Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate

Grudinin, S.; Büldt, G.; Gordeliy, I. L.; Baumgaertner, A.

doi:10.1529/biophysj.104.047993

Journal Article

Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate

Grudinin, S.FZJ* ; Büldt, G.FZJ* ; Gordeliy, I. L.FZJ* ; Baumgaertner, A.FZJ*

2005
Rockefeller Univ. Press New York, NY

Biophysical journal 88, 3252 - 3261 (2005) [10.1529/biophysj.104.047993]

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Please use a persistent id in citations: http://hdl.handle.net/2128/1516 doi:10.1529/biophysj.104.047993

Abstract: 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.

Keyword(s): Bacteriorhodopsins: chemistry (MeSH) ; Biological Transport (MeSH) ; Biophysics: methods (MeSH) ; Computer Simulation (MeSH) ; Crystallography, X-Ray (MeSH) ; Diffusion (MeSH) ; Dimerization (MeSH) ; Halobacterium: metabolism (MeSH) ; Hydrogen Bonding (MeSH) ; Models, Chemical (MeSH) ; Models, Molecular (MeSH) ; Models, Statistical (MeSH) ; Phosphatidylcholines: chemistry (MeSH) ; Protein Conformation (MeSH) ; Protein Structure, Tertiary (MeSH) ; Protons (MeSH) ; Software (MeSH) ; Time Factors (MeSH) ; Water: chemistry (MeSH) ; Phosphatidylcholines ; Protons ; Bacteriorhodopsins ; 1-palmitoyl-2-oleoylphosphatidylcholine ; Water ; J