Molecular mechanisms of respiratory complex I

Abstract

Respiratory complex I transduces about half of the chemical energy used in a cell by catalyzing the transfer of electrons from the NADH metabolite to coenzyme-Q coupled to proton pumping and the generation of a transmembrane electrochemical gradient. Although decades of research, including impressive recent structural advances, have contributed to unveil the molecular functioning of complex I, fundamental doubts still persist, mainly regarding the coupling mechanism. Here we propose to apply advanced molecular simulation methodologies in combination with experimental results obtained by collaborators to elucidate different mechanistic aspects of complex I. In particular, we will investigate how the re-protonation of the catalytic residues involved in the reduction of the coenzyme-Q substrate and the proton pumping in transmembrane regions occur. We will determine internal hydration properties and free energy profiles for proton transfer processes with simulations of molecular dynamics and hybrid potentials of Quantum Chemistry and Molecular Mechanics (QM/MM). We will use simulations at constant pH to identify conformational changes correlated with alterations in protonation states in residues exposed to coenzyme-Q binding sites and in the central transmembrane region, in different substrate occupation and composition. We will also simulate the binding of rotenone and derivatives to understand its mechanisms of inhibitory activity. The research proposed here is ambitious but totally feasible given the experience of the candidate and our research group, pioneer in Brazil in the use of hybrid QM/MM potentials and in molecular simulations of the electron transport chain. This proposal will be developed in close collaboration with the group of Prof. Judy Hirst (University of Cambridge, United Kingdom), authority on complex I experimental research, whose structural and kinetic studies will be used in direct comparison, refinement and validation of our simulations. (AU)