Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase

Biochimica Et Biophysica Acta. Bioenergetics
Xiuhong CaiM R Gunner

Abstract

Cytochrome c Oxidase (CcO) reduces O2, the terminal electron acceptor, to water in the aerobic, respiratory electron transport chain. The energy released by O2 reductions is stored by removing eight protons from the high pH, N-side, of the membrane with four used for chemistry in the active site and four pumped to the low pH, P-side. The proton transfers must occur along controllable proton pathways that prevent energy dissipating movement towards the N-side. The CcO N-side has well established D- and K-channels to deliver protons to the protein interior. The P-side has a buried core of hydrogen-bonded protonatable residues designated the Proton Loading Site cluster (PLS cluster) and many protonatable residues on the P-side surface, providing no obvious unique exit. Hydrogen bond pathways were identified in Molecular Dynamics (MD) trajectories of Rb. sphaeroides CcO prepared in the PR state with the heme a3 propionate and Glu286 in different protonation states. Grand Canonical Monte Carlo sampling of water locations, polar proton positions and residue protonation states in trajectory snapshots identify a limited number of water mediated, proton paths from PLS cluster to the surface via a (P-exit) cluster of residues. Key P-exit...Continue Reading

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Citations

Apr 16, 2020·Proceedings of the National Academy of Sciences of the United States of America·Amandine MaréchalPeter R Rich
Oct 19, 2019·Journal of Molecular Biology·Giuseppe CapitanioSergio Papa
Jun 13, 2020·Biochimica Et Biophysica Acta. Bioenergetics·Xiuhong CaiM R Gunner
Jun 13, 2020·Biochimica Et Biophysica Acta. Bioenergetics·Umesh KhaniyaM R Gunner
May 9, 2021·Biochimica Et Biophysica Acta. Bioenergetics·Divya KaurM R Gunner
Jul 3, 2021·Frontiers in Chemistry·Divya KaurM R Gunner
Aug 25, 2021·The Journal of Physical Chemistry. B·Jovan DrageljErnst Walter Knapp
Dec 4, 2021·Proceedings of the National Academy of Sciences of the United States of America·Chenghan Li, Gregory A Voth

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