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Biochim Biophys Acta. 2016 Sep;1857(9):1594-1606. doi: 10.1016/j.bbabio.2016.06.005. Epub 2016 Jun 16.

Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.

Author information

1
Department of Chemistry, Nanchang University, 999 Xuefudadao, Nanchang, Jiangxi 330031, China; San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA.
2
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway.
3
Department of Integrative Structural and Computational Biology, GAC1118, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
4
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA; Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. Electronic address: ross@rosswalker.co.uk.
5
San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, CA 92093, USA. Electronic address: agoetz@sdsc.edu.

Abstract

Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

KEYWORDS:

Computer simulation; Cytochrome c oxidase; Molecular dynamics; Proton pumping mechanism; Proton transport; Water exit pathway

PMID:
27317965
PMCID:
PMC4995112
DOI:
10.1016/j.bbabio.2016.06.005
[Indexed for MEDLINE]
Free PMC Article

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