TY - JOUR
T1 - Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex i
AU - Gupta, Chitrak
AU - Khaniya, Umesh
AU - Chan, Chun Kit
AU - Dehez, Francois
AU - Shekhar, Mrinal
AU - Gunner, M. R.
AU - Sazanov, Leonid
AU - Chipot, Christophe
AU - Singharoy, Abhishek
N1 - Funding Information:
A.S. and C.G. acknowledge start-up funds from the SMS and CASD at Arizona State University, and the resources of the OLCF at the Oak Ridge National Laboratory, which is supported by the Office of Science at DOE under Contract No. DE-AC05-00OR22725, made available via the INCITE program. A.S. acknowledges CAREER award from NSF (MCB-1942763) and MCB-1616590. C.C. and F.D. are grateful to the Contrat Plan État Région (CPER) IT2MP and to the Fonds Européen de Développement en Région (FEDER) for generous funding. M.G. and U.K. acknowledge funding from the National Science Foundation (grant number MCB-1519640).
Publisher Copyright:
© 2020 American Chemical Society.
PY - 2020/5/20
Y1 - 2020/5/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85086518472&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85086518472&partnerID=8YFLogxK
U2 - 10.1021/jacs.9b13450
DO - 10.1021/jacs.9b13450
M3 - Article
C2 - 32347721
AN - SCOPUS:85086518472
SN - 0002-7863
VL - 142
SP - 9220
EP - 9230
JO - Journal of the American Chemical Society
JF - Journal of the American Chemical Society
IS - 20
ER -