Volume 9, Number 1, p.p. 27–35
Investigating oxido-reduction kinetics using protein dynamics
N. Parisey and M. Beurton-Aimar
Laboratoire Bordelais de Recherche en Informatique, CNRS UMR5800, Université Bordeaux 1, 351 Cours de la Libération, 33405 Talence, France
For twenty years, more and more crystallographic structures of enzymatic macromolecular complexes are available in international data banks. At the same time, there is always an interest in the better understanding of enzyme functionalities. The movements of large protein structures are key components in ligand docking and enzymatic catalysis. Hence, simulations of enzymatic reactions must take into account such structural movements. Our aim is to combine modelling of the redox reactions and modelling of the conformational changes of enzyme structures in order to describe the dynamical functioning of redox enzymes. An agent-based system has been developed to simulate internal enzymatic movements and redox reactions. We applied our approach to the complexes II and III of the mitochondrial respiratory chain. Using this model, we are able to assess quantitative and qualitative enzymatic kinetic behaviours such as conversion rate of the overall reaction, the path of individual electrons within the complexes and potentially pathological short-circuits.
Keywords:
electron transfer, multiagent systems, respiratory chain, stochastic simulation