ArticleProceedings of the National Academy of Sciences of the United States of America2007
Structures and spectral signatures of protonated water networks in bacteriorhodopsin.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 142 citations in OpenAlex.
- Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin.Journal of chemical theory and computation · 2021Article
- Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism.Nature communications · 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
- Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study.IEEE transactions on terahertz science and technology · 2017Article
- A delocalized proton-binding site within a membrane protein.Biophysical journal · 2014Article
- Detection of an intermediary, protonated water cluster in photosynthetic oxygen evolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway.Structure (London, England : 1993) · 2013Article
- Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase.PLoS computational biology · 2012Article
- Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift.Biophysics (Nagoya-shi, Japan) · 2012Article
- Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks.Journal of biological physics · 2012Article
- Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra.Journal of the American Chemical Society · 2011Article
- 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
- A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties.The Journal of biological chemistry · 2011Article
- Real-time structural transitions are coupled to chemical steps in ATP hydrolysis by Eg5 kinesin.The Journal of biological chemistry · 2010Article
- Visualizing water molecules in transmembrane proteins using radiolytic labeling methods.Biochemistry · 2010Review
- H(aq)+ structures in proton wires inside nanotubes.Journal of the American Chemical Society · 2009Article
- Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.Journal of molecular modeling · 2009Article
- Long-distance proton transfer with a break in the bacteriorhodopsin active site.Journal of the American Chemical Society · 2009Article
- Active water in protein-protein communication within the membrane: the case of SRII-HtrII signal relay.Biochemistry · 2009Article
- Protons and how they are transported by proton pumps.Pflugers Archiv : European journal of physiology · 2009Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.
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