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

Abstract

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 first analyze the allosteric transition, where cyclic-AMP binds to CRP, then model how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. We examine data from a recent beautiful experiment that created a single-chain version of the CRP homodimer, thereby enabling each subunit to be mutated separately. Using this construct, six mutants were created using every possible combination of 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.

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