ArticleBiophysical journal2003
A computer simulation study of the hydrated proton in a synthetic proton channel.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 63 citations in OpenAlex.
- Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction.bioRxiv : the preprint server for biology · 2026Article
- A proton-gated channel identified in the centipede antenna.EMBO reports · 2025Article
- Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.Chemical reviews · 2020Review
- Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel.Journal of chemical theory and computation · 2014Article
- Water networks in fast proton transfer during catalysis by human carbonic anhydrase II.Biochemistry · 2013Article
- Proton transfer in catalysis and the role of proton shuttles in carbonic anhydrase.Biochimica et biophysica acta · 2010Article
- Article
- Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB.The journal of physical chemistry. B · 2009Article
- Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations.The journal of physical chemistry. B · 2007Review
- Charge delocalization in proton channels, I: the aquaporin channels and proton blockage.Biophysical journal · 2007Article
- Charge delocalization in proton channels, II: the synthetic LS2 channel and proton selectivity.Biophysical journal · 2007Article
- Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps.The journal of physical chemistry. A · 2006Article
- Energy transduction: proton transfer through the respiratory complexes.Annual review of biochemistry · 2006Review
- Hydroxide and proton migration in aquaporins.Biophysical journal · 2005Article
- Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway.Proceedings of the National Academy of Sciences of the United States of America · 2005Article
- Protons may leak through pure lipid bilayers via a concerted mechanism.Biophysical journal · 2005Article
- OmpT: molecular dynamics simulations of an outer membrane enzyme.Biophysical journal · 2004Article
- Water alignment, dipolar interactions, and multiple proton occupancy during water-wire proton transport.Biophysical journal · 2004Article
- What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals.Biophysical journal · 2003Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Classical molecular dynamics simulations using the multistate empirical valence bond model for aqueous proton transport were performed to characterize the hydration structure of an excess proton inside a leucine-serine synthetic ion channel, LS2. For such a nonuniform pore size ion channel, it is found that the Zundel ion (H(5)O(2)(+)) solvation structure is generally more stable in narrow channel regions than in wider channel regions, which is in agreement with a recent study on idealized hydrophobic proton channels. However, considerable diversity in the relative stability of the Zundel to Eigen cation (H(9)O(4)(+)) was observed. Three of the five wide channel regions, one located at the channel's center and the other two located near the channel mouths, are found to show extraordinary preference for the Eigen solvation structure. This implies that proton hopping is inhibited in these regions and therefore suggests that these regions may behave as barriers in the proton conducting pathway inside the channel. The proton solvation is also greatly influenced by the local molecular environment of the protein. In particular, the polar side chains of the Ser residues, which are intimately involved in the solvation structure, can greatly influence proton solvation. However, no preference of the influence by the various Ser side chains was found; they can either promote or prevent the formation of certain solvation structures.
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