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Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics
Author(s) -
Chan Hue Sun,
Dill Ken A.
Publication year - 1998
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/(sici)1097-0134(19980101)30:1<2::aid-prot2>3.0.co;2-r
Subject(s) - energy landscape , kinetics , folding (dsp implementation) , chevron (anatomy) , kinetic energy , protein folding , statistical physics , arrhenius equation , arrhenius plot , exponential function , relaxation (psychology) , chemistry , downhill folding , thermodynamics , folding funnel , chemical physics , physics , phi value analysis , mathematics , geology , biology , classical mechanics , paleontology , mathematical analysis , biochemistry , neuroscience , electrical engineering , engineering
We use two simple models and the energy landscape perspective to study protein folding kinetics. A major challenge has been to use the landscape perspective to interpret experimental data, which requires ensemble averaging over the microscopic trajectories usually observed in such models. Here, because of the simplicity of the model, this can be achieved. The kinetics of protein folding falls into two classes: multiple‐exponential and two‐state (single‐exponential) kinetics. Experiments show that two‐state relaxation times have “chevron plot” dependences on denaturant and non‐Arrhenius dependences on temperature. We find that HP and HP+ models can account for these behaviors. The HP model often gives bumpy landscapes with many kinetic traps and multiple‐exponental behavior, whereas the HP+ model gives more smooth funnels and two‐state behavior. Multiple‐exponential kinetics often involves fast collapse into kinetic traps and slower barrier climbing out of the traps. Two‐state kinetics often involves entropic barriers where conformational searching limits the folding speed. Transition states and activation barriers need not define a single conformation; they can involve a broad ensemble of the conformations searched on the way to the native state. We find that unfolding is not always a direct reversal of the folding process. Proteins 30:2–33, 1998. © 1998 Wiley‐Liss, Inc.