Figure 2. The deprotonation distance and angle in the epimerization reaction catalyzed by NocTE. (A) The distributions of the distance d(H1901-LSub) and the angle a(H1901-LSub-LSub) in six MD simulation trajectories; (B) The most representative structures for md2 and md6 MD simulation trajectories.
For proton transfer step, reasonable deprotonation distances and angles are of great importance, so the reaction distance d(H1901-LSub) and angle a(H1901-LSub-LSub) were analyzed (Figure 2). Among these MD simulation trajectories, only md2 and md6 exhibited abundant proper conformations for deprotonation. For these two trajectories, the averages of the distance d(H1901-LSub) were 3.45 Å and 3.65 Å, while above 4.50 Å in other trajectories. Besides, the angle a(H1901-LSub-LSub) was mainly concentrated around 120° that is beneficial for the proton transfer. Hence, md2 and md6 trajectories were rich in pre-reaction conformations and selected to be lengthened to 310 ns for further study (Figure S3).