ArticleBiophysical journal2005
Water molecules and hydrogen-bonded networks in bacteriorhodopsin--molecular dynamics simulations of the ground state and the M-intermediate.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 52 citations in OpenAlex.
- Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake.International journal of molecular sciences · 2022Article
- Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway.Structure (London, England : 1993) · 2013Article
- Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps.Computational and structural biotechnology journal · 2013Review
- Exploring cavity dynamics in biomolecular systems.BMC bioinformatics · 2013Article
- Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase.PLoS computational biology · 2012Article
- Water pathways in the bacteriorhodopsin proton pump.The Journal of membrane biology · 2011Article
- Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach.BMC structural biology · 2010Article
- Dynamics of the internal water molecules in squid rhodopsin.Biophysical journal · 2009Article
- Dynamics of voltage profile in enzymatic ion transporters, demonstrated in electrokinetics of proton pumping rhodopsin.Biophysical journal · 2008Article
- Structures and spectral signatures of protonated water networks in bacteriorhodopsin.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- External electric control of the proton pumping in bacteriorhodopsin.European biophysics journal : EBJ · 2007Article
- pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin.Biophysical journal · 2006Article
- Molecular dynamics simulations of proteins in lipid bilayers.Current opinion in structural biology · 2005Review
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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