Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I

The
mitochondrial respiratory chain, formed by five protein complexes,
utilizes energy from catabolic processes to synthesize ATP. Complex
I, the first and the largest protein complex of the chain, harvests
electrons from NADH to reduce quinone, while pumping protons across
the mitochondrial membrane. Detailed knowledge of the working principle
of such coupled charge-transfer processes remains, however, fragmentary
due to bottlenecks in understanding redox-driven conformational transitions
and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur
clusters, reduced by electrons from NADH. Here, employing the latest
crystal structure of T. thermophilus complex I, we
have used microsecond-scale molecular dynamics simulations to study
the chemo-mechanical coupling between redox changes of the iron–sulfur
clusters and conformational transitions across complex I. First, we
identify the redox switches within complex I, which allosterically
couple the dynamics of the quinone binding pocket to the site of NADH
reduction. Second, our free-energy calculations reveal that the affinity
of the quinone, specifically menaquinone, for the binding-site is
higher than that of its reduced, menaquinol forma design essential
for menaquinol release. Remarkably, the barriers to diffusive menaquinone
dynamics are lesser than that of the more ubiquitous ubiquinone, and
the naphthoquinone headgroup of the former furnishes stronger binding
interactions with the pocket, favoring menaquinone for charge transport
in T. thermophilus. Our computations are consistent
with experimentally validated mutations and hierarchize the key residues
into three functional classes, identifying new mutation targets. Third,
long-range hydrogen-bond networks connecting the quinone-binding site
to the transmembrane subunits are found to be responsible for proton
pumping. Put together, the simulations reveal the molecular design
principles linking redox reactions to quinone turnover to proton translocation
in complex I.