Protonation dynamics in the K-channel of cytochrome C oxidase estimated from molecular dynamics simulations

Stegmaier V, Gorriz RF, Imhof P (2021)

Publication Type: Journal article

Publication year: 2021

Journal

Processes MDPI

Book Volume: 9

Pages Range: 1-24

Article Number: 265

Journal Issue: 2

DOI: 10.3390/pr9020265

Abstract

Proton transfer reactions are one of the most fundamental processes in biochemistry. We present a simplistic approach for estimating proton transfer probabilities in a membrane protein, cytochrome c oxidase. We combine short molecular dynamics simulations at discrete protonation states with a Monte Carlo approach to exchange between those states. Requesting for a proton transfer the existence of a hydrogen-bonded connection between the two source and target residues of the exchange,restricts the acceptance of transfers to only those in which a proton-relay is possible. Together with an analysis of the hydrogen-bonded connectivity in one of the proton-conducting channels of cytochrome c oxidase, this approach gives insight into the protonation dynamics of the hydrogen-bonded networks. The connectivity and directionality of the networks are coupled to the conformation of an important protein residue in the channel, K362, rendering proton transfer in the entire channel feasible in only one of the two major conformations. Proton transport in the channel can thus be regulated by K362 not only through its possible role as a proton carrier itself, but also by allowing or preventing proton transport via water residues.

Authors with CRIS profile

Petra Imhof Professur für Computational Chemistry

Involved external institutions

Freie Universität Berlin

Germany (DE)

How to cite

APA:

Stegmaier, V., Gorriz, R.F., & Imhof, P. (2021). Protonation dynamics in the K-channel of cytochrome C oxidase estimated from molecular dynamics simulations. Processes, 9(2), 1-24. https://dx.doi.org/10.3390/pr9020265

MLA:

Stegmaier, Vincent, Rene F. Gorriz, and Petra Imhof. "Protonation dynamics in the K-channel of cytochrome C oxidase estimated from molecular dynamics simulations." Processes 9.2 (2021): 1-24.

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