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Folding free‐energy landscape of a 10‐residue mini‐protein, chignolin
Author(s) -
Satoh Daisuke,
Shimizu Kentaro,
Nakamura Shugo,
Terada Tohru
Publication year - 2006
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2006.05.015
Subject(s) - energy landscape , molecular dynamics , protein folding , folding (dsp implementation) , chemistry , crystallography , residue (chemistry) , statistical physics , physics , chemical physics , root mean square , biological system , computational chemistry , thermodynamics , biology , biochemistry , quantum mechanics , electrical engineering , engineering
Chignolin is an artificial mini‐protein composed of 10 residues (GYDPETGTWG) that has been shown to cooperatively fold into a β‐hairpin structure in water. We extensively explored the conformational space of chignolin using a 180‐ns multicanonical molecular dynamics (MD) simulation and analyzed its folding free‐energy landscape. In the MD trajectory, we found structures that satisfy 99% of the experimental restraints and are quite close to the experimentally determined structures with C α root‐mean‐square‐deviations of less than 0.5 Å. These structures formed a large cluster in the conformational space with the largest probability of existence, agreeing well with the experiment.