Figure 2. The deprotonation distance and angle in the
epimerization reaction catalyzed by NocTE. (A) The distributions of the
distance
d(H1901Nε-LSubHα)
and the angle
a(H1901Nε-LSubHα-LSubCα)
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(H1901Nε-LSubHα) and angle
a(H1901Nε-LSubHα-LSubCα)
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(H1901Nε-LSubHα) were 3.45 Å and 3.65
Å, while above 4.50 Å in other trajectories. Besides, the angle
a(H1901Nε-LSubHα-LSubCα)
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).