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Modeling the structure of the respiratory syncytial virus small hydrophobic protein by silent‐mutation analysis of global searching molecular dynamics
Author(s) -
Kochva Uzi,
Leonov Hadas,
Arkin Isaiah T.
Publication year - 2003
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.03151103
Subject(s) - transmembrane domain , transmembrane protein , molecular dynamics , mutation , virus , protein structure , protein domain , helix bundle , biophysics , biology , ion channel , chemistry , computational biology , biochemistry , genetics , amino acid , gene , receptor , computational chemistry
Human respiratory syncytial virus (RSV) encodes a small hydrophobic (SH) protein, whose function in the life cycle of the virus is unknown. Recent channel activity measurements of the protein suggest that like other viroporins, SH may assemble into a homo‐oligomeric ion channel. To further our understanding of this potentially important protein, a new strategy was implemented in order to model the transmembrane oligomeric bundle of the protein. Global searching molecular dynamic simulations of SH proteins from eight different viral strains, each at different oligomeric states, as well as different lengths of the putative transmembrane domain, were undertaken. Taken together, a total of 45 different global molecular dynamic simulations pointed to a single pentameric structure for the protein that was found in all of the different variants. The model of the structure obtained is a channel‐like homopentamer whose minimal transmembrane pore diameter is 1.46 Å.