Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins

TL;DR

This study uses molecular simulations to explain why m-values in protein denaturation are constant at high denaturant concentrations but vary at lower levels, linking surface area changes to denatured state collapse.

Contribution

It provides a molecular explanation for the constant and variable m-values in protein unfolding by analyzing surface area changes and denatured state collapse through simulations.

Findings

m-values are constant above 3 M denaturant concentration

denatured state collapses at low denaturant concentrations

residue-specific transition midpoints vary significantly

Abstract

Experiments show that for many two state folders the free energy of the native state DG_ND([C]) changes linearly as the denaturant concentration [C] is varied. The slope, m = d DG_ND([C])/d[C], is nearly constant. The m-value is associated with the difference in the surface area between the native (N) and the denatured (D) state, which should be a function of DR_g^2, the difference in the square of the radius of gyration between the D and N states. Single molecule experiments show that the denatured state undergoes an equilibrium collapse transition as [C] decreases, which implies m also should be [C]-dependent. We resolve the conundrum between constant m-values and [C]-dependent changes in Rg using molecular simulations of a coarse-grained representation of protein L, and the Molecular Transfer Model, for which the equilibrium folding can be accurately calculated as a function of denaturant concentration. We find that over a large range of denaturant concentration (> 3 M) the m-value is a constant, whereas under strongly renaturing conditions (< 3 M) it depends on [C]. The m-value is a constant above [C]> 3 M because the [C]-dependent changes in the surface area of the backbone groups, which make the largest contribution to m, is relatively narrow in the denatured state. The burial of the backbone gives rise to substantial surface area changes below [C]< 3 M, leading to collapse in the denatured state. The midpoint of transition of individual residues vary significantly even though global folding can be described as an all-or-none transition. Collapse driven by the loss of favorable residue-solvent interactions and a concomitant increase in the strength of intrapeptide interactions with decreasing [C]. These interactions are non-uniformly distributed throughout the native structure of protein L.