title: Bundles consisting of extended transmembrane segments of Vpu from HIV-1: computer simulations and conductance measurements.
abstract: Part of the genome of the human immunodeficiency virus type 1 (HIV-1) encodes for a short membrane protein Vpu, which has a length of 81 amino acids. It has two functional roles: (i) to downregulate CD4 and (ii) to support particle release. These roles are attributed to two distinct domains of the peptide, the cytoplasmic and transmembrane (TM) domains, respectively. It has been suggested that the enhanced particle release function is linked to the ion channel activity of Vpu, with a slight preference for cations over anions. To allow ion flux across the membrane Vpu would be required to assemble in homooligomers to form functional water-filled pores. In this study molecular dynamics simulations are used to address the role of particular amino acids in 4, 5, and 6 TM helix bundle structures. The helices (Vpu(6-33)) are extended to include hydrophilic residues such as Glu, Tyr, and Arg (EYR motif). Our simulations indicate that this motif destabilizes the bundles at their C-terminal ends. The arginines point into the pore to form a positive charged ring that could act as a putative selectivity filter. The helices of the bundles adopt slightly higher average tilt angles with decreasing number of helices. We also suggest that the helices are kinked. Conductance measurements on a peptide (Vpu(1-32)) reconstituted into lipid membranes show that the peptide forms ion channels with several conductance levels.
authors.affiliation: Biomembrane Structure Unit, Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, U.K.
authors.forename: F S
authors.initials: FS
authors.lastname: Cordes
authors.forename: A D
authors.initials: AD
authors.lastname: Tustian
authors.forename: M S P
authors.initials: MS
authors.lastname: Sansom
authors.forename: A
authors.initials: A
authors.lastname: Watts
authors.forename: W B
authors.initials: WB
authors.lastname: Fischer
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D004553:Electric Conductivity; D015497:HIV-1 / Q000737:chemistry* / Q000502:physiology; D054298:Human Immunodeficiency Virus Proteins; D006801:Humans; D008564:Membrane Potentials; D008565:Membrane Proteins / Q000737:chemistry* / Q000502:physiology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D018408:Patch-Clamp Techniques; D010446:Peptide Fragments / Q000737:chemistry* / Q000502:physiology; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000502:physiology; D014867:Water / Q000737:chemistry; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D008565:Membrane Proteins; D010446:Peptide Fragments; D054334:Viral Regulatory and Accessory Proteins; D014867:Water; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins