Molecular dynamics simulations reveal the HIV-1 Vpu transmembrane protein to form stable pentamers

• Published in: PloS one Vol. 8; no. 11; p. e79779
• Main Authors: Padhi, Siladitya, Khan, Nabab, Jameel, Shahid, Priyakumar, U Deva
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 06.11.2013; Public Library of Science (PLoS)
• Subjects: Analysis; Atomic structure; Bioinformatics; Cell Membrane - metabolism; Channel gating; Computer simulation; Entropy; Fourier transforms; Genetic engineering; HIV; HIV (Viruses); Human immunodeficiency virus; Human Immunodeficiency Virus Proteins - chemistry; Hydrophobic and Hydrophilic Interactions; Information technology; Ion channels; Lipids; Membrane lipids; Molecular dynamics; Molecular Dynamics Simulation; Oligomerization; Oligomers; Protein Multimerization; Protein Stability; Protein Structure, Quaternary; Protein Structure, Tertiary; Proteins; Residues; Simulation; Studies; Transmembrane proteins; Viral Regulatory and Accessory Proteins - chemistry; Viruses; Vpu protein; India
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0079779

The human immunodeficiency virus type I (HIV-1) Vpu protein is 81 residues long and has two cytoplasmic and one transmembrane (TM) helical domains. The TM domain oligomerizes to form a monovalent cation selective ion channel and facilitates viral release from host cells. Exactly how many TM domains oligomerize to form the pore is still not understood, with experimental studies indicating the existence of a variety of oligomerization states. In this study, molecular dynamics (MD) simulations were performed to investigate the propensity of the Vpu TM domain to exist in tetrameric, pentameric, and hexameric forms. Starting with an idealized α-helical representation of the TM domain, a thorough search for the possible orientations of the monomer units within each oligomeric form was carried out using replica-exchange MD simulations in an implicit membrane environment. Extensive simulations in a fully hydrated lipid bilayer environment on representative structures obtained from the above approach showed the pentamer to be the most stable oligomeric state, with interhelical van der Waals interactions being critical for stability of the pentamer. Atomic details of the factors responsible for stable pentamer structures are presented. The structural features of the pentamer models are consistent with existing experimental information on the ion channel activity, existence of a kink around the Ile17, and the location of tetherin binding residues. Ser23 is proposed to play an important role in ion channel activity of Vpu and possibly in virus propagation.