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

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005     20240610120257.0
017 _ _ |a This version is available at the following Publisher URL: http://www.biophysj.org/
024 7 _ |a pmid:15731388
|2 pmid
024 7 _ |a pmc:PMC1305474
|2 pmc
024 7 _ |a 10.1529/biophysj.104.047993
|2 DOI
024 7 _ |a WOS:000228688800021
|2 WOS
024 7 _ |a 2128/1516
|2 Handle
037 _ _ |a PreJuSER-44759
041 _ _ |a eng
082 _ _ |a 570
084 _ _ |2 WoS
|a Biophysics
100 1 _ |a Grudinin, S.
|b 0
|u FZJ
|0 P:(DE-Juel1)VDB10417
245 _ _ |a Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
260 _ _ |a New York, NY
|b Rockefeller Univ. Press
|c 2005
300 _ _ |a 3252 - 3261
336 7 _ |a Journal Article
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336 7 _ |a JOURNAL_ARTICLE
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336 7 _ |a article
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440 _ 0 |a Biophysical Journal
|x 0006-3495
|0 882
|v 88
500 _ _ |a Record converted from VDB: 12.11.2012
520 _ _ |a 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.
536 _ _ |a Kondensierte Materie
|c M02
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536 _ _ |a Neurowissenschaften
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588 _ _ |a Dataset connected to Web of Science, Pubmed
650 _ 2 |2 MeSH
|a Bacteriorhodopsins: chemistry
650 _ 2 |2 MeSH
|a Biological Transport
650 _ 2 |2 MeSH
|a Biophysics: methods
650 _ 2 |2 MeSH
|a Computer Simulation
650 _ 2 |2 MeSH
|a Crystallography, X-Ray
650 _ 2 |2 MeSH
|a Diffusion
650 _ 2 |2 MeSH
|a Dimerization
650 _ 2 |2 MeSH
|a Halobacterium: metabolism
650 _ 2 |2 MeSH
|a Hydrogen Bonding
650 _ 2 |2 MeSH
|a Models, Chemical
650 _ 2 |2 MeSH
|a Models, Molecular
650 _ 2 |2 MeSH
|a Models, Statistical
650 _ 2 |2 MeSH
|a Phosphatidylcholines: chemistry
650 _ 2 |2 MeSH
|a Protein Conformation
650 _ 2 |2 MeSH
|a Protein Structure, Tertiary
650 _ 2 |2 MeSH
|a Protons
650 _ 2 |2 MeSH
|a Software
650 _ 2 |2 MeSH
|a Time Factors
650 _ 2 |2 MeSH
|a Water: chemistry
650 _ 7 |0 0
|2 NLM Chemicals
|a Phosphatidylcholines
650 _ 7 |0 0
|2 NLM Chemicals
|a Protons
650 _ 7 |0 53026-44-1
|2 NLM Chemicals
|a Bacteriorhodopsins
650 _ 7 |0 6753-55-5
|2 NLM Chemicals
|a 1-palmitoyl-2-oleoylphosphatidylcholine
650 _ 7 |0 7732-18-5
|2 NLM Chemicals
|a Water
650 _ 7 |a J
|2 WoSType
700 1 _ |a Büldt, G.
|b 1
|u FZJ
|0 P:(DE-Juel1)131957
700 1 _ |a Gordeliy, I. L.
|b 2
|u FZJ
|0 P:(DE-Juel1)VDB32237
700 1 _ |a Baumgaertner, A.
|b 3
|u FZJ
|0 P:(DE-Juel1)VDB17756
773 _ _ |a 10.1529/biophysj.104.047993
|g Vol. 88, p. 3252 - 3261
|p 3252 - 3261
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|x 0006-3495
856 7 _ |2 Pubmed Central
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856 4 _ |u https://juser.fz-juelich.de/record/44759/files/65846.pdf
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