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Entropic barriers, transition states, funnels, and exponential protein folding kinetics: A simple model
Author(s) -
Bicout D. J.,
Szabo Attila
Publication year - 2000
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.9.3.452
Subject(s) - funnel , folding funnel , protein folding , energy landscape , downhill folding , statistical physics , simple (philosophy) , exponential function , physics , folding (dsp implementation) , contact order , kinetics , relaxation (psychology) , chemical physics , thermodynamics , chemistry , phi value analysis , classical mechanics , mathematics , engineering , psychology , mathematical analysis , social psychology , philosophy , organic chemistry , epistemology , nuclear magnetic resonance , electrical engineering
This paper presents an analytically tractable model that captures the most elementary aspect of the protein folding problem, namely that both the energy and the entropy decrease as a protein folds. In this model, the system diffuses within a sphere in the presence of an attractive spherically symmetric potential. The native state is represented by a small sphere in the center, and the remaining space is identified with unfolded states. The folding temperature, the time‐dependence of the populations, and the relaxation rate are calculated, and the folding dynamics is analyzed for both golf‐course and funnel‐like energy landscapes. This simple model allows us to illustrate a surprising number of concepts including entropic barriers, transition states, funnels, and the origin of single exponential relaxation kinetics.