ArticleBiophysical journal2005
Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Start Me Up: How Can Surrounding Gangliosides Affect Sodium-Potassium ATPase Activity and Steer towards Pathological Ion Imbalance in Neurons?Biomedicines · 2022Review
- Nicotinic receptor pharmacology in silico: Insights and challenges.Neuropharmacology · 2020Review
- Probing the Secondary Structure of Membrane Peptides Using (2)H-Labeled d(10)-Leucine via Site-Directed Spin-Labeling and Electron Spin Echo Envelope Modulation Spectroscopy.The journal of physical chemistry. B · 2016Article
- Article
- Solid-state NMR (31)P paramagnetic relaxation enhancement membrane protein immersion depth measurements.The journal of physical chemistry. B · 2014Article
- Activation and proton transport mechanism in influenza A M2 channel.Biophysical journal · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
- GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study.Biophysical journal · 2012Article
- Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation.Journal of computational and theoretical nanoscience · 2010Article
- Normal mode gating motions of a ligand-gated ion channel persist in a fully hydrated lipid bilayer model.ACS chemical neuroscience · 2010Article
- On the functional significance of soft modes predicted by coarse-grained models for membrane proteins.The Journal of general physiology · 2010Article
- Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.Chemical reviews · 2010Review
- Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptor.Biophysical journal · 2009Article
- Behavioral differences between phosphatidic acid and phosphatidylcholine in the presence of the nicotinic acetylcholine receptor.Biophysical journal · 2008Article
- In silico models for the human alpha4beta2 nicotinic acetylcholine receptor.The journal of physical chemistry. B · 2008Article
- End-point targeted molecular dynamics: large-scale conformational changes in potassium channels.Biophysical journal · 2008Article
- Structural answers and persistent questions about how nicotinic receptors work.Frontiers in bioscience : a journal and virtual library · 2008Review
- Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation.Protein science : a publication of the Protein Society · 2008Article
- Mechanics of channel gating of the nicotinic acetylcholine receptor.PLoS computational biology · 2008Article
- Opened by a twist: a gating mechanism for the nicotinic acetylcholine receptor.European biophysics journal : EBJ · 2007Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Multiple nanosecond duration molecular dynamics simulations were performed on the transmembrane region of the Torpedo nicotinic acetylcholine receptor embedded within a bilayer mimetic octane slab. The M2 helices and M2-M3 loop regions were free to move, whereas the outer (M1, M3, M4) helix bundle was backbone restrained. The M2 helices largely retain their hydrogen-bonding pattern throughout the simulation, with some distortions in the helical end and loop regions. All of the M2 helices exhibit bending motions, with the hinge point in the vicinity of the central hydrophobic gate region (corresponding to residues alphaL251 and alphaV255). The bending motions of the M2 helices lead to a degree of dynamic narrowing of the pore in the region of the proposed hydrophobic gate. Calculations of Born energy profiles for various structures along the simulation trajectory suggest that the conformations of the M2 bundle sampled correspond to a closed conformation of the channel. Principal components analyses of each of the M2 helices, and of the five-helix M2 bundle, reveal concerted motions that may be relevant to channel function. Normal mode analyses using the anisotropic network model reveal collective motions similar to those identified by principal components analyses.
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