Computational study of the conformational domains of peptide T.
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.
Filizola
M
M
Istituto di Biochimica delle Macromolecole, Seconda Università degli Studi di Napoli, Italy.
Centeno
N B
NB
Perez
J J
JJ
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
D015699:HIV Envelope Protein gp120; D012996:Solutions; D015717:Peptide T