Figure 7.

Effect of additional kinetic energy in selective protein vibrational modes (a) Increased amount of kinetic energy in a mode coupled to the enzyme reaction allows the trajectory to cross the barrier successfully from the reactant side to the product side. The solid black curve represents the native trajectory (no additional kinetic energy), and δ indicates the fraction of system kinetic energy added to the protein vibrational mode. (b)-(d) representative trajectories from simulations with increased kinetic energy in network protein vibrational modes and a non promoting mode. 2% of system kinetic energy was added to protein vibrations mode. Five representative trajectories from each mode are shown in different colors. Not all protein vibrational modes show increased barrier recrossing; much less effect on the barrier crossing is seen in a mode not coupled to the reaction [12]. Reprinted with permission from Agarwal et al., J. Am. Chem. Soc. (2005) 127, 15248–15256. Copyright (2005) American Chemical Society.