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Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β‐hairpins
Author(s) -
Imamura Hideo,
Chen Jeff Z. Y.
Publication year - 2006
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20846
Subject(s) - reptation , folding (dsp implementation) , nucleation , lattice protein , downhill folding , chemical physics , molecular dynamics , protein folding , monte carlo method , stability (learning theory) , chemistry , statistical physics , crystallography , hydrophobic effect , physics , thermodynamics , phi value analysis , computational chemistry , computer science , mathematics , biochemistry , statistics , organic chemistry , machine learning , electrical engineering , engineering , polymer
We study the dependence of folding time, nucleation site, and stability of a model β‐hairpin on the location of a cross‐strand hydrophobic pair, using a coarse‐grained off‐lattice model with the aid of Monte Carlo simulations. Our simulations have produced 6500 independent folding trajectories dynamically, forming the basis for extensive statistical analysis. Four folding pathways, zipping‐out, middle‐out, zipping‐in, and reptation, have been closely monitored and discussed in all seven sequences studied. A hydrophobic pair placed near the β‐turn or in the middle section effectively speed up folding; a hydrophobic pair placed close to the terminal ends or next to the β‐turn encourages stability of the entire chain. Proteins 2006. © 2006 Wiley‐Liss, Inc.