ArticleBiophysical journal1999
Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer.
Article in Biophysical journal, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Defining Viral Defective Ribosomal Products: Standard and Alternative Translation Initiation Events Generate a Common Peptide from Influenza A Virus M2 and M1 mRNAs.Journal of immunology (Baltimore, Md. : 1950) · 2016Article
- Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.Faraday discussions · 2014Article
- Voltage-gated proton channels: molecular biology, physiology, and pathophysiology of the H(V) family.Physiological reviews · 2013Review
- Multiple Proton Confinement in the M2 Channel from the Influenza A Virus.The journal of physical chemistry. C, Nanomaterials and interfaces · 2010Article
- Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Structure and dynamics of the influenza A M2 channel: a comparison of three structures.Journal of molecular modeling · 2009Article
- Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.Biophysical journal · 2008Article
- Solid-state NMR characterization of conformational plasticity within the transmembrane domain of the influenza A M2 proton channel.Biochimica et biophysica acta · 2007Article
- A structural model of EmrE, a multi-drug transporter from Escherichia coli.Biophysical journal · 2004Article
- Molecular dynamics simulation of human immunodeficiency virus protein U (Vpu) in lipid/water Langmuir monolayer.Journal of molecular modeling · 2003Article
- Pores formed by the nicotinic receptor m2delta Peptide: a molecular dynamics simulation study.Biophysical journal · 2003Article
- Deuterium/hydrogen exchange factors measured by solution nuclear magnetic resonance spectroscopy as indicators of the structure and topology of membrane proteins.Biophysical journal · 2002Article
- Mapping the energy surface of transmembrane helix-helix interactions.Biophysical journal · 2001Article
- Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL 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
- Structure and dynamics of K channel pore-lining helices: a comparative simulation study.Biophysical journal · 2000Article
- Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer.Biophysical journal · 2000Article
- Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane.Biophysical journal · 1999Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Integral membrane proteins containing at least one transmembrane (TM) alpha-helix are believed to account for between 20% and 30% of most genomes. There are several algorithms that accurately predict the number and position of TM helices within a membrane protein sequence. However, these methods tend to disagree over the beginning and end residues of TM helices, posing problems for subsequent modeling and simulation studies. Molecular dynamics (MD) simulations in an explicit lipid and water environment are used to help define the TM helix of the M2 protein from influenza A virus. Based on a comparison of the results of five different secondary structure prediction algorithms, three different helix lengths (an 18mer, a 26mer, and a 34mer) were simulated. Each simulation system contained 127 POPC molecules plus approximately 3500-4700 waters, giving a total of approximately 18,000-21,000 atoms. Two simulations, each of 2 ns duration, were run for the 18mer and 26mer, and five separate simulations were run for the 34mer, using different starting models generated by restrained in vacuo MD simulations. The total simulation time amounted to 11 ns. Analysis of the time-dependent secondary structure of the TM segments was used to define the regions that adopted a stable alpha-helical conformation throughout the simulation. This analysis indicates a core TM region of approximately 20 residues (from residue 22 to residue 43) that remained in an alpha-helical conformation. Analysis of atomic density profiles suggested that the 18mer helix revealed a local perturbation of the lipid bilayer. Polar side chains on either side of this region form relatively long-lived H-bonds to lipid headgroups and water molecules.
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