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Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations

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Olkhova,  Elena
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Hutter,  Michael C.
Max Planck Research Group of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Lill,  Markus A.
Max Planck Research Group of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Helms,  Volkhard
Max Planck Research Group of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society;

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Michel,  Hartmut
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society;

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Citation

Olkhova, E., Hutter, M. C., Lill, M. A., Helms, V., & Michel, H. (2004). Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations. Biophysical Journal, 86(4), 1873-1889. doi:10.1016/S0006-3495(04)74254-X.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0024-DACE-0
Abstract
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