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Speeding protein folding beyond the Gō model: How a little frustration sometimes helps
Author(s) -
Plotkin Steven S.
Publication year - 2001
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.1154
Subject(s) - frustration , energy landscape , protein folding , statistical physics , folding (dsp implementation) , physics , kinetics , chemical physics , hamiltonian (control theory) , thermodynamics , chemistry , classical mechanics , condensed matter physics , mathematics , engineering , nuclear magnetic resonance , mathematical optimization , electrical engineering
By perturbing a Gō model toward a realistic protein Hamiltonian by adding non‐native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and flexible. Eventually, the rate drops rapidly toward zero when ruggedness significantly slows conformational transitions. Energy landscape arguments for thermodynamics and kinetics are coupled with a treatment of non‐native collapse to elucidate this effect. Proteins 2001;45:337–345. © 2001 Wiley‐Liss, Inc.