Abstract
The aerobic electron transfer chain builds a proton gradient by proton coupled electron transfer reactions through multiple proteins. Complex I is the first enzyme in this chain. On transfer of two electrons from NADH to quinone four protons are pumped from the N- (negative, higher pH) to the P- (positive, lower) side. Protons move pthrough three linear antiporter paths, with a few amino acids and waters providing the route and the E-channel, which is a complex of competing paths, with clusters of interconnected protonatable residues.
Proton loading sites (PLS) are residues that transiently bind protons as they are transported from N- to P-compartments. PLS can be individual residues or extended clusters. The program MCCE uses Monte Carlos sampling to analyze the E-channel proton binding in equilibrium with individual Molecular Dynamics snapshots from trajectories of Thrmus thermuphillus Complex I in the apo, quinone or quinol bound states. At pH 7, the five E-channel subunits (Nqo4, Nqo7, Nqo8, Nqo10, and Nqo11) have accepted >25,000 protonation microstates, each with different residues protonated. The microstate explosion is tamed by analyzing interconnected clusters of residues along the proton transfer paths. A proton is bound and released to five coupled residues in a cluster on the protein N-side and to six coupled residues in the protein center. Loaded microstates bind protons to sites closer to the P-side in the forward pumping direction. MCCE microstate analysis shows the strong coupling of proton binding amongst individual residues in the two PLS clusters.
Competing Interest Statement
The authors have declared no competing interest.
