title: Optimal allosteric stabilization sites using contact stabilization analysis.
abstract: Proteins can be destabilized by a number of environmental factors such as temperature, pH, and mutation. The ability to subsequently restore function under these conditions by adding small molecule stabilizers, or by introducing disulfide 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 to 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 Gō-like model, we examine the dynamics of the enzyme β-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. We have carried out this analysis for three different scaling strengths for the intramolecular contacts, and we examine how the calculated stabilization factors depend on the ensemble of destabilized conformations. We further examine a locally destabilized mutant of β-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. © 2016 Wiley Periodicals, Inc.
authors: Department of Biochemistry & Molecular Biology and the Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan, 48824.
authors: Alex
authors: A
authors: Dickson
authors: Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan, 48824.
authors: Christopher T
authors: CT
authors: Bailey
authors: Department of Molecular Biosciences and Center for Computational Biology, University of Kansas, Lawrence, Kansas, 66045.
authors: John
authors: J
authors: Karanicolas
mesh_terms: D000495:Allosteric Site; D001665:Binding Sites; D020134:Catalytic Domain; D004795:Enzyme Stability; D005966:Glucuronidase / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D005966:Glucuronidase
keywords: allostery; chemical rescue; coarse-grained model; molecular dynamics; protein re-activation; protein stabilization