In Silico Modeling of the Mitochondrial Pumping Complexes with Markov State Models

Methods Mol Biol. 2021:2276:425-439. doi: 10.1007/978-1-0716-1266-8_31.

Abstract

The mechanism of proton pumping by the mitochondrial electron transport chain complexes is still enigmatic after decades of research. Recently, there has been interest in in silico Markov state models to model the mitochondrial pumping complexes at the microscopic level, and this chapter describes the methods of constructing and simulating such models.

Keywords: Gillespie algorithm; Markov state models; Mitochondria; Proton pumping; Rate constants.

MeSH terms

  • Algorithms
  • Animals
  • Computer Simulation / statistics & numerical data*
  • Electron Transport
  • Humans
  • Markov Chains
  • Mitochondria / physiology*
  • Models, Biological
  • Proton Pumps / metabolism*

Substances

  • Proton Pumps