title: Computational investigation of the conformational profile of the four stereomers of Ac-L-Pro-c3Phe-NHMe (c3Phe= 2,3-methanophenylalanine).
abstract: The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace-Pro-c3Phe-NMe, previously reported to exhibit beta-turn structures in dichloromethane with different type I/type II beta-turn profiles. Molecular systems were represented at the molecular mechanics level using the parm96 parameterization of the AMBER force field. Calculations were carried out in dichloromethane using an implicit solvent approach. Characterization of the conformational features of the peptide analogs was carried out using simulated annealing (SA), molecular dynamics (MD) and replica exchange molecular dynamics (REMD). Present results show that MD calculations do not provide a reasonable sampling after 300 ns. In contrast, both SA and REMD provide similar results and agree well with experimental observations.
authors.affiliation: Department of Chemical Engineering (ETSEIB), Technical University of Catalonia (UPC), Barcelona 08028, Spain.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Rodriguez
authors.forename: Josep
authors.initials: J
authors.lastname: Canto
authors.forename: Francesc J
authors.initials: FJ
authors.lastname: Corcho
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Perez
mesh_terms: D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013237:Stereoisomerism
chemical_list: D009842:Oligopeptides