Interplay of Flavin's Redox States and Protein Dynamics: An Insight from QM/MM Simulations of Dihydronicotinamide Riboside Quinone Oxidoreductase 2

Dihydronicotinamide riboside quinone oxidor- eductase 2 is known to catalyze a two-electron reduction of quinone to hydroquinone using its cofactor, flavin adenine dinucleotide. Using quantum mechanical/molecular mecha- nical simulations, we have computed the reorganization free energies of the electron and proton transfer processes of flavin inthefreestateaswellaswhenitisboundintheactivesiteofthe enzyme. The calculated energetics for electron transfer pro- cesses demonstrate that the enzyme active site lowers the reorganization energy for the redox process as compared to the enzyme-free aqueous state. This is most apparent in the two electron reduction step, which eliminates the possibility of flavosemiquinone generation. In addition, essential dynamics study of the simulated motions revealed spectacular changes in the principalcomponentsofatomic fluctuationsuponreduction of flavin.Thisalteration ofactivesitedynamicsprovides aninsightinto the "ping-pong" kinetics exhibited by the enzyme upon a change in the redox state of the enzyme-bound flavin. A charge perturbation analysis provides further support that the observed change in dynamics is correlated with the change in energetics due to the altered electrostatic interactions between the flavin ring and the active site residues. This study shows that the effect of electrostatic preorganization goes beyond the chemical catalysis as it strongly impacts the postcatalytic intrinsic protein dynamics.