Hydrogen-Bonded Network and Water Dynamics in the D-channel of Cytochrome c Oxidase
- 178 Downloads
Proton transfer in cytochrome c oxidase (CcO) from the cellular inside to the binuclear redox centre as well as proton pumping through the membrane takes place through proton entrance via two distinct pathways, the D- and K-channel. Both channels show a dependence of their hydration level on the protonation states of their key residues, K362 for the K-channel, and E286 or D132 for the D-channel. In the oxidative half of CcO’s catalytic cycle the D-channel is the proton-conducting path. For this channel, an interplay of protonation state of the D-channel residues with the water and hydrogen-bond dynamics has been observed in molecular dynamics simulations of the CcO protein, embedded in a lipid bi-layer, modelled in different protonation states. Protonation of residue E286 at the end of the D-channel results in a hydrogen-bonded network pointing from E286 to N139, that is against proton transport, and favouring N139 conformations which correspond to a closed asparagine gate (formed by residues N121 and N139). Consequently, the hydration level is lower than with unprotonated E286. In those models, the Asn gate is predominantly open, allowing water molecules to pass and thus increase the hydration level. The hydrogen-bonded network in these states exhibits longer life times of the Asn residues with water than other models and shows the D-channel to be traversable from the entrance, D132, to exit, E286. The D-channel can thus be regarded as auto-regulated with respect to proton transport, allowing proton passage only when required, that is the proton is located at the lower part of the D-channel (D132 to Asn gate) and not at the exit (E286).
KeywordsMembrane protein Cytochrome c oxidase Proton transfer
We are grateful for computational resources provided by the North-German Supercomputing Alliance (HLRN). IT support by Jens Dreger of the Physics department at Freie Universität Berlin is gratefully acknowledged.
This study was funded by the Deutsche Forschungsgemeinschaft (DFG) provided through project C5 “Redox-state dependent communication and protonation dynamics in cytochrome c oxidase” in the Sonderforschungsbereich 1078 (SFB 1078) on ’Protonation Dynamics in Protein Function’.
Compliance with Ethical Standards
Conflict of interest
The authors declare that they have no conflict of interest.
Research Involving Human and Animal Participants
This article does not contain any studies with human participants or animals performed by any of the authors.
- Son CY, Yethiraj A, Cui Q (2017) Cavity hydration dynamics in cytochrome c oxidase and functional implications. Proc Natl Acad Sci USA 114(42):E8830–E8836Google Scholar
- Cover TM, Thomas JA (2006) Elements of information theory. Wiley, New York, p 19Google Scholar
- Henry RM, Caplan D, Fadda E, Pomès RA (2011) Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase. J Phys 23(23):234102Google Scholar
- Konstantinov AA, Siletsky S, Mitchell D, Kaulen A, Gennis Robert B (1997) The roles of the two proton input channels in cytochrome c oxidase from Rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transfer. Proc Natl Acad Sci USA 94(17):9085–9090CrossRefPubMedGoogle Scholar
- MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616Google Scholar
- Pawate AS, Morgan J, Namslauer A, Mills D, Brzezinski P, Ferguson-Miller S, Gennis RB (2002) A mutation in subunit I of cytochrome oxidase from Rhodobacter sphaeroides results in an increase in steady-state activity but completely eliminates proton pumping. Biochemistry 41:13417–13423CrossRefPubMedGoogle Scholar
- Zhu J, Han H, Pawate A, Gennis RB (2010) Decoupling mutations in the d-channel of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides suggest that a continuous hydrogen-bonded chain of waters is essential for proton pumping. Biochemistry 49(21):4476–4482CrossRefPubMedPubMedCentralGoogle Scholar