English
 
Help Privacy Policy Disclaimer
  Advanced SearchBrowse

Item

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

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.

Item is

Files

show Files

Locators

show

Creators

show
hide
 Creators:
Olkhova, Elena1, Author              
Hutter, Michael C.2, Author              
Lill, Markus A.2, Author              
Helms, Volkhard2, Author              
Michel, Hartmut1, Author              
Affiliations:
1Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society, ou_2068290              
2Max Planck Research Group of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068294              

Content

show
hide
Free keywords: -
 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

Details

show
hide
Language(s): eng - English
 Dates: 2003-08-132003-11-102009-01-062004-04
 Publication Status: Published in print
 Pages: 17
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1016/S0006-3495(04)74254-X
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Biophysical Journal
  Other : Biophys. J.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: Cambridge, Mass. : Cell Press
Pages: - Volume / Issue: 86 (4) Sequence Number: - Start / End Page: 1873 - 1889 Identifier: ISSN: 0006-3495
CoNE: https://pure.mpg.de/cone/journals/resource/954925385117