Structural implications of mutations assessed by molecular dynamics: Vpu1-32 from HIV-1.
Structural pore models are generated for Vpu(1-32)WT from HIV-1 as well as for three mutants W23L, S24L and R31V. A computational methodology is employed which samples the whole conformational space of the pentameric assemblies of Vpu. The analysis of the related energy landscape reveals a small set of reasonable pore models, which are thoroughly investigated regarding their structural properties as well as their putative stability under native-like conditions. The models are also discussed in respect of earlier experimental findings about their channel activities. The study proposes functional pores reflecting the experimentally found conductance states of Vpu and its mutants.
Krüger
J
J
Institute of Biophotonics, School of Biomedical Science and Engineering, National Yang-Ming University, 155, Sec. 2, Li-Nong St., Taipei, 112, Taiwan.
Fischer
Wolfgang B
WB
D015497:HIV-1 / Q000737:chemistry* / Q000235:genetics; D054298:Human Immunodeficiency Virus Proteins / Q000737:chemistry* / Q000235:genetics*; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D010713:Phosphatidylcholines / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D054334:Viral Regulatory and Accessory Proteins / Q000737:chemistry* / Q000235:genetics*; D000086082:Viroporin Proteins
D054298:Human Immunodeficiency Virus Proteins; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D054334:Viral Regulatory and Accessory Proteins; C514859:vpu protein, Human immunodeficiency virus 1; D000086082:Viroporin Proteins; C028694:1-palmitoyl-2-oleoylphosphatidylcholine