Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

To explore how distal mutations affect binding sites and how binding sites in proteins communicate, an ensemble-based model of the native state was us ed to define the energetic connectivities between the different structural elements of Escherichia coli dihydrofolate reductase. Analysis of this mode l protein has allowed us to identify two important aspects of intramolecula r communication. First,:within a protein, pair-wise couplings exist that de fine the magnitude and extent to which mutational effects propagate from th e point of origin. These pair-wise couplings can be identified from a quant ity we define as the residue-specific connectivity. second, in addition to the pair-wise energetic coupling between residues, there exists functional connectivity, which identifies energetic coupling between entire functional elements (i.e,, binding sites) and the rest of the protein. Analysis of th e energetic couplings provides access to the thermodynamic domain structure in dihydrofolate reductase as well as the susceptibility of the different regions of the protein to both small-scale (e.g., point mutations) and larg e-scale perturbations (e.g., binding ligand), The results point toward a vi ew of allosterism and signal transduction wherein perturbations do not nece ssarily propagate through structure via a series of conformational distorti ons that extend from one active site to another, Instead, the observed beha vior is a manifestation of the distribution of states in the ensemble and h ow the distribution is affected by the perturbation.