Qualitative computational bioanalytics: assembly of viral channel-forming peptides around mono and divalent ions.
A fine-grained docking protocol was used to generate a bundle-like structure of the bitopic membrane protein Vpu from HIV-1. Vpu is a type I membrane protein with 81 amino acids. It is proposed that Vpu forms ion- and substrate-conducting bundles, which are located at the plasma membrane in the infected cell. The Vpu1-32 peptide that includes the transmembrane domain (TMD) is assembled into homo-pentameric bundles around prepositioned Na, K, Ca or Cl ions. For bundles with the lowest energy, the TMDs generate a hydrophobic pore. Bundles in which Ser-24 faces the pore have higher energy. The tilt of the helices in the lowest energy bundles is larger than bundles with serines facing the pore. Left-handed bundles are lowest in energy where the ions are located at the serines.
Institute of Biophotonics, School of Biomedical Science and Engineering, Biophotonics & Molecular Imaging Research Center (BMIRC), National Yang-Ming University, Taipei 112, Taiwan.
Li-Hua
LH
Li
Hao-Jen
HJ
Hsu
Wolfgang B
WB
Fischer
D002413:Cations, Divalent / Q000737:chemistry; D002414:Cations, Monovalent / Q000737:chemistry; D019295:Computational Biology; D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D007473:Ion Channels / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry*; D000086082:Viroporin Proteins
D002413:Cations, Divalent; D002414:Cations, Monovalent; D054298:Human Immunodeficiency Virus Proteins; D007473:Ion Channels; D008565:Membrane Proteins; D010455:Peptides; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins
Assembly; Docking approach; HIV-1; Membrane protein; Molecular dynamics simulations; Vpu protein