This title appears in the Scientific Report :
2005
Please use the identifier:
http://dx.doi.org/10.1529/biophysj.104.047993 in citations.
Please use the identifier: http://hdl.handle.net/2128/1516 in citations.
Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
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 bacte...
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Personal Name(s): | Grudinin, S. |
---|---|
Büldt, G. / Gordeliy, I. L. / Baumgaertner, A. | |
Contributing Institute: |
Theorie II; IFF-TH-II Biologische Strukturforschung; IBI-2 |
Published in: | Biophysical journal, 88 (2005) S. 3252 - 3261 |
Imprint: |
New York, NY
Rockefeller Univ. Press
2005
|
Physical Description: |
3252 - 3261 |
DOI: |
10.1529/biophysj.104.047993 |
PubMed ID: |
15731388 |
Document Type: |
Journal Article |
Research Program: |
Neurowissenschaften Kondensierte Materie |
Series Title: |
Biophysical Journal
88 |
Subject (ZB): | |
Link: |
Get full text OpenAccess |
Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/1516 in citations.
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. |