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Updated: Jul 5, 2026

Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
Published on: September 15, 2010
Exploring the conformational space of Vpu from HIV-1: a versatile adaptable protein
Jens Krüger1, Wolfgang B Fischer
1Institute of Biophotonics, School of Medical Science and Engineering, National Yang Ming University, 155, Sec. 2, Li-Nong St., Taipei 112, Taiwan.
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.
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