  Allosteric transcription factors undergo binding events both at their inducer
binding sites as well as at distinct DNA binding domains, and it is often
difficult to disentangle the structural and functional consequences of these
two classes of interactions. In this work, we compare the ability of two
statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the
Koshland-N\'emethy-Filmer (KNF) models of protein conformational change - to
characterize the multi-step activation mechanism of the broadly acting
cyclic-AMP receptor protein (CRP). We first consider the allosteric transition
resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its
operator, and finally investigate the ability of CRP to activate gene
expression. In light of these models, we examine data from a beautiful recent
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 all possible combinations of the wild type subunit,
a D53H mutant subunit, and an S62F mutant subunit. We demonstrate that both the
MWC and KNF models can explain the behavior of all six mutants using a small,
self-consistent set of parameters. In comparing the results, we find that the
MWC model slightly outperforms the KNF model in the quality of its fits, but
more importantly the parameters inferred by the MWC model are more in line with
structural knowledge of CRP. In addition, we discuss how the conceptual
framework developed here for CRP enables us to not merely analyze data
retrospectively, but has the predictive power to determine how combinations of
mutations will interact, how double mutants will behave, and how each construct
would regulate gene expression.
