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The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
Reprint requests to: Isaiah T. Arkin, The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel; e-mail: arkin{at}cc.huji.ac.il; fax: 972-(0)2-6584329.
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.
Keywords: HRSV; membrane protein; molecular dynamics; SH protein; protein structure; viroporin
Abbreviations: RMSD, root mean square deviation • CNS, crystallography and NMR system • CHI, CNS searching of helix interactions • HRSV, human respiratory syncytial virus • SH, small hydrophobic
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