title: An investigation of the conformation of peptide-T and its D-Ala analog by NMR and molecular dynamics simulations.
abstract: Peptide-T (ASTTTNYT) and its D-Ala analog (D-ASTTTNYT-NH2) have been designed to block the adsorption of HIV to CD4 receptors on T-cell lymphocytes, thus inhibiting viral infectivity. The conformation of these important peptides has been investigated by 2D-NMR and molecular dynamics simulations. The NMR studies in DMSO show that the peptides exist in solution as a mixture of conformations. beta-Turns and non-specific folded conformations are present in a small proportion in the ensemble of conformations, which is largely dominated by more or less extended structures. This result is in line with molecular dynamics simulations where beta-turns were found to occur with a low frequency and with energies 10 to 17 kcal/mole higher than the global minimum structure. Our findings differ from previous reports on the conformation of peptide-T determined by NMR.
authors.affiliation: Physics Department, Gorakhpur University.
authors.forename: R P
authors.initials: RP
authors.lastname: Ojha
authors.forename: A
authors.initials: A
authors.lastname: Saran
authors.forename: S
authors.initials: S
authors.lastname: Kamath
authors.forename: E
authors.initials: E
authors.lastname: Coutinho
mesh_terms: D000998:Antiviral Agents / Q000737:chemistry; D006678:HIV / Q000187:drug effects; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D015717:Peptide T / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013601:T-Lymphocytes / Q000821:virology
chemical_list: D000998:Antiviral Agents; D015717:Peptide T