title: Exploring the conformational space of Vpu from HIV-1: a versatile adaptable protein.
abstract: The dynamic behavior of monomeric Vpu(1-32) from HIV-1 in different lipid environments has been studied. The peptide shows highly flexible behavior during the simulations and easily adapts to changing lipid environments as it experiences when travelling through the Golgi apparatus. Protein-lipid interactions do not show any significant correlation towards lipid type or thickness based on multiple 10 ns simulations. The averaged structure of a series of 16 independent simulations suggest kink around Ser-24, which compensates the polarity of its side chain by forming hydrogen bonds with the carbonyl backbone of adjacent amino acids towards the N-terminus.
authors.affiliation: Institute of Biophotonics, School of Medical Science and Engineering, National Yang Ming University, 155, Sec. 2, Li-Nong St., Taipei 112, Taiwan.
authors.forename: Jens
authors.initials: J
authors.lastname: Krüger
authors.forename: Wolfgang B
authors.initials: WB
authors.lastname: Fischer
mesh_terms: D003198:Computer Simulation; D015497:HIV-1 / Q000737:chemistry* / Q000378:metabolism; D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry* / Q000378:metabolism; D050356:Lipid Metabolism; D008055:Lipids / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000378:metabolism; D000086082:Viroporin Proteins
chemical_list: D054298:Human Immunodeficiency Virus Proteins; D008055:Lipids; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins