Conformational study of vasoactive intestinal peptide by computational methods.
The conformational profile of vasoactive intestinal peptide (VIP) was characterized using computational methods. The strategy devised included a close examination of the conformational profile of the first 11 residues fragment followed by a study that considered the compatibility of the different conformations found with a continuation of the polypeptide chain in a alpha-helical conformation. Accordingly, a detailed analysis of the conformational preferences of the N-terminal fragment of VIP(1-11) was carried out within the framework of the molecular mechanics approach, using simulated annealing in an iterative fashion as the sampling technique. In a second step, low-energy structures of the fragment were fused to the remainder of the VIP chain in the form of two noninteracting alpha-helices, according to a model of the structure of the peptide proposed from NMR studies. After investigation for compatibility of each of the low-energy structures of VIP(1-11) with the two helical regions by energy minimization, only 5 of 35 structures were discarded. Analysis of the structures characterized indicates that most of the conformations of VIP(1-11), including the global minimum, can be described as bent conformations. Conformations exhibiting alpha-turns and beta-turns, previously proposed by NMR studies were also characterized. The conformational analysis also suggests that the common structural features found in VIP(1-11) should also be present in VIP. Finally, because of the sequence homology between VIP and Peptide T, and the fact that both are ligands of the CD4 receptor, both sets of low-energy conformations were compared for similarity. The relevance of these results as guidance of the design of new peptide analogs targeted to the CD4 receptor is also discussed.
Filizola
M
M
Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche (CRISCEB), Seconda Universitá degli Studi di Napoli, Italy.
Cartenì-Farina
M
M
Perez
J J
JJ
D015704:CD4 Antigens / Q000378:metabolism; D019295:Computational Biology; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry* / Q000378:metabolism; D015717:Peptide T / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D014660:Vasoactive Intestinal Peptide / Q000737:chemistry* / Q000378:metabolism
D015704:CD4 Antigens; D008024:Ligands; D010446:Peptide Fragments; D015717:Peptide T; C072440:vasoactive intestinal peptide (1-11); D014660:Vasoactive Intestinal Peptide