Simple Two-State Protein Folding Kinetics Requires Near-Levinthal Thermodynamic Cooperativity

TL;DR

This paper demonstrates that simple two-state protein folding kinetics require near-Levinthal thermodynamic cooperativity, which can be achieved through models with many-body interactions, providing insights into protein energetics and folding behavior.

Contribution

The study introduces models with many-body interactions that reproduce two-state folding kinetics and high thermodynamic cooperativity, highlighting the importance of native structure recognition beyond pairwise interactions.

Findings

Models with many-body interactions achieve two-state kinetics.

High thermodynamic cooperativity correlates with native and denatured state separation.

Folding rate decreases with increasing native contact order, aligning with experimental trends.

Abstract

Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a 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 G\=o 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 G\=o-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. Consistent with experiments, comparison among the present models with extra native favorabilities indicate that their folding rate at a given interaction strength decreases with increasing native contact order, although the dependence is weaker than the corresponding trend in real proteins. 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 ...