An investigation of the conformation of peptide-T and its D-Ala analog by NMR and molecular dynamics simulations.

Ojha, R P; Saran, A; Kamath, S; Coutinho, E

An investigation of the conformation of peptide-T and its D-Ala analog by NMR and molecular dynamics simulations.

Date

1998-06-06

Authors

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.

Citation

Ojha RP, Saran A, Kamath S, Coutinho E. An investigation of the conformation of peptide-T and its D-Ala analog by NMR and molecular dynamics simulations. Indian Journal of Biochemistry & Biophysics. 1998 Jun; 35(3): 133-41