Allostery can convert binding free energies into concerted domain motions in enzymes

Abstract Enzymes’ mechanisms are typically inferred from structural data. However, understanding proteins’ functions requires unravelling the intricate dynamic interplay between dynamics, conformational substates and multiple protein structures. Here, we investigate the catalytic cycle of adenylate kinase (AK), an enzyme that catalyzes the interconversion of the various adenosine phosphates (ATP, ADP, and AMP). Our findings reveal that allosteric interactions enable converting ligands and cofactor binding energies into directional conformational changes of the two catalytic domains of AK. These coordinated motions emerged to control the exact sequence of ligand binding, the affinity for the three different substrates, and guiding the reactants along the reaction coordinates. Interestingly, we found that about 10% of enzymes showed altered allosteric regulation and ligand affinities, indicating that a subset of enzymes folded in alternative catalytically active forms. Since molecules or proteins might be able to selectively stabilize one of these multiple folds, this observation suggests an evolutionary path for allostery in enzymes. In AK, this complex catalytic framework has likely emerged to prevent futile ATP/ADP hydrolysis and to finely tune the enzyme for different energy needs of the cell.