Energetics and Dynamics of Proton-Coupled Electron Transfer in the NADH/FMN Site of Respiratory Complex I.

Complex I functions as an initial electron acceptor in aerobic respiratory chains that reduces quinone and pumps protons across a biological membrane. This remarkable charge transfer process extends ca. 300 Å and it is initiated by a poorly understood proton-coupled electron transfer (PCET) reaction between NADH and a protein-bound flavin (FMN) cofactor. We combine here large-scale density functional theory (DFT) calculations and quantum/classical (QM/MM) models with atomistic molecular dynamics (MD) simulations to probe the energetics and dynamics of the NADH-driven PCET reaction in complex I. We find that the reaction takes place by concerted hydrogen atom (H•) transfer that couples to an electron transfer (eT) between the aromatic ring systems of the cofactors, and further triggers reduction of the nearby FeS centers. In bacterial, E. coli-like complex I-isoforms, reduction of the N1a FeS center increases the binding affinity of the oxidized NAD+ that prevents the nucleotide from leaving prematurely. This electrostatic trapping could provide a protective gating mechanism against reactive oxygen species (ROS) formation. We also find that proton transfer from the transient FMNH• to a nearby conserved glutamate (Glu97) residue favors eT from N1a onwards along the FeS chain, and modulates the binding of a new NADH molecule. The PCET in complex I-isoforms with low-potential N1a centers is also discussed. Based on our combined results, we propose a putative mechanistic model for the NADH-driven proton/electron-transfer reaction in complex I.