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Transmembrane domains of viral ion channel proteins: A molecular dynamics simulation study
Author(s) -
Fischer Wolfgang B.,
Forrest Lucy R.,
Smith Graham R.,
Sansom Mark S. P.
Publication year - 2000
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(200006)53:7<529::aid-bip1>3.0.co;2-6
Subject(s) - chemistry , molecular dynamics , transmembrane protein , dynamics (music) , ion channel , biophysics , transmembrane domain , ion , chemical physics , computational biology , membrane , biochemistry , computational chemistry , physics , organic chemistry , receptor , biology , acoustics
Nanosecond molecular dynamics simulations in a fully solvated phospholipid bilayer have been performed on single transmembrane α‐helices from three putative ion channel proteins encoded by viruses: NB (from influenza B), CM2 (from influenza C), and Vpu (from HIV‐1). α‐Helix stability is maintained within a core region of ca. 28 residues for each protein. Helix perturbations are due either to unfavorable interactions of hydrophobic residues with the lipid headgroups or to the need of the termini of short helices to extend into the surrounding interfacial environment in order to form H‐bonds. The requirement of both ends of a helix to form favorable interactions with lipid headgroups and/or water may also lead to tilting and/or kinking of a transmembrane α‐helix. Residues that are generally viewed as poor helix formers in aqueous solution (e.g., Gly, Ile, Val) do not destabilize helices, if located within a helix that spans a lipid bilayer. However, helix/bilayer mismatch such that a helix ends abruptly within the bilayer core destabilizes the end of the helix, especially in the presence of Gly and Ala residues. Hydrogen bonding of polar side‐chains with the peptide backbone and with one another occurs when such residues are present within the bilayer core, thus minimizing the energetic cost of burying such side‐chains. © 2000 John Wiley & Sons, Inc. Biopoly 53: 529–538, 2000