the biotechnology industry. There is a need for improving its enzyme production efficiency. The use of metabolic modeling for the simulation and prediction of this organism's metabolism is potentially a valuable tool for improving its capabilities. An accurate metabolic model is needed to perform metabolic modeling analysis.A whole-genome metabolic model of T. reesei has been reconstructed together with metabolic models of 55 related species using the metabolic model reconstruction algorithm CoReCo. The previously published CoReCo method has been improved to obtain better quality models. The main improvements are the creation of a unified database of reactions and compounds and the use of reaction directions as constraints in the gap-filling step of the algorithm. In addition, the biomass composition of T. reesei has been measured experimentally to build and include a specific biomass equation in the model.The improvements presented in this work on the CoReCo pipeline for metabolic model reconstruction resulted in higher-quality metabolic models compared with previous versions. A metabolic model of T. reesei has been created and is publicly available in the BIOMODELS database. The model contains a biomass equation, reaction boundaries and uptake/export reactions which make it ready for simulation. To validate the model, we dem1onstrate that the model is able to predict biomass production accurately and no stoichiometrically infeasible yields are detected. The new T. reesei model is ready to be used for simulations of protein production processes. link: http://identifiers.org/pubmed/27895706