ArticleJournal of the American Chemical Society2011
Proton storage site in bacteriorhodopsin: new insights from quantum mechanics/molecular mechanics simulations of microscopic pK(a) and infrared spectra.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 63 citations in OpenAlex.
- Revisiting the Proposed Protonated Water Cluster at the Exit Site of the Proton Transfer Pathway in Bacteriorhodopsin.The journal of physical chemistry. B · 2025Article
- Proteorhodopsin insights into the molecular mechanism of vectorial proton transport.Science advances · 2025Article
- Origin of the unique topology of the triangular water cluster inBiophysics and physicobiology · 2025Article
- Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.Annual review of biophysics · 2023Review
- Archaeal Lipids Regulating the Trimeric Structure Dynamics of Bacteriorhodopsin for Efficient Proton Release and Uptake.International journal of molecular sciences · 2022Article
- True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins.Nature structural & molecular biology · 2022Article
- O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter.Biochemistry · 2021Article
- 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
- Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.Journal of computational chemistry · 2017Article
- The Existence of an Isolated Hydronium Ion in the Interior of Proteins.Angewandte Chemie (International ed. in English) · 2017Article
- Perspective: Quantum mechanical methods in biochemistry and biophysics.The Journal of chemical physics · 2016Article
- Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models.The journal of physical chemistry. B · 2014Article
- Density functional tight binding: values of semi-empirical methods in an ab initio era.Physical chemistry chemical physics : PCCP · 2014Article
- A delocalized proton-binding site within a membrane protein.Biophysical journal · 2014Article
- Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications.Journal of chemical theory and computation · 2014Article
- Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.Journal of chemical theory and computation · 2014Article
- A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.Journal of chemical theory and computation · 2012Article
- Factors that differentiate the H-bond strengths of water near the Schiff bases in bacteriorhodopsin and Anabaena sensory rhodopsin.The Journal of biological chemistry · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as the PRG would require the protein to raise the pK(a) of a hydronium by almost 11 pK(a) units, which is difficult considering known cases of pK(a) shifts in proteins. Our recent quantum mechanics/molecular mechanics (QM/MM) simulations suggested an alternative "intermolecular proton bond" model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pK(a) values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting X-ray structure, and nuclear quantum effects, the "intermolecular proton bond" model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the "intermolecular proton bond" model is likely applicable to the PRG in biomolecular proton pumps in general.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.