title: Computational study of the conformational domains of peptide T.
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.
authors.affiliation: Istituto di Biochimica delle Macromolecole, Seconda Università degli Studi di Napoli, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Filizola
authors.forename: N B
authors.initials: NB
authors.lastname: Centeno
authors.forename: J J
authors.initials: JJ
authors.lastname: Perez
mesh_terms: D003198:Computer Simulation; D015699:HIV Envelope Protein gp120 / Q000737:chemistry; D008958:Models, Molecular; D015717:Peptide T / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012996:Solutions; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D015699:HIV Envelope Protein gp120; D012996:Solutions; D015717:Peptide T