ArticleBiophysical journal2000
Structure and dynamics of K channel pore-lining helices: a comparative simulation study.
Article in Biophysical journal, 2000. 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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20 citing papers in PubMed, 71 citations in OpenAlex.
- Unraveling the mechanism of selective ion transport in hydrophobic subnanometer channels.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The pore of voltage-gated potassium ion channels is strained when closed.Nature communications · 2013Article
- Structural rearrangements underlying ligand-gating in Kir channels.Nature communications · 2012Article
- Cooperative nature of gating transitions in K(+) channels as seen from dynamic importance sampling calculations.Proteins · 2010Article
- The effects of lipids on channel function.Journal of biology · 2009Article
- Coupled and independent contributions of residues in IS6 and IIS6 to activation gating of CaV1.2.The Journal of biological chemistry · 2009Article
- End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.Biophysical journal · 2008Article
- Single mutations convert an outward K+ channel into an inward K+ channel.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Analysis of side-chain rotamers in transmembrane proteins.Biophysical journal · 2004Article
- In silico activation of KcsA K+ channel by lateral forces applied to the C-termini of inner helices.Biophysical journal · 2004Article
- Anion pathway and potential energy profiles along curvilinear bacterial ClC Cl- pores: electrostatic effects of charged residues.Biophysical journal · 2004Article
- Interactions of the designed antimicrobial peptide MB21 and truncated dermaseptin S3 with lipid bilayers: molecular-dynamics simulations.The Biochemical journal · 2003Article
- Localization of divalent cation-binding site in the pore of a small conductance Ca(2+)-activated K(+) channel and its role in determining current-voltage relationship.Biophysical journal · 2002Article
- Open-state models of a potassium channel.Biophysical journal · 2002Article
- Cholesterol-induced modifications in lipid bilayers: a simulation study.Biophysical journal · 2002Article
- Hierarchical approach to predicting permeation in ion channels.Biophysical journal · 2001Article
- Side-chain ionization states in a potassium channel.Biophysical journal · 2001Article
- Molecular dynamics study of peptide-bilayer adsorption.Biophysical journal · 2001Article
- Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel.Biophysical journal · 2000Article
- Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer.Biophysical journal · 2000Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Isolated pore-lining helices derived from three types of K-channel have been analyzed in terms of their structural and dynamic features in nanosecond molecular dynamics (MD) simulations while spanning a lipid bilayer. The helices were 1) M1 and M2 from the bacterial channel KcsA (Streptomyces lividans), 2) S5 and S6 from the voltage-gated (Kv) channel Shaker (Drosophila melanogaster), and 3) M1 and M2 from the inward rectifier channel Kir6.2 (human). In the case of the Kv and Kir channels, for which x-ray structures are not known, both short and long models of each helix were considered. Each helix was incorporated into a lipid bilayer containing 127 palmitoyloleoylphosphatidylcholine molecules, which was solvated with approximately 4000 water molecules, yielding approximately 20, 000 atoms in each system. Nanosecond MD simulations were used to aid the definition of optimal lengths for the helix models from Kv and Kir. Thus the study corresponds to a total simulation time of 10 ns. The inner pore-lining helices (M2 in KcsA and Kir, S6 in Shaker) appear to be slightly more flexible than the outer pore-lining helices. In particular, the Pro-Val-Pro motif of S6 results in flexibility about a molecular hinge, as was suggested by previous in vacuo simulations (, Biopolymers. 39:503-515). Such flexibility may be related to gating in the corresponding intact channel protein molecules. Analysis of H-bonds revealed interactions with both water and lipid molecules in the water/bilayer interfacial region. Such H-bonding interactions may lock the helices in place in the bilayer during the folding of the channel protein (as is implicit in the two-stage model of membrane protein folding). Aromatic residues at the extremities of the helices underwent complex motions on both short (<10 ps) and long (>100 ps) time scales.
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