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Exploring the conformational space of Vpu from HIV‐1: A versatile adaptable protein
Author(s) -
Krüger Jens,
Fischer Wolfgang B.
Publication year - 2008
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.20986
Subject(s) - monomer , hydrogen bond , side chain , polarity (international relations) , molecular dynamics , human immunodeficiency virus (hiv) , crystallography , chemical physics , chemistry , biophysics , space (punctuation) , biological system , molecule , computer science , computational chemistry , biology , biochemistry , organic chemistry , immunology , cell , polymer , operating system
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. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008.