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Probing the role of local propensity in peptide turn formation
Author(s) -
Mohanty D.,
Elber R.,
Thirumalai D.
Publication year - 2000
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 - 10.1002/1097-461x(2000)80:4/5<1125::aid-qua62>3.0.co;2-j
Subject(s) - folding (dsp implementation) , turn (biochemistry) , molecular dynamics , chemistry , maxima and minima , peptide , scaling , potential of mean force , protein folding , chemical physics , computational chemistry , mathematical analysis , biochemistry , mathematics , geometry , electrical engineering , engineering
Abstract We use atomically detailed molecular dynamics simulations with explicit solvent (water) to investigate the effects of local propensity on the dynamics of turn formation in a class of peptides. In particular, we computed the potential of mean force for the pair PY and PG and showed a significant tendency to form a structure in the pair PY. The PG tendency to form a structure is significantly smaller. The current results are discussed with the peptides SYPYD and SYPGD in mind. We suggest a detailed folding mechanism based on the potential of mean force calculations and earlier simulation studies. The mechanism includes the PY/PG pair that acts as mininuclei in consolidating the turn formation. In accord with structural information obtained using nuclear magnetic resonance (NMR) experiments, we find that PY has a single dominant minimum while PG in SYPGD has two minima. Estimates of folding times used in conjunction with scaling theory are employed to predict the typical folding rates in 16‐mer peptide that forms a β‐hairpin. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 1125–1128, 2000