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A theoretical study of pentacyclo‐undecane cage peptides of the type [Ac‐X‐Y‐NHMe]
Author(s) -
Bisetty Krishna,
Corcho Francesc J.,
Canto Josep,
Kruger Hendrik G.,
Perez Juan J.
Publication year - 2006
Publication title -
journal of peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.475
H-Index - 66
eISSN - 1099-1387
pISSN - 1075-2617
DOI - 10.1002/psc.692
Subject(s) - chemistry , peptide , dipeptide , conformational isomerism , cage , molecular dynamics , bent molecular geometry , stereochemistry , residue (chemistry) , computational chemistry , molecule , organic chemistry , biochemistry , mathematics , combinatorics
The conformational preferences of peptides of the type, Ac‐X‐Y‐NHMe, where X and Y = Ala, cage and Pro, were studied by means of computational techniques within the framework of a molecular mechanics approach. For each of the eight peptide analogues, extensive conformational searches were carried out using molecular dynamics (MD) and simulated annealing (SA) protocols in an iterative fashion. Both results are in good agreement and complement each other. The conformational search indicates that the cage residue restricts the conformational freedom of the dipeptide considerably in comparison with the other model residues used. This study revealed that proline exhibits a greater tendency in promoting reverse‐turn characteristics in comparison to the cage peptides, which show promising β‐turn characteristics. It was also found that 300–500 K is not sufficient to overcome rotational barriers for cage peptides. In all cases, the low‐energy conformers have a tendency to form bent structures. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.