TY - CHAP
T1 - Computational modeling of mitochondrial function
AU - Cortassa, Sonia
AU - Aon, Miguel A.
PY - 2012
Y1 - 2012
N2 - The advent of techniques with the ability to scan massive changes in cellular makeup (genomics, proteomics, etc.) has revealed the compelling need for analytical methods to interpret and make sense of those changes. Computational models built on sound physico-chemical mechanistic basis are unavoidable at the time of integrating, interpreting, and simulating high-throughput experimental data. Another powerful role of computational models is predicting new behavior provided they are adequately validated. Mitochondrial energy transduction has been traditionally studied with thermodynamic models. More recently, kinetic or thermo-kinetic models have been proposed, leading the path toward an understanding of the control and regulation of mitochondrial energy metabolism and its interaction with cytoplasmic and other compartments. In this work, we outline the methods, step-by-step, that should be followed to build a computational model of mitochondrial energetics in isolation or integrated to a network of cellular processes. Depending on the question addressed by the modeler, the methodology explained herein can be applied with different levels of detail, from the mitochondrial energy producing machinery in a network of cellular processes to the dynamics of a single enzyme during its catalytic cycle.
AB - The advent of techniques with the ability to scan massive changes in cellular makeup (genomics, proteomics, etc.) has revealed the compelling need for analytical methods to interpret and make sense of those changes. Computational models built on sound physico-chemical mechanistic basis are unavoidable at the time of integrating, interpreting, and simulating high-throughput experimental data. Another powerful role of computational models is predicting new behavior provided they are adequately validated. Mitochondrial energy transduction has been traditionally studied with thermodynamic models. More recently, kinetic or thermo-kinetic models have been proposed, leading the path toward an understanding of the control and regulation of mitochondrial energy metabolism and its interaction with cytoplasmic and other compartments. In this work, we outline the methods, step-by-step, that should be followed to build a computational model of mitochondrial energetics in isolation or integrated to a network of cellular processes. Depending on the question addressed by the modeler, the methodology explained herein can be applied with different levels of detail, from the mitochondrial energy producing machinery in a network of cellular processes to the dynamics of a single enzyme during its catalytic cycle.
KW - Kinetic and thermo-kinetic models
KW - Mitochondrial energy transduction
KW - Model parameters
KW - Ordinary differential equations
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=82355161908&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=82355161908&partnerID=8YFLogxK
U2 - 10.1007/978-1-61779-382-0_19
DO - 10.1007/978-1-61779-382-0_19
M3 - Chapter
C2 - 22057575
AN - SCOPUS:82355161908
SN - 9781617793813
T3 - Methods in Molecular Biology
SP - 311
EP - 326
BT - Mitochondrial Bioenergetics
ER -