Full length Vpu from HIV-1: combining molecular dynamics simulations with NMR spectroscopy.

Journal article

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.

Authors: Lemaitre, V; Willbold, D; Watts, A; Fischer, W

• Publication status: Published
• Journal: Journal of biomolecular structure and dynamics
• Volume: 23
• Issue: 5
• Pages: 485-496
• Publication date: 2006-04-01
• DOI: 10.1080/07391102.2006.10507074
• EISSN: 1538-0254
• ISSN: 0739-1102
• Language: English
• Keywords: Binding Sites; Humans; Models, Molecular; Water; Human Immunodeficiency Virus Proteins; Magnetic Resonance Spectroscopy; Amino Acid Sequence; HIV-1; Protein Folding; Membrane Lipids; Viral Regulatory and Accessory Proteins; Computer Simulation; Phosphorylation; Lipid Bilayers; Protein Conformation; Molecular Sequence Data