title: Conformation of N-terminal HIV-1 Tat (fragment 1-9) peptide by NMR and MD simulations.
abstract: The N-terminal portion of HIV-1 Tat covering residues 1-9 is a competitive inhibitor of dipeptidyl peptidase IV (DP IV). We have used 1H NMR techniques, coupled with molecular dynamics methods, to determine the conformation of this peptide in the three diverse media: DMSO-d6, water (pH 2.7) and 40% HFA solution. The results indicate that in both DMSO-d6 and HFA the peptide has a tendency to acquire a type I beta-turn around the segment Asp5-Pro6-Asn7-IIe8. The N-terminal end is seen to be as a random coil. In water, the structure is best described as a left-handed polyproline type II (PPII) helix for the mid segment region Asp2 to Pro6. The structures obtained in this study have been compared with an earlier report on Tat (1-9).
authors.affiliation: Department of Pharmaceutical Chemistry, Bombay College of Pharmacy, Kalina, Mumbai 400 098, India.
authors.forename: M
authors.initials: M
authors.lastname: Kanyalkar
authors.forename: S
authors.initials: S
authors.lastname: Srivastava
authors.forename: E
authors.initials: E
authors.lastname: Coutinho
mesh_terms: D000096:Acetone / Q000031:analogs & derivatives* / Q000737:chemistry; D003198:Computer Simulation; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D018819:Dipeptidyl Peptidase 4 / Q000378:metabolism; D004791:Enzyme Inhibitors / Q000494:pharmacology; D005466:Fluorocarbons / Q000737:chemistry; D015696:Gene Products, tat / Q000737:chemistry* / Q000494:pharmacology; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry* / Q000494:pharmacology; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012984:Software; D014867:Water / Q000737:chemistry; D054322:tat Gene Products, Human Immunodeficiency Virus; D006845:Hydrocarbons, Fluorinated
chemical_list: D000096:Acetone; D004121:Dimethyl Sulfoxide; D018819:Dipeptidyl Peptidase 4; D004791:Enzyme Inhibitors; D005466:Fluorocarbons; D015696:Gene Products, tat; D010446:Peptide Fragments; D014867:Water; D054322:tat Gene Products, Human Immunodeficiency Virus; C415751:tat peptide (1-9), Human immunodeficiency virus 1; C017366:hexafluoroacetone; D006845:Hydrocarbons, Fluorinated