%0 Journal Article
%A Grudinin, S.
%A Büldt, G.
%A Gordeliy, I. L.
%A Baumgaertner, A.
%T Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
%J Biophysical journal
%V 88
%@ 0006-3495
%C New York, NY
%I Rockefeller Univ. Press
%M PreJuSER-44759
%P 3252 - 3261
%D 2005
%Z Record converted from VDB: 12.11.2012
%X Protein crystallography provides the structure of a protein, averaged over all elementary cells during data collection time. Thus, it has only a limited access to diffusive processes. This article demonstrates how molecular dynamics simulations can elucidate structure-function relationships in bacteriorhodopsin (bR) involving water molecules. The spatial distribution of water molecules and their corresponding hydrogen-bonded networks inside bR in its ground state (G) and late M intermediate conformations were investigated by molecular dynamics simulations. The simulations reveal a much higher average number of internal water molecules per monomer (28 in the G and 36 in the M) than observed in crystal structures (18 and 22, respectively). We found nine water molecules trapped and 19 diffusive inside the G-monomer, and 13 trapped and 23 diffusive inside the M-monomer. The exchange of a set of diffusive internal water molecules follows an exponential decay with a 1/e time in the order of 340 ps for the G state and 460 ps for the M state. The average residence time of a diffusive water molecule inside the protein is approximately 95 ps for the G state and 110 ps for the M state. We have used the Grotthuss model to describe the possible proton transport through the hydrogen-bonded networks inside the protein, which is built up in the picosecond-to-nanosecond time domains. Comparing the water distribution and hydrogen-bonded networks of the two different states, we suggest possible pathways for proton hopping and water movement inside bR.
%K Bacteriorhodopsins: chemistry
%K Biological Transport
%K Biophysics: methods
%K Computer Simulation
%K Crystallography, X-Ray
%K Diffusion
%K Dimerization
%K Halobacterium: metabolism
%K Hydrogen Bonding
%K Models, Chemical
%K Models, Molecular
%K Models, Statistical
%K Phosphatidylcholines: chemistry
%K Protein Conformation
%K Protein Structure, Tertiary
%K Protons
%K Software
%K Time Factors
%K Water: chemistry
%K Phosphatidylcholines (NLM Chemicals)
%K Protons (NLM Chemicals)
%K Bacteriorhodopsins (NLM Chemicals)
%K 1-palmitoyl-2-oleoylphosphatidylcholine (NLM Chemicals)
%K Water (NLM Chemicals)
%K J (WoSType)
%F PUB:(DE-HGF)16
%9 Journal Article
%$ pmid:15731388
%2 pmc:PMC1305474
%U <Go to ISI:>//WOS:000228688800021
%R 10.1529/biophysj.104.047993
%U https://juser.fz-juelich.de/record/44759