Dynamic water networks in cytochrome C oxidase from Paracoccus denitrificans investigated by molecular dynamics simulations.
We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water molecules and their corresponding hydrogen-bonded networks inside cytochrome c oxidase. The majority of the water molecules had residence times shorter than 100 ps, but a few water molecules are fixed inside the protein for up to 1.125 ns. The hydrogen-bonded network in cytochrome c oxidase is not uniformly distributed, and the degree of water arrangement is variable. The average number of solvent sites in the proton-conducting K- and D-pathways was determined. In contrast to single water files in narrow geometries we observe significant diffusion of individual water molecules along these pathways. The highly fluctuating hydrogen-bonded networks, combined with the significant diffusion of individual water molecules, provide a basis for the transfer of protons in cytochrome c oxidase, therefore leading to a better understanding of the mechanism of proton pumping.
Olkhova
Elena
E
Max-Planck-Institute of Biophysics, Department of Molecular Membrane Biology, Frankfurt am Main, Germany.
Hutter
Michael C
MC
Lill
Markus A
MA
Helms
Volkhard
V
Michel
Hartmut
H
D003198:Computer Simulation; D003576:Electron Transport Complex IV / Q000737:chemistry*; D006860:Hydrogen Bonding; D008051:Lipid Bilayers / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D010084:Oxidation-Reduction; D010231:Paracoccus denitrificans / Q000737:chemistry; D011522:Protons; D014867:Water / Q000737:chemistry*
D008051:Lipid Bilayers; D011522:Protons; D014867:Water; D003576:Electron Transport Complex IV