Binding Leverage and Leverage Coupling as Determinants of Allosteric Regulation and Communication

Abstract

Allosteric regulation involves collective conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules [1]. The states involved are inherent to the protein, in the sense that they are visited by the protein also in the absence of effector ligands. We developed the measure binding leverage [2] to find sites where ligand binding can shift the conformational equilibrium of a protein. Binding leverage is calculated for a set of motion vectors representing independent conformational degrees of freedom. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. To analyze allosteric communication between binding sites, we introduce the concept of leverage coupling [3], based on the assumption that only pairs of sites that couple to the same conformational degrees of freedom can be allosterically connected. We demonstrate how leverage coupling can be used to analyze allosteric communication in a range of enzymes (regulated by both ligand binding and post-translational modifications) and huge molecular machines such as chaperones. Because binding leverage and leverage coupling can be calculated from a single crystal structure it should be a useful tool for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design.1. Mitternacht, S. & Berezovsky, I.N. 2011. A geometry-based generic predictor for catalytic and allosteric sites. Protein Engineering, Design & Selection 24, 405–409.2. Mitternacht, S. & Berezovsky, I.N. 2011. Binding leverage as a molecular basis for allosteric regulation. PLoS Comp Biol 7, e1002148.3. Mitternacht, S. & Berezovsky, I.N. 2011. Coherent conformational degrees of freedom as a structural basis for allosteric communication, Submitted.