Computational study of the conformational domains of peptide T

J Pept Sci. Mar-Apr 1997;3(2):85-92. doi: 10.1002/(SICI)1099-1387(199703)3:2%3C85::AID-PSC84%3E3.0.CO;2-0.

Abstract

The conformational preferences of peptide T (ASTTTNYT) were analysed by means of computational methods. A thorough exploration of the conformational space was carried out within the framework of the molecular mechanics approach, using simulated annealing as a searching strategy. Specifically, in order to obtain a subset of low-energy conformations with energies close to the global minimum as complete as possible, a simulated annealing protocol was repeated several times in a recursive fashion. The results of the search indicate that the peptide exhibits a alpha-helical character although most of the conformations characterized, including the global minimum, can be described as bent conformations. Conformations exhibiting beta-turn motives previously proposed from NMR studies were also characterized, although they are not very predominant in the set of low-energy conformations.

MeSH terms

  • Computer Simulation*
  • HIV Envelope Protein gp120 / chemistry
  • Models, Molecular*
  • Peptide T / chemistry*
  • Protein Conformation
  • Protein Structure, Tertiary*
  • Solutions
  • Structure-Activity Relationship
  • Thermodynamics

Substances

  • HIV Envelope Protein gp120
  • Solutions
  • Peptide T