Full length Vpu from HIV-1: combining molecular dynamics simulations with NMR spectroscopy.
Based on structures made available by solution NMR, molecular models of the protein Vpu from HIV-1 were built and refined by 6 ns MD simulations in a fully hydrated lipid bilayer. Vpu is an 81 amino acid type I integral membrane protein encoded by the human immunodeficiency virus type-1 (HIV-1) and closely related simian immunodeficiency viruses (SIVs). Its role is to amplify viral release. Upon phosphorylation, the cytoplasmic domain adopts a more compact shape with helices 2 and 3 becoming almost parallel to each other. A loss of helicity for several residues belonging to the helices adjacent to both ends of the loop region containing serines 53 and 57 is observed. A fourth helix, present in one of the NMR-based structures of the cytoplasmic domain and located near the C-terminus, is lost upon phosphorylation.
Biomembrane Structure Unit, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, UK.
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D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry*; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D008051:Lipid Bilayers; D009682:Magnetic Resonance Spectroscopy; D008563:Membrane Lipids / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010766:Phosphorylation; D011487:Protein Conformation; D017510:Protein Folding; D054334:Viral Regulatory and Accessory Proteins / Q000138:chemical synthesis / Q000737:chemistry*; D014867:Water / Q000737:chemistry*; D000086082:Viroporin Proteins
D054298:Human Immunodeficiency Virus Proteins; D008051:Lipid Bilayers; D008563:Membrane Lipids; D054334:Viral Regulatory and Accessory Proteins; D014867:Water; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins