Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle.
The transmembrane domain of oligomeric protein Vpu encoded by HIV-1 has been studied by means of a molecular dynamics simulation. A pentameric bundle of unconstrained helices (residues 6-28 of Vpu) with a water filled pore was initially assembled in a membrane mimetic octane/water system. This system was simulated, using the CHARMm19 and OPLS united atom force fields with no constraints at a temperature of 300 K and a pressure of 1 atm. For these forcefields and the initial conditions tested, the oligomeric bundle expelled most of the pore water molecules. The resulting bundle and residual waters adopt a conical structural motif with some resemblance to a potassium channel.
Moore
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Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadephia 19104-6323, USA. moore@cmm.chem.upenn.edu
Zhong
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Husslein
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Klein
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D000595:Amino Acid Sequence; D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry*; D054298:Human Immunodeficiency Virus Proteins; D007473:Ion Channels / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry*; D000086082:Viroporin Proteins
D054298:Human Immunodeficiency Virus Proteins; D007473:Ion Channels; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins