Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)

  public model
Model Identifier
BIOMD0000000579
Short description
Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)

This model is described in the article:

HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual.
Sengupta A, Grover M, Chakraborty A, Saxena S.
PLoS ONE 2015; 10(6): e0127918

Abstract:

HEPNet is an electronic representation of metabolic reactions occurring within human cellular organization focusing on inflow and outflow of the energy currency ATP, GTP and other energy associated moieties. The backbone of HEPNet consists of primary bio-molecules such as carbohydrates, proteins and fats which ultimately constitute the chief source for the synthesis and obliteration of energy currencies in a cell. A series of biochemical pathways and reactions constituting the catabolism and anabolism of various metabolites are portrayed through cellular compartmentalization. The depicted pathways function synchronously toward an overarching goal of producing ATP and other energy associated moieties to bring into play a variety of cellular functions. HEPNet is manually curated with raw data from experiments and is also connected to KEGG and Reactome databases. This model has been validated by simulating it with physiological states like fasting, starvation, exercise and disease conditions like glycaemia, uremia and dihydrolipoamide dehydrogenase deficiency (DLDD). The results clearly indicate that ATP is the master regulator under different metabolic conditions and physiological states. The results also highlight that energy currencies play a minor role. However, the moiety creatine phosphate has a unique character, since it is a ready-made source of phosphoryl groups for the rapid synthesis of ATP from ADP. HEPNet provides a framework for further expanding the network diverse age groups of both the sexes, followed by the understanding of energetics in more complex metabolic pathways that are related to human disorders.

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Format
SBML (L2V4)
Related Publication
  • HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual.
  • Sengupta A, Grover M, Chakraborty A, Saxena S
  • PloS one , 0/ 2015 , Volume 10 , pages: e0127918 , PubMed ID: 26053019
  • Amity Institute of Biotechnology, Amity University Uttar Pradesh, U.P., India.
  • HEPNet is an electronic representation of metabolic reactions occurring within human cellular organization focusing on inflow and outflow of the energy currency ATP, GTP and other energy associated moieties. The backbone of HEPNet consists of primary bio-molecules such as carbohydrates, proteins and fats which ultimately constitute the chief source for the synthesis and obliteration of energy currencies in a cell. A series of biochemical pathways and reactions constituting the catabolism and anabolism of various metabolites are portrayed through cellular compartmentalization. The depicted pathways function synchronously toward an overarching goal of producing ATP and other energy associated moieties to bring into play a variety of cellular functions. HEPNet is manually curated with raw data from experiments and is also connected to KEGG and Reactome databases. This model has been validated by simulating it with physiological states like fasting, starvation, exercise and disease conditions like glycaemia, uremia and dihydrolipoamide dehydrogenase deficiency (DLDD). The results clearly indicate that ATP is the master regulator under different metabolic conditions and physiological states. The results also highlight that energy currencies play a minor role. However, the moiety creatine phosphate has a unique character, since it is a ready-made source of phosphoryl groups for the rapid synthesis of ATP from ADP. HEPNet provides a framework for further expanding the network diverse age groups of both the sexes, followed by the understanding of energetics in more complex metabolic pathways that are related to human disorders.
Contributors
Abhishek Sengupta

Metadata information

is
BioModels Database MODEL1507210000
BioModels Database BIOMD0000000579
isDescribedBy
PubMed 26053019
hasTaxon
Taxonomy Homo sapiens
isVersionOf
Gene Ontology generation of precursor metabolites and energy
hasProperty
Mathematical Modelling Ontology Ordinary differential equation model
Curation status
Curated
Modelling approach(es)
ordinary differential equation model
Original model(s)
HEPNET:Human Energy Pool Network
Tags
Name Description Size Actions

Model files
BIOMD0000000579_url.xml SBML L2V4 representation of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet) 1.45 MB Preview | Download

Additional files
BIOMD0000000579.pdf Auto-generated PDF file 1.23 MB Preview | Download
BIOMD0000000579.svg Auto-generated Reaction graph (SVG) 630.32 KB Preview | Download
BIOMD0000000579.m Auto-generated Octave file 76.75 KB Preview | Download
BIOMD0000000579-biopax2.owl Auto-generated BioPAX (Level 2) 406.04 KB Preview | Download
BIOMD0000000579.sci Auto-generated Scilab file 154.00 bytes Preview | Download
BIOMD0000000579-biopax3.owl Auto-generated BioPAX (Level 3) 625.90 KB Preview | Download
BIOMD0000000579.xpp Auto-generated XPP file 60.78 KB Preview | Download
BIOMD0000000579.png Auto-generated Reaction graph (PNG) 9.32 MB Preview | Download
BIOMD0000000579_urn.xml Auto-generated SBML file with URNs 1.22 MB Preview | Download
BIOMD0000000579.vcml Auto-generated VCML file 52.00 bytes Preview | Download

  • Model originally submitted by : Abhishek Sengupta
  • Submitted: 21-Jul-2015 18:52:50
  • Last Modified: 08-Apr-2016 19:17:35
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 08-Apr-2016 19:17:35
    • Submitted by: Abhishek Sengupta
    • With comment: Current version of Sengupta2015 - Knowledge base model of human energy pool network (HEPNet)
  • Version: 1 public model Download this version
    • Submitted on: 21-Jul-2015 18:52:50
    • Submitted by: Abhishek Sengupta
    • With comment: Original import of BIOMD0000000579.xml.origin
Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
NAD+

NAD+ ; NAD(+) 		24.0 mol
Malate

Malate ; malic acid 		3.2 mol
Limit Dextrin

Limit dextrin ; limit dextrin 		0.0 mol
Lactate

(S)-Lactate ; (S)-lactic acid 		740.0 mol
Isocitrate

Isocitrate ; isocitric acid 		6.0 mol
HMGCoA

(S)-3-Hydroxy-3-methylglutaryl-CoA ; (3S)-3-hydroxy-3-methylglutaryl-CoA 		0.25 mol
Glutamine

L-Glutamine ; L-glutamine 		586.0 mol
Glutamate

L-Glutamate ; L-glutamic acid 		7.9 mol
Glucose

D-Glucose ; D-glucopyranose 		4440.0 mol
Reactions
Reactions Rate Parameters
(C12 L-3-hydroxyacyl-CoA + NAD+) => (C12 Ketoacyl-CoA + NADH + H+)

([(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA] + [NAD+; NAD(+)]) => ([C12 Ketoacyl-CoA] + [NADH; NADH] + [H+; hydron])		 v1*s104/(k1+s104)

v1*[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA]/(k1+[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA])		 k1=34.5 substance; v1=1.0 substance
(C10 L-3-hydroxyacyl-CoA + NAD+) => (C10 Ketoacyl-CoA + NADH + H+)

([(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA] + [NAD+; NAD(+)]) => ([C10 Ketoacyl-CoA] + [NADH; NADH] + [H+; hydron])		 v1*s107/(k1+s107)

v1*[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA]/(k1+[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA])		 k1=34.5 substance; v1=1.0 substance
(C8 L-3-hydroxyacyl-CoA + NAD+) => (C8 Ketoacyl-CoA + NADH + H+)

([(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA] + [NAD+; NAD(+)]) => ([C8 Ketoacyl-CoA] + [NADH; NADH] + [H+; hydron])		 v1*s112/(k1+s112)

v1*[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA]/(k1+[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA])		 k1=34.5 substance; v1=1.0 substance
(C6 L-3-hydroxyacyl-CoA + NAD+) => (C6 Ketoacyl-CoA + NADH + H+)

([(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA] + [NAD+; NAD(+)]) => ([C6 Ketoacyl-CoA] + [NADH; NADH] + [H+; hydron])		 v1*s115/(k1+s115)

v1*[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA]/(k1+[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA])		 k1=34.5 substance; v1=1.0 substance
(C4 L-3-hydroxyacyl-CoA + NAD+) => (C4 Ketoacyl-CoA + NADH + H+)

([(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA] + [NAD+; NAD(+)]) => ([C4 Ketoacyl-CoA] + [NADH; NADH] + [H+; hydron])		 v1*s120/(k1+s120)

v1*[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA]/(k1+[(3S)-3-Hydroxyacyl-CoA; (S)-3-hydroxyacyl-CoA])		 k1=34.5 substance; v1=1.0 substance
(Malate + NAD+) => (OAA + NADH + H+)

([Malate; malic acid] + [NAD+; NAD(+)]) => ([Oxaloacetate; oxaloacetic acid] + [NADH; NADH] + [H+; hydron])		 v1*s9/(k1+s9)

v1*[Malate; malic acid]/(k1+[Malate; malic acid])		 k1=3.8E-4 substance; v1=1.0 substance
(Glycogen) => (G1P + Limit Dextrin)

([Glycogen; glycogen]) => ([D-Glucose 1-phosphate; alpha-D-glucose 1-phosphate] + [Limit dextrin; limit dextrin])		 v1*s198/(k1+s198)

v1*[Glycogen; glycogen]/(k1+[Glycogen; glycogen])		 k1=0.1 substance; v1=1.0 substance
(Limit Dextrin) => (Unbranched alpha(1,4)polymer + Glucose)

([Limit dextrin; limit dextrin]) => ([Unbranched alpha(1,4)polymer] + [D-Glucose; D-glucopyranose])		 v1*s252/(k1+s252)

v1*[Limit dextrin; limit dextrin]/(k1+[Limit dextrin; limit dextrin])		 v1=1.0 substance; k1=0.08 substance
(Pyruvate) => (Lactate)

([Pyruvate; pyruvic acid]) => ([(S)-Lactate; (S)-lactic acid])		 s11*k1

[Pyruvate; pyruvic acid]*k1		 k1=1.0 substance
(Isocitrate + NAD+) => (Alpha-KG + CO2 + NADH + H+)

([Isocitrate; isocitric acid] + [NAD+; NAD(+)]) => ([2-Oxoglutarate; 2-oxoglutaric acid] + [CO2; carbon dioxide] + [NADH; NADH] + [H+; hydron])		 v1*s52/(k1+s52)

v1*[Isocitrate; isocitric acid]/(k1+[Isocitrate; isocitric acid])		 k1=73.0 substance; v1=1.0 substance
(AcetoacetylCoA + AcetylCoA + H2O) => (HMGCoA + CoA-SH)

([Acetoacetyl-CoA; acetoacetyl-CoA] + [Acetyl-CoA; acetyl-CoA] + [H2O; water]) => ([(S)-3-Hydroxy-3-methylglutaryl-CoA; (3S)-3-hydroxy-3-methylglutaryl-CoA] + [CoA; coenzyme A])		 v1*s321/(k1+s321)

v1*[Acetoacetyl-CoA; acetoacetyl-CoA]/(k1+[Acetoacetyl-CoA; acetoacetyl-CoA])		 k1=294.0 substance; v1=1.0 substance
(Glutamine) => (Glutamine)

([L-Glutamine; L-glutamine]) => ([L-Glutamine; L-glutamine])		 s378*k2

[L-Glutamine; L-glutamine]*k2		 k1=1.0 substance; k2=1.0 substance
(Glutamate + OAA) => (Glutamate + Aspartate)

([L-Glutamate; L-glutamic acid] + [Oxaloacetate; oxaloacetic acid]) => ([L-Glutamate; L-glutamic acid] + [L-Aspartate; L-aspartic acid])		 s379*s50*k1

[L-Glutamate; L-glutamic acid]*[Oxaloacetate; oxaloacetic acid]*k1		 k1=1.0 substance
(Amino acids + Alpha keto acid) => (Glutamate + Alpha KG)

([Amino acids] + [2-Oxoglutarate; 2-oxoglutaric acid]) => ([L-Glutamate; L-glutamic acid] + [2-Oxoglutarate; 2-oxoglutaric acid])		 s12*s17*k1

[Amino acids]*[2-Oxoglutarate; 2-oxoglutaric acid]*k1		 k1=1.0 substance
(Lactate + NADH) => (Glucose + NAD+)

([(S)-Lactate; (S)-lactic acid] + [NADH; NADH]) => ([D-Glucose; D-glucopyranose] + [NAD+; NAD(+)])		 s296*s67*k1

[(S)-Lactate; (S)-lactic acid]*[NADH; NADH]*k1		 k1=1.0 substance
Curator's comment:
(added: 07 Aug 2015, 16:25:48, updated: 07 Aug 2015, 16:25:48)
Figure 5A of the reference publication has been reproduced using SBML odeSolver.