title: Computational study of the dynamics of mannose disaccharides free in solution and bound to the potent anti-HIV virucidal protein cyanovirin.
abstract: In this paper, we present a computational study of the dynamics of the potent anti-HIV virucidal protein cyanovirin in complex with mannose disaccharides. Recently, it has been experimentally demonstrated that cyanovirin binds mannose oligomers on the surface of glycoprotein gp120. gp120, a protein on the surface of the HIV virus, is key in the process of viral docking and transfer of genetic material into human cells. Cyanovirin prevents the transfer of viral RNA into human cells. In this study, we found that, among all residues that show nuclear Overhauser effects in the solution NMR experiments, residues Glu41 and Arg76 appear to interact with the sugar at the high-affinity binding site through stronger Coulombic interactions. In particular, Arg76 participates in a dynamical mechanism that caps and locks the sugar once it is bound to the protein. We also studied the distribution of glycosidic torsional angles of mannose disaccharides in solution and compared it with those when bound at the high- and low-affinity sites of the protein. Throughout our 20 ns simulations, we find that the sugar bound to the high-affinity site preserves the most favorable conformation in solution while the sugar bound at the low-affinity site does not. The sugar at the low-affinity site can adopt both conformations, but we find it most predominantly on the one that is least probable for the free sugar in solution. We also carried out a detailed study of the interactions between the disaccharides and different amino acids as well as between the disaccharide and the solvent at both binding locations.
authors.affiliation: Department of Chemistry, University of Iowa, 319 Chemistry Building, Iowa City, Iowa 52242, USA.
authors.forename: C J
authors.initials: CJ
authors.lastname: Margulis
mesh_terms: D019380:Anti-HIV Agents / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D002352:Carrier Proteins / Q000737:chemistry*; D004187:Disaccharides / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008358:Mannose / Q000737:chemistry*; D008956:Models, Chemical; D008968:Molecular Conformation; D012984:Software; D013816:Thermodynamics
chemical_list: D019380:Anti-HIV Agents; D001426:Bacterial Proteins; D002352:Carrier Proteins; D004187:Disaccharides; D015699:HIV Envelope Protein gp120; C107733:cyanovirin N; D018698:Glutamic Acid; D001120:Arginine; D008358:Mannose