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Int. J. Mol. Sci. 2019, 20(2), 260; https://doi.org/10.3390/ijms20020260

Effects of CD4 Binding on Conformational Dynamics, Molecular Motions, and Thermodynamics of HIV-1 gp120

1
State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China
2
College of Mathematics and Computer, Dali University, Dali 671003, China
3
College of Agriculture and Biological Science, Dali University, Dali 671003, China
*
Authors to whom correspondence should be addressed.
Received: 7 November 2018 / Revised: 19 December 2018 / Accepted: 19 December 2018 / Published: 10 January 2019
(This article belongs to the Collection Proteins and Protein-Ligand Interactions)
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Abstract

Human immunodeficiency virus type-1 (HIV-1) infection is triggered by its envelope (Env) glycoprotein gp120 binding to the host-cell receptor CD4. Although structures of Env/gp120 in the liganded state are known, detailed information about dynamics of the liganded gp120 has remained elusive. Two structural models, the CD4-free gp120 and the gp120-CD4 complex, were subjected to µs-scale multiple-replica molecular dynamics (MD) simulations to probe the effects of CD4 binding on the conformational dynamics, molecular motions, and thermodynamics of gp120. Comparative analyses of MD trajectories in terms of structural deviation and conformational flexibility reveal that CD4 binding effectively suppresses the overall conformational fluctuations of gp120. Despite the largest fluctuation amplitude of the V1/V2 region in both forms of gp120, the presence of CD4 prevents it from approaching the gp120 core. Comparison of the constructed free energy landscapes (FELs) shows that CD4 binding reduces the conformational entropy and conformational diversity while enhancing the stability of gp120. Further comparison of the representative structures extracted from free energy basins/minima of FELs reveals that CD4 binding weakens the reorientation ability of V1/V2 and hence hinders gp120 from transitioning out of the liganded state to the unliganded state. Therefore, locking gp120 conformation via restraining V1/V2 reorientation with small molecules seems to be a promising strategy to control HIV-1 infection. Our computer simulation results support the conformational selection mechanism for CD4 binding to gp120 and facilitate the understanding of HIV-1 immune evasion mechanisms. View Full-Text
Keywords: molecular dynamics simulation; conformational transition; free energy landscape; conformational selection; structure-dynamics-function relationship molecular dynamics simulation; conformational transition; free energy landscape; conformational selection; structure-dynamics-function relationship
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Li, Y.; Deng, L.; Yang, L.-Q.; Sang, P.; Liu, S.-Q. Effects of CD4 Binding on Conformational Dynamics, Molecular Motions, and Thermodynamics of HIV-1 gp120. Int. J. Mol. Sci. 2019, 20, 260.

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