Protonation Dynamics in the K-Channel of Cytochrome c Oxidase Estimated from Molecular Dynamics Simulations

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