ArticleBiophysical journal2006
The influence of amino acid protonation states on molecular dynamics simulations of the bacterial porin OmpF.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.PLoS computational biology · 2025Article
- TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations.Journal of chemical theory and computation · 2025Article
- Interaction of Tryptophan- and Arginine-Rich Antimicrobial Peptide withInternational journal of molecular sciences · 2023Article
- Advances in Computational and Bioinformatics Tools and Databases for Designing and Developing a Multi-Epitope-Based Peptide Vaccine.International journal of peptide research and therapeutics · 2023Review
- The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway.Antibiotics (Basel, Switzerland) · 2022Article
- Role of internal loop dynamics in antibiotic permeability of outer membrane porins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Rationalizing the generation of broad spectrum antibiotics with the addition of a positive charge.Chemical science · 2021Article
- Outer Membrane Protein F Is Involved in Biofilm Formation, Virulence and Antibiotic Resistance inMicroorganisms · 2021Article
- Permeation of β-Lactamase Inhibitors through the General Porins of Gram-Negative Bacteria.Molecules (Basel, Switzerland) · 2020Article
- Article
- Structural and activity characterization of human PHPT1 after oxidative modification.Scientific reports · 2016Article
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.Biophysical journal · 2016Article
- Understanding Voltage Gating of Providencia stuartii Porins at Atomic Level.PLoS computational biology · 2015Article
- A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.Journal of the American Chemical Society · 2013Article
- Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.The Journal of general physiology · 2013Article
- The binding of antibiotics in OmpF porin.Structure (London, England : 1993) · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics.BMC genomics · 2010Article
- The ionization state of D37 in E. coli porin OmpF and the nature of conductance fluctuations in D37 mutants.European biophysics journal : EBJ · 2010Article
- Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin.Biophysical journal · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
Several groups, including our own, have found molecular dynamics (MD) calculations to result in the size of the pore of an outer membrane bacterial porin, OmpF, to be reduced relative to its size in the x-ray crystal structure. At the narrowest portion of its pore, loop L3 was found to move toward the opposite face of the pore, resulting in decreasing the cross-section area by a factor of approximately 2. In an earlier work, we computed the protonation states of titratable residues for this system and obtained values different from those that had been used in previous MD simulations. Here, we show that MD simulations carried out with these recently computed protonation states accurately reproduce the cross-sectional area profile of the channel lumen in agreement with the x-ray structure. Our calculations include the investigation of the effect of assigning different protonation states to the one residue, D(127), whose protonation state could not be modeled in our earlier calculation. We found that both assumptions of charge states for D(127) reproduced the lumen size profile of the x-ray structure. We also found that the charged state of D(127) had a higher degree of hydration and it induced greater mobility of polar side chains in its vicinity, indicating that the apparent polarizability of the D(127) microenvironment is a function of the D(127) protonation state.
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