ArticleBiophysical journal2004
Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 44 citations in OpenAlex.
- Atomistic Characterization of Gramicidin Channel Formation.Journal of chemical theory and computation · 2021Article
- Molecular Mechanism for Gramicidin Dimerization and Dissociation in Bilayers of Different Thickness.Biophysical journal · 2019Article
- Time-resolved measurements of an ion channel conformational change driven by a membrane phase transition.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Gramicidin A Channel Formation Induces Local Lipid Redistribution I: Experiment and Simulation.Biophysical journal · 2017Article
- Gramicidin A Channel Formation Induces Local Lipid Redistribution II: A 3D Continuum Elastic Model.Biophysical journal · 2017Article
- Linear rate-equilibrium relations arising from ion channel-bilayer energetic coupling.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Solvation free energies of glutamate and its metal complexes: a computer simulation study.Journal of molecular modeling · 2011Article
- A one-dimensional continuum elastic model for membrane-embedded gramicidin dimer dissociation.PloS one · 2011Article
- Amphiphile regulation of ion channel function by changes in the bilayer spring constant.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Electroelastic coupling between membrane surface fluctuations and membrane-embedded charges: continuum multidielectric treatment.The Journal of chemical physics · 2010Article
- Shape-Dependent Global Deformation Modes of Large Protein Structures.Journal of molecular structure · 2010Article
- Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes.Journal of the Royal Society, Interface · 2010Review
- Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information.The Journal of chemical physics · 2009Article
- Lipid bilayer-mediated regulation of ion channel function by amphiphilic drugs.The Journal of general physiology · 2008Article
- Water and ion permeation in bAQP1 and GlpF channels: a kinetic Monte Carlo study.Biophysical journal · 2004Article
- Anion pathway and potential energy profiles along curvilinear bacterial ClC Cl- pores: electrostatic effects of charged residues.Biophysical journal · 2004Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The dissociation of gramicidin A (gA) channels into monomers is the simplest example of a channel gating process. The initial steps in this process are studied via a computational model that simulates the reaction coordinate for dimer-monomer dissociation. The nonbonded interaction energy between the monomers is determined, allowing for their free relative translational and rotational motion. Lowest energy pathways and reaction coordinates of the gating process are determined. Partial rupture of the six hydrogen bonds (6HB) at the dimer junction takes place by coupling monomer rotation and lateral displacement. Coupling rotation with axial separation is far more expensive energetically. The transition state for channel dissociation occurs when monomers are displaced laterally by approximately 4-6 A, separated by approximately 1.6-2 A, and rotated by approximately 120 degrees, breaking two hydrogen bonds. In membranes with significant hydrophobic mismatch there is a much greater likelihood of forming 4HB and possibly even 2HB states. In the 4HB state the pore remains fully open and conductive. However, transitions from the 6HB to 4HB and 4HB to 2HB states take place via intermediates in which the gA pore is closed and nonconductive. These lateral monomer displacements give rise to transitory pore occlusion at the dimer junction, which provides a rationale for fast closure events (flickers). Local dynamics of gA monomers also leads to lateral and rotational diffusion of the whole gA dimer, giving rise to diffusional rotation of the dimer about the channel axis.
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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.