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Simulation of oligopeptide dynamics and folding. The use of NMR chemical shifts to analyse the MD trajectories
Author(s) -
Busetta Bernard,
Picard Philippe,
Précigoux Gilles
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.694
Subject(s) - folding (dsp implementation) , chemistry , dihedral angle , molecular dynamics , chemical shift , hydrogen bond , protein secondary structure , crystallography , protein folding , side chain , chemical physics , computational chemistry , molecule , organic chemistry , biochemistry , electrical engineering , engineering , polymer
In this paper, a simulation of the folding process, based on a random perturbations of the ϕ, ψ, χ 1 dihedral angles, is proposed to approach the formation at the atom level of both principal elements of protein secondary structure, the α‐helix and the β‐hairpin structures. Expecting to understand what may happen in solution during the formation of such structures, the behaviour of large sets of random conformations that are generated for small oligopeptides was analysed. Different factors that may influence the folding (as conformational propensity, hydrophobic interactions and side‐chain mobility) were investigated. The difference between the corresponding theoretical folding and the real conformational diversity that is observed in solution is appraised by a comparison between the calculated and observed NMR secondary chemical shifts. From this study it appears that hydrophobic interactions and mobility represent the principal factors that initiate folding and determine the observed hydrogen‐bond pattern, which subsequently allows packing between the peptide side chains. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.