The thermodynamics of molecular recognition by proteins is a central determinant of complex biochemistry. For over a half-century detailed cryogenic structures have provided deep insight into the energetic contributions to ligand binding by proteins. We have been pursuing the elusive contributions of conformational entropy. The development of a dynamical proxy based on solution NMR-relaxation methods has revealed an unexpected richness in the contributions of conformational entropy to the thermodynamics of ligand binding. The evolution of the so-called “entropy meter” from its model-dependent roots to its current empirically calibrated form will be presented. From this work, it is now abundantly clear that conformational entropy is often a critical element of molecular recognition by <u>soluble</u> proteins. Recently, we have approached integral membrane proteins, which have eluded a similar characterization. The first examples, pSRII and Omp W, are found to be more dynamic in the ps-ns time regime than any previously characterized protein. The corresponding conformational entropy apparently stabilizes the folded state in the absence of the classic hydrophobic effect. Finally, despite these insights, there remains a discomforting disconnect between protein structure and conformational entropy. Prompted by the dynamical response of barnase to high pressure, we performed an analysis of the small packing imperfections or voids surrounding over 2,500 methyl-bearing side chains having determined order parameters. Changes in unoccupied volume as small as a water molecule surrounding buried side chains greatly affects fast motion. The discovered relationship begins to permit construction of a united view of the relationship between changes in the internal energy, provided by structural analysis, and the conformational entropy, as represented by fast internal motion, in the thermodynamics of protein function.

Molecular recognition by proteins: The dark energy of proteins comes to light

ACS Fall 2021

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