In most of the systems we obtain activation free energies ~1 kcal mol -1 higher than the corresponding experimental values, as for wild-type HisA. However, for D130A in PriA and S202A in HisA, we underestimate the activation free energies by 1.5 -2.0 kcal mol -1 in comparison with the experimental value, suggesting that the experimental effect is due to either a change in substrate positioning or loop conformation or dynamics, which we are unable to capture in our simulations when simply starting from the wild-type crystal structure and manually truncating these residues.