Journal of Molecular Modeling

, Volume 14, Issue 9, pp 857–870 | Cite as

Molecular motions of human HIV-1 gp120 envelope glycoproteins

Original Paper

Abstract

The HIV-1 gp120 exterior envelope glycoprotein undergoes a series of conformational rearrangements while sequentially interacting with the receptor CD4 and the coreceptor CCR5 or CXCR4 on the surface of host cells to initiate virus entry. Both the crystal structures of the HIV-1 gp120 core bound by CD4 and antigen 17b, and the SIV gp120 core pre-bound by CD4 are known. Despite the wealth of knowledge on these static snapshots of molecular conformations, the details of molecular motions crucial to intervention remain elusive. We presented a comprehensive comparative analysis of dynamic behavior of gp120 in its CD4-complexed, CD4-free and CD4-unliganded states based on the homology models with modeled V3 and V4 loops. CONCOORD computer simulation was utilized to generate ensembles of feasible protein structures, which were subsequently analyzed by essential dynamics technique to identify preferred concerted motions. The revealed collective fluctuations are dominated by complex motional modes such as rotation/twisting, flexing/closing, and shortness/elongation between or within the inner, outer, and bridging-sheet domains. An attempt has been made to relate these modes to receptor/coreceptor association and neutralization avoidance. Covariance web analysis revealed four subdomains that undergo concerted motion in gp120. The structural components in gp120 that move in concert with CD4 were also identified, which may be the suitable target for inhibitor design to interrupt CD4-gp120 interaction. The differences in B-factors between the three gp120 states revealed certain structural regions that could be related either to CD4 association or to subsequent dissociation of gp120 from gp41. These dynamics data provide new insights into the structure-function relationship of gp120 and may aid in structure-based anti-HIV vaccine design.

Keywords

B-factor Collective fluctuation Comparative modeling CONCOORD simulation Covariance web Essential dynamics HIV-1 gp120 

Abbreviations

HIV

Human immunodeficiency virus

AIDS

Acquired immunodeficiency syndrome

Fab

Antigen binding fragment

SIV

Simian immunodeficiency virus

V

Variable loop

MD

Molecular dynamics

ED

Essential Dynamics

PANC

Per-atom normalized covariance

MSF

Mean square fluctuation

RMSD

Root mean square deviation

CD4-BL

CD4-binding-loop

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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  1. 1.Laboratory for Conservation and Utilization of Bio-resourcesYunnan UniversityKunmingPeople’s Republic of China
  2. 2.School of Chemical Science and TechnologyYunnan UniversityKunmingPeople’s Republic of China
  3. 3.Human Genetics CenterThe University of Texas Helth Science CenterHoustonUSA

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