Conformational analysis of the highly potent bradykinin antagonist Hoe-140 by means of two different computational methods.
The AMBER 4.0 force field was used to perform the characterization of the conformational profile of the highly potent bradykinin antagonist Hoe-140 (D-Arg0-Arg1-Pro2-Hyp3-Gly4-Thi5-Ser6-D-++ +Tic7-Oic8-Arg9). The structural features of the peptide were assessed using two different computational methods, both capable to provide a good sampling of the low-energy conformations of the molecule. Specifically, the conformational space of the peptide was explored: i) computing molecular dynamics trajectories in cycles of high (900 K) and low (300 K) temperature and ii) using simulated annealing (SA) in an iterative fashion. Analysis of the structures characterized indicates that most of the low-energy conformations of the peptide exhibit a betaII'-turn motif at its C-terminus, in agreement with previous experimental and theoretical studies. On the other hand, about a 50% of the low-energy conformations characterized also exhibit different beta-turn type motifs at the N-terminus, whereas the rest of the conformations can be described as bends. Finally, in order to get new insights into the structural requirements necessary to design more potent and selective antagonists of bradykinin, present results were compared with those previously reported by this laboratory on the conformational preferences of the native nonapeptide and its DPhe7 analog.
Filizola
M
M
Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche, Seconda Universitá degli Studi di Napoli, Italy.
Centeno
N B
NB
Cartení-Farina
M
M
Perez
J J
JJ
D001920:Bradykinin / Q000031:analogs & derivatives* / Q000737:chemistry; D003198:Computer Simulation; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics
C065679:icatibant; D001920:Bradykinin