title: Enhanced dynamics of HIV gp120 glycoprotein by small molecule binding.
abstract: HIV cell entry and infection are driven by binding events to the CD4 and chemokine receptors with associated conformational change of the viral glycoprotein, gp120. Scyllatoxin miniprotein CD4 mimetics and a small molecule inhibitor of CD4 binding, NBD-556, also effectively induce gp120 conformational change. In this study we examine the fluctuation profile of gp120 in context of CD4, a miniprotein mimetic, and NBD-556 with the aim of understanding the effect of ligand binding on gp120 conformational dynamics. Analysis of molecular dynamics trajectories indicate that NBD-556 binding in the Phe 43 cavity enhances the overall mobility of gp120, especially in the outer domain in comparison to CD4 or miniprotein bound complex. Interactions with the more flexible bridging sheet strengthen upon NBD-556 binding and may contribute to gp120 restructuring. The enhanced mobility of D368, E370, and I371 with NBD-556 bound in the Phe 43 cavity suggests that interactions with α3-helix in the outer domain are not optimal, providing further insights into gp120--small molecule interactions that may impact small molecule designs.
authors.affiliation: Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, 3083 Biomedical Science Tower 3, Pittsburgh, Pennsylvania 15213, United States.
authors.forename: Indira
authors.initials: I
authors.lastname: Shrivastava
authors.forename: Judith M
authors.initials: JM
authors.lastname: LaLonde
mesh_terms: D000818:Animals; D015704:CD4 Antigens / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D010070:Oxalates / Q000737:chemistry / Q000378:metabolism; D010649:Phenylalanine / Q000737:chemistry / Q000378:metabolism; D010880:Piperidines / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics; D055550:Protein Stability; D017433:Protein Structure, Secondary / Q000235:genetics; D017434:Protein Structure, Tertiary / Q000235:genetics; D058767:Protein Unfolding; D012604:Scorpion Venoms / Q000737:chemistry / Q000378:metabolism; D012605:Scorpions
chemical_list: D015704:CD4 Antigens; D015699:HIV Envelope Protein gp120; C514246:N-(4-chlorophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)oxalamide; D010070:Oxalates; D010880:Piperidines; D012604:Scorpion Venoms; C056574:leiurotoxin I; D010649:Phenylalanine