The ability of enzymes to preserve reactive conformations with well-positioned residues during enzyme-catalyzed reactions can be an important factor for efficient catalysis: a case study of CARNMT1

Determining the origin of high catalytic efficiency of enzymes has been a central goal in biochemical research. But our understanding of the mechanisms by which enzymes achieve enormous rate enhancements is still incomplete. One of wildly accepted strategies to achieve rate enhancements by enzymes is to position catalytic residues precisely in enzyme-substrate complexes and form reactive conformations for catalysis. Such catalytic strategy through positioning may also serve as the basis for transition state stabilization. Although considerable efforts have been made to determine relationships between enzyme activities and the formation of reactive conformations of enzyme-substrate complexes, there is considerable uncertainty concerning the ability of enzymes to preserve reactive conformations during enzyme-catalyzed reactions. The failure of properly maintaining reactive conformations during reactions may prevent residues from exerting catalytic effects and lead to significant reductions of activities. Here QM/MM MD and free energy simulations are performed for CARNMT1 to determine the importance and requirements for preservation of catalytic competent reactive conformations during enzyme-catalyzed reactions. For CARNMT1, the existence of wild-type reactive conformation is directly related to the conformation of His347. Therefore, the conformation of His347 can be used to monitor preservation or collapse of the reactive conformation during catalysis. It is found that for wild-type the reactive conformation can not only be formed in the enzyme-substrate complex but also be preserved well after the reaction passes TS. For the Tyr386Ala, Tyr396Asp and Tyr398Ala mutants, the wild-type like reactive conformations can be formed in the mutant-substrate complexes but collapse in the early stage of reaction. Such pre-mature collapse of the reactive conformation in the mutants prevents the residues to fully exert catalytic effects and leads to a significant reduction of catalytic efficiency. The results suggest that the ability of enzymes to preserve reactive conformations with well-positioned catalytic residues during enzyme-catalyzed reactions can be an important factor for efficient catalysis, and this property of enzymes deserves attention.