title: Conformational study of palindromic tripeptides (GPG, IPI and KPK) in HIV-1 protease--a density functional theory study.
abstract: A comparative study has been carried out on three palindromic tripeptides Gly-Pro-Gly, Ile-Pro-Ile and Lys-Pro-Lys which were present in HIV protein along with their analogues applying density functional computation at B3LYP/6-31G* level of theory. Discrepancy from the structural analysis has been noted for all the systems and it was found to be more for amide capped structure at the C terminal of proline. The puckering amplitude A and Phase angle P of the pyrrolidine ring of proline in the chosen palindromic tripeptides and their analogues were calculated from the endocyclic torsion angles. The minimum energy conformers lying well within the prescribed region of proline were obtained for the derived compounds from potential energy surface scan mentioning that no role has been played by its terminal residues. This is further supported by the simulated amide bands identifying the helical structure for all three palindromic tripeptides signifying the importance of proline. The molecular properties such as stabilization energy, chemical hardness along with dipole moment were calculated and interpreted. The values of Calpha-H(s) and the peptide backbone N-Calpha-CO for all the selected conformers specify the three palindromic tripeptides to have a symmetrical achiral structure.
authors.affiliation: Department of Physics, Bharathiar University, Coimbatore-641 046, India.
authors.forename: A
authors.initials: A
authors.lastname: Abiram
authors.forename: P
authors.initials: P
authors.lastname: Kolandaivel
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D003198:Computer Simulation; D016333:HIV Protease / Q000737:chemistry* / Q000378:metabolism*; D015497:HIV-1 / Q000201:enzymology*; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary
chemical_list: D009842:Oligopeptides; D016333:HIV Protease