Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants

Allosteric transcription factors undergo binding events both at their operator binding sites as well as at distinct allosteric sites, and it is often difficult to disentangle the structural and functional consequences of the two types of binding. In this work, we compare the ability of two statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the Koshland-Némethy-Filmer (KNF) models of allostery - to characterize the multi-step activation mechanism of the cyclic-AMP receptor protein (CRP). We examine data from a recent experiment that created a single-chain version of the CRP homodimer, enabling each subunit to be mutated separately. Using this construct, six mutants were created using the wild type subunit, a D53H mutant subunit, and an S62F mutant subunit. We show that both the MWC and KNF models can simultaneously characterize the cyclic-AMP and DNA binding of all six CRP constructs based solely on their subunit compositions, thereby tying together the behavior of the mutants to a small, self-consistent set of parameters.