The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding

Allostery is the process by which perturbation at one site in a protein affects distal sites. For many years the understanding of allostery and other functions was influenced by the high-resolution, ground state structure obtained through X-ray crystallography. Ample evidence has meanwhile accumulated that this ground state structure is only one member of the biologically relevant group of conformations, known as the protein ensemble, which collectively affect the observed biological response. This review aims to; (1) focus statistical thermodynamic formalisms on quantitative description of the ensemble, (2) illustrate the functional implications of ensembles for allostery, and (3) highlight ensemble redistribution as a unifying principle underlying all biological processes. Emphasis is placed on the importance of locally unfolded regions, i.e. excited states, underpinning two theoretical treatments developed in this laboratory: a coarse-grained Ensemble Allosteric Model (EAM) and an atomic-detail model named COREX. Locally unfolded conformations are profiled with case studies of allosteric proteins that are mostly denatured (Glucocorticoid Receptor), that are mostly folded (Adenylate Kinase), and that populate alternative folded structures (Metamorphic Proteins). These examples demonstrate that redistribution of states within the thermodynamic ensemble is sufficient to explain disparate biological phenomena including allostery, epistatic effects, and responses to environmental stimuli such as temperature - often without reliance on the structural details. The coarse-grained nature of the models highlights the degeneracy of molecular mechanisms that have evolved to facilitate function, and thus draws attention to the importance of relative energy differences between states, as opposed to the specific interactions that stabilize them.