ArticleBiophysical journal2002
Open-state models of a potassium channel.
Article in Biophysical journal, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Conduction through a narrow inward-rectifier KThe Journal of general physiology · 2019Article
- Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating.Scientific reports · 2017Article
- Side chain flexibility and the pore dimensions in the GABAA receptor.Journal of computer-aided molecular design · 2016Article
- Probing the energy landscape of activation gating of the bacterial potassium channel KcsA.PLoS computational biology · 2013Article
- Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.Proteins · 2010Article
- Computational analysis of membrane proteins: the largest class of drug targets.Drug discovery today · 2009Review
- Generation, comparison, and merging of pathways between protein conformations: gating in K-channels.Biophysical journal · 2008Article
- Cooperative transition between open and closed conformations in potassium channels.PLoS computational biology · 2008Article
- End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.Biophysical journal · 2008Article
- Ion conductance vs. pore gating and selectivity in KcsA channel: modeling achievements and perspectives.Journal of molecular modeling · 2007Article
- Common mechanism of pore opening shared by five different potassium channels.Biophysical journal · 2006Article
- Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating.Biophysical journal · 2005Article
- Molecular dynamics study of gating in the mechanosensitive channel of small conductance MscS.Biophysical journal · 2004Article
- In silico activation of KcsA K+ channel by lateral forces applied to the C-termini of inner helices.Biophysical journal · 2004Article
- Ion permeation of pores in model membranes: selectivity, fluctuations and the role of surface charge.European biophysics journal : EBJ · 2004Article
- Theory and simulation of water permeation in aquaporin-1.Biophysical journal · 2004Article
- Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA.Biophysical journal · 2003Article
- Gating of MscL studied by steered molecular dynamics.Biophysical journal · 2003Article
- Pores formed by the nicotinic receptor m2delta Peptide: a molecular dynamics simulation study.Biophysical journal · 2003Article
- A molecular model of the inner pore of the Ca channel in its open state.Channels (Austin, Tex.)Article
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2 authors.
Funding
Abstract
The structure of the bacterial potassium channel, KcsA, corresponds to the channel in a closed state. Two lines of evidence suggest that the channel must widen its intracellular mouth when in an open state: 1) internal block by a series of tetraalkylammonium ions and 2) spin labeling experiments. Thus it is known that the protein moves in this region, but it is unclear by how much and the mechanisms that are involved. To address this issue we have applied a novel approach to generate plausible open-state models of KcsA. The approach can be thought of as placing a balloon inside the channel and gradually inflating it. Only the protein sees the balloon, and so water is free to move in and out of the channel. The balloon is a van der Waals sphere whose parameters change by a small amount at each time step, an approach similar to methods used in free energy perturbation calculations. We show that positioning of this balloon at various positions along the pore axis generates similar open-state models, thus indicating that there may be a preferred pathway to an open state. We also show that the resulting structures from this process are conformationally unstable and need to undergo a relaxation process for up to 4 ns. We show that the channel can relax into a new state that has a larger pore radius at the region of the intracellular mouth. The resulting models may be useful in exploring models of the channel in the context of ion permeation and blocking agents.
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