TY  - JOUR
AU  - Grudinin, S.
AU  - Büldt, G.
AU  - Gordeliy, I. L.
AU  - Baumgaertner, A.
TI  - Water Molecules and Hydrogen-Bonded Networks in Bacteriorhodopsin-Molecular Dynamics Simulations of the Ground State and the M-Intermediate
JO  - Biophysical journal
VL  - 88
SN  - 0006-3495
CY  - New York, NY
PB  - Rockefeller Univ. Press
M1  - PreJuSER-44759
SP  - 3252 - 3261
PY  - 2005
N1  - Record converted from VDB: 12.11.2012
AB  - 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.
KW  - Bacteriorhodopsins: chemistry
KW  - Biological Transport
KW  - Biophysics: methods
KW  - Computer Simulation
KW  - Crystallography, X-Ray
KW  - Diffusion
KW  - Dimerization
KW  - Halobacterium: metabolism
KW  - Hydrogen Bonding
KW  - Models, Chemical
KW  - Models, Molecular
KW  - Models, Statistical
KW  - Phosphatidylcholines: chemistry
KW  - Protein Conformation
KW  - Protein Structure, Tertiary
KW  - Protons
KW  - Software
KW  - Time Factors
KW  - Water: chemistry
KW  - Phosphatidylcholines (NLM Chemicals)
KW  - Protons (NLM Chemicals)
KW  - Bacteriorhodopsins (NLM Chemicals)
KW  - 1-palmitoyl-2-oleoylphosphatidylcholine (NLM Chemicals)
KW  - Water (NLM Chemicals)
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:15731388
C2  - pmc:PMC1305474
UR  - <Go to ISI:>//WOS:000228688800021
DO  - DOI:10.1529/biophysj.104.047993
UR  - https://juser.fz-juelich.de/record/44759
ER  -