Allostery and Evolution: A Molecular Journey Through the Structural and Dynamical Landscape of an Enzyme Super Family

Allosteric regulation is a powerful mechanism for controlling the efficiency of enzymes. Deciphering the evolutionary mechanisms by which allosteric properties have been acquired in enzymes is of fundamental importance. We used the malate (MalDH) and lactate deydrogenases (LDHs) superfamily as model to elucidate this phenomenon. By introducing a few of mutations associated to the emergence of allosteric LDHs into the non-allosteric MalDH from Methanopyrus kandleri, we have gradually shifted its enzymatic profile toward that typical of allosteric LDHs. We first investigated the process triggering homotropic activation. The structures of the resulting mutants show the typical compact organization of the R-active state of LDHs, but a distorted (T-like) catalytic site demonstrating that they corresponds to hybrid states. Molecular dynamics simulations and free energy calculations confirmed the capability of these mutants to sample the T-inactive state. By adding a final single mutation to fine-tune the flexibility of the catalytic site, we obtained an enzyme with both sigmoid (homotropic) and hyperbolic (heterotropic) substrate activation profiles. Its structure shows a typical extended T-state as in LDHs, whereas its catalytic state has as a restored configuration favorable for catalysis. Free energy calculations indicate that the T and R catalytic site configurations are in an equilibrium that depends on solvent conditions. We observed long-range communication between monomers as required for allosteric activation. Our work links the evolution of allosteric regulation in the LDH/MDH superfamily to the ensemble model of allostery at molecular level, and highlights the important role of the underlying protein dynamics.