Simple two-state protein folding kinetics requires near-levinthal thermodynamic cooperativity. 2003

Hüseyin Kaya, and Hue Sun Chan
Protein Engineering Network of Centres of Excellence, Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.

Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with an apparent two-state description of equilibrium thermodynamics. This phenomenon is hereby recognized as a nontrivial heteropolymer property capable of providing fundamental insight into protein energetics. Many current protein chain models, including common lattice and continuum Gō models with explicit native biases, fail to reproduce this generic protein property. Here we show that simple two-state kinetics is obtainable from models with a cooperative interplay between core burial and local conformational propensities or an extra strongly favorable energy for the native structure. These predictions suggest that intramolecular recognition in real two-state proteins is more specific than that envisioned by common Gō-like constructs with pairwise additive energies. The many-body interactions in the present kinetically two-state models lead to high thermodynamic cooperativity as measured by their van't Hoff to calorimetric enthalpy ratios, implying that the native and denatured conformational populations are well separated in enthalpy by a high free-energy barrier. It has been observed experimentally that deviations from Arrhenius behavior are often more severe for folding than for unfolding. This asymmetry may be rationalized by one of the present modeling scenarios if the effective many-body cooperative interactions stabilizing the native structure against unfolding is less dependent on temperature than the interactions that drive the folding kinetics.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D013816 Thermodynamics A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed) Thermodynamic
D017510 Protein Folding Processes involved in the formation of TERTIARY PROTEIN STRUCTURE. Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular

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