Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation.

Here, we present a protocol to examine asymmetric pairwise pre-reaction and transition states in enzymatic catalysis. We describe steps to set up the calculated systems, run umbrella sampling molecular dynamics simulation, and conduct quantum mechanics/molecular mechanics calculations. We also provide analytical scripts to yield potential of mean force of pre-reaction states and reaction barriers.