Proteins can be destabilized by a number of environmental factors such as temperature, pH and mutation. The ability to restore function by small molecule stabilizers, or the introduction of disulde bonds, would be a very powerful tool, but the physical principles that drive this stabilization are not well understood. The first problem lies is in choosing an appropriate binding site or disulfide bond location that will best confer stability to the active site and restore function. Here we present a general framework for predicting which allosteric binding sites correlate with stability in the active site. Using the Karanicolas-Brooks Go-like model, we examine the dynamics of the glycosidase enzyme beta-glucuronidase using an Umbrella Sampling method to thoroughly sample the conformational landscape. Each intramolecular contact is assigned a score termed a “stabilization factor” that measures its correlation with structural changes in the active site. This is done for three different scaling strengths for the intramolecular contacts, and we examine how the calculated stabilization factors depend on the makeup of the ensemble of destabilized conformations. We further examine a locally destabilized mutant of beta-glucuronidase that has been characterized experimentally, and show that this brings about local changes in the stabilization factors. We find that the proximity to the active site is not sufficient to determine which contacts can confer active site stability.

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