Parametrization of synthetic amino acids

• Type: Article in International Scientific Journal
• Date: 2003

Authors

Preto, MAC (Author) Other; Melo, A (Author) FCUP; Costa, SPG (Author) Other; Maia, HLS (Author) Other; Ramos, MJ (Author) FCUP

Journal

Title: Journal of Physical Chemistry B

Vol. 107

Pages: 14556-14562

ISSN: 1520-6106

Publisher: American Chemical Society

Indexing

ISI Web of Knowledge - 9 Citations

Scopus - 8 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-000-E26

DOI: 10.1021/jp030544y

Abstract (EN): C(alpha)-C(alpha)dialkylglycines, sarcosine, O-methyltyrosine and beta-(imidazol-1-yl)-alanine are noncoded amino acids with a large pharmaceutical potential. We have developed a set of parameters for these amino acids, consistent with the AMBER force field. Several dipeptide and tripeptide models were built to simulate the different possibilities for insertion of the noncoded amino acids in a peptide backbone. Bonding parameters were obtained from both existing force fields and quantum calculations. The Coulombic parameters have been determined using a multiconformational weighted approach and a restricted electrostatic potential fitting, at a 6-31G* ab initio level. Molecular dynamics simulations have been carried out on the model peptides to validate the parameters obtained. The characteristic geometry features such as the planarity of peptide bonds have been conserved on these models. The peptide models, which included monosubstituted residues, have revealed considerable backbone flexibility. The conformational flexibility of the peptides containing disubstituted residues has been significantly restricted by the length and volume of their side chains.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 7