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000044759 0247_ $$2DOI$$a10.1529/biophysj.104.047993
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000044759 084__ $$2WoS$$aBiophysics
000044759 1001_ $$0P:(DE-Juel1)VDB10417$$aGrudinin, S.$$b0$$uFZJ
000044759 245__ $$aWater Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
000044759 260__ $$aNew York, NY$$bRockefeller Univ. Press$$c2005
000044759 300__ $$a3252 - 3261
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000044759 520__ $$aProtein 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.
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000044759 650_2 $$2MeSH$$aBacteriorhodopsins: chemistry
000044759 650_2 $$2MeSH$$aBiological Transport
000044759 650_2 $$2MeSH$$aBiophysics: methods
000044759 650_2 $$2MeSH$$aComputer Simulation
000044759 650_2 $$2MeSH$$aCrystallography, X-Ray
000044759 650_2 $$2MeSH$$aDiffusion
000044759 650_2 $$2MeSH$$aDimerization
000044759 650_2 $$2MeSH$$aHalobacterium: metabolism
000044759 650_2 $$2MeSH$$aHydrogen Bonding
000044759 650_2 $$2MeSH$$aModels, Chemical
000044759 650_2 $$2MeSH$$aModels, Molecular
000044759 650_2 $$2MeSH$$aModels, Statistical
000044759 650_2 $$2MeSH$$aPhosphatidylcholines: chemistry
000044759 650_2 $$2MeSH$$aProtein Conformation
000044759 650_2 $$2MeSH$$aProtein Structure, Tertiary
000044759 650_2 $$2MeSH$$aProtons
000044759 650_2 $$2MeSH$$aSoftware
000044759 650_2 $$2MeSH$$aTime Factors
000044759 650_2 $$2MeSH$$aWater: chemistry
000044759 650_7 $$00$$2NLM Chemicals$$aPhosphatidylcholines
000044759 650_7 $$00$$2NLM Chemicals$$aProtons
000044759 650_7 $$053026-44-1$$2NLM Chemicals$$aBacteriorhodopsins
000044759 650_7 $$06753-55-5$$2NLM Chemicals$$a1-palmitoyl-2-oleoylphosphatidylcholine
000044759 650_7 $$07732-18-5$$2NLM Chemicals$$aWater
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000044759 7001_ $$0P:(DE-Juel1)131957$$aBüldt, G.$$b1$$uFZJ
000044759 7001_ $$0P:(DE-Juel1)VDB32237$$aGordeliy, I. L.$$b2$$uFZJ
000044759 7001_ $$0P:(DE-Juel1)VDB17756$$aBaumgaertner, A.$$b3$$uFZJ
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000044759 8567_ $$2Pubmed Central$$uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305474
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