Investigating Oxidoreduction Kinetics using Protein Dynamics.
Résumé
For twenty years, there are more and more crystallographic structures of enzymatic macromolecular complexes available in international data banks. At the same time, there is always an interest in better understanding 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 modeling of the redox reactions and modeling of the conformational changes of enzymes 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 complex II and III of the mitochondrial respiratory chain. Using this model, we are able to assess quantitative and qualitative enzymatic kinetic behaviors such as conversion rate of the overall reaction, individual electrons path within the complexes and potentially pathological short-circuits.