ArticleBiophysical journal2004
Dynamics of water molecules in the bacteriorhodopsin trimer in explicit lipid/water environment.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 83 citations in OpenAlex.
- Voltage Imaging with Engineered Proton-Pumping Rhodopsins: Insights from the Proton Transfer Pathway.ACS physical chemistry Au · 2023Review
- Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake.International journal of molecular sciences · 2022Article
- Collective exchange processes reveal an active site proton cage in bacteriorhodopsin.Communications biology · 2020Article
- Multiscale modelization in a small virus: Mechanism of proton channeling and its role in triggering capsid disassembly.PLoS computational biology · 2018Article
- pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The Activation Pathway of Human Rhodopsin in Comparison to Bovine Rhodopsin.The Journal of biological chemistry · 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
- Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol:fumarate reductase.Biophysical journal · 2012Article
- An internal water-retention site in the rhomboid intramembrane protease GlpG ensures catalytic efficiency.Structure (London, England : 1993) · 2012Article
- In channelrhodopsin-2 Glu-90 is crucial for ion selectivity and is deprotonated during the photocycle.The Journal of biological chemistry · 2012Article
- Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase.PLoS computational biology · 2012Article
- Proton transfer via a transient linear water-molecule chain in a membrane protein.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Velocity-dependent mechanical unfolding of bacteriorhodopsin is governed by a dynamic interaction network.Biophysical journal · 2011Article
- 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
- Molecular dynamics simulations of proteins in lipid bilayers.Current opinion in structural biology · 2005Review
- Water molecules and hydrogen-bonded networks in bacteriorhodopsin--molecular dynamics simulations of the ground state and the M-intermediate.Biophysical journal · 2005Article
- Proton binding within a membrane protein by a protonated water cluster.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- The assignment of the different infrared continuum absorbance changes observed in the 3000-1800-cm(-1) region during the bacteriorhodopsin photocycle.Biophysical journal · 2004Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protonated networks of internal water molecules appear to be involved in proton transfer in various integral membrane proteins. High-resolution x-ray studies of protein crystals at low temperature deliver mean positions of most internal waters, but only limited information about fluctuations within such H-bonded networks formed by water and residues. The question arises as to how water molecules behave inside and on the surface of a fluctuating membrane protein under more physiological conditions. Therefore, as an example, long-time molecular dynamics simulations of bacteriorhodopsin were performed with explicit membrane/water environment. Based on a recent x-ray model the bacteriorhodopsin trimer was inserted in a fully solvated 16 x 16 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-bilayer patch, resulting in a system of approximately 84,000 atoms. Unrestrained molecular dynamics calculations of 5 ns were performed using the GROMACS package and force field. Mean water densities were computed to describe the anisotropic distribution of internal water molecules. In the whole protein two larger areas of higher water density are identified. They are located between the central proton binding site, the Schiff base, and the extracellular proton release site. Separated by Arg-82 these water clusters could provide a proton release pathway in a Grotthus-like mechanism as indicated by a continuum absorbance change observed during the photocycle by time-resolved Fourier transform infrared spectroscopy. Residues are identified which are H-bonded to the water clusters and are therefore facilitating proton conduction. Their influence on proton transfer via the H-bonded network as indicated by the continuum absorbance change is predicted. This may explain why several site-directed mutations alter the proton release kinetics without a direct involvement in proton transfer.
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