Premium
Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation
Author(s) -
Moradi Mahmoud,
Lee JungGoo,
Babin Volodymyr,
Roland Christopher,
Sagui Celeste
Publication year - 2010
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.22875
Subject(s) - polyproline helix , molecular dynamics , chemistry , isomerization , ab initio , conformational isomerism , computational chemistry , chemical physics , energy landscape , statistical physics , peptide , molecule , physics , organic chemistry , biochemistry , catalysis
Depending on their environment, polyproline peptides form chiral helices that may be either left‐ (PPII) or right‐handed (PPI). Here, we have characterized both the structure and free energy landscapes of Ace‐(Pro) n ‐Nme ( n an integer less than 13) peptides, in vacuo and in implicit water environments. Both ab initio and classical molecular dynamics methods were used. In terms of the latter, we used a recently developed Adaptively Biased Molecular Dynamics (ABMD) method in conjunction with three different force fields (ff99, ff99SB, ff03) and two different Generalized Born models for the implicit solvent environment. Specifically, the ABMD method provides for an accurate description of the free energy landscapes in terms of a set of collective variables, which were carefully chosen as to reflect the “slow modes” of the polyproline peptides. These are primarily based on the cis ‐ trans isomerization associated with the prolyl bonds. In agreement with recent experimental results, the peptides form not only the pure PPII or PPI structures but also a large number of stable conformers having more or less similar free energies, whose distributions we have characterized. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010