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Computational investigation of the conformational profile of the four stereomers of Ac‐L‐Pro‐c 3 Phe‐NHMe (c 3 Phe= 2,3‐methanophenylalanine)
Author(s) -
Rodriguez Alejandro,
Canto Josep,
Corcho Francesc J.,
Perez Juan J.
Publication year - 2009
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21293
Subject(s) - chemistry , molecular dynamics , force field (fiction) , dichloromethane , preprint , computational chemistry , peptide , solvent , crystallography , chemical physics , organic chemistry , physics , biochemistry , quantum mechanics
The present report regards a computational study aimed at assessing the conformational profile of the four stereoisomers of the peptide Ace‐Pro‐c 3 Phe‐NMe, previously reported to exhibit β‐turn structures in dichloromethane with different type I/type II β‐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. © 2009 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 518–524, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com