ArticleThe journal of physical chemistry. A2006
Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.
Article in The journal of physical chemistry. A, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Ultrafast excited-state proton transfer dynamics using linearized pair-density functional theory.Chemical science · 2026Article
- A carboxylate switch point controls long-range energy transduction in respiratory Complex I.Nature communications · 2026Article
- Quinones operate as proton-collecting antennas in energy-transducing membranes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions.Journal of chemical theory and computation · 2025Article
- Redox-Activated Proton Transfer through a Redundant Network in the QJournal of chemical information and modeling · 2025Article
- Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.Annual review of biophysics · 2023Review
- Generalized Transition State Theory Treatment of Water-Assisted Proton Transport Processes in Proteins.The journal of physical chemistry. B · 2022Article
- Molecular-scale mechanisms of CONature reviews. Chemistry · 2022Review
- Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.Journal of the American Chemical Society · 2022Article
- Improved Indicator Algorithms for Tracking a Hydrated Proton as A Local Structural Defect in Grotthuss Diffusion in Aqueous Solutions.Chemical physics letters · 2021Article
- 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
- Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface.Journal of chemical theory and computation · 2021Article
- Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.Chemical reviews · 2020Review
- Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.The journal of physical chemistry. B · 2020Article
- Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1.Nucleic acids research · 2018Article
- Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations.Methods in enzymology · 2018Article
- Behavior of BsoBI endonuclease in the presence and absence of DNA.Journal of molecular modeling · 2017Article
- Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.Biochemistry · 2017Article
- Acid activation mechanism of the influenza A M2 proton channel.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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7 authors.
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Abstract
Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.
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