2.2 Molecular dynamic simulations
Through AMBER 18 program suite,
NocTE-LSub and NocTE-DSub systems were subjected to molecular dynamic
(MD) simulations using ff14SB force field23.
Firstly, energy minimizations were
carried out for these complexes to rationalize crystal structures.
Afterwards, each system was heated from 0 K to 300 K
and
equilibrated for 50 ps under the isothermal−isobaric ensemble. Starting
from this preprocessed conformation, six replicas of MD simulation
trajectories were collected. Long-range electrostatic interactions and
bond lengths in simulations were described using Particle Mesh Ewald
(PME) method24 and the SHAKE
algorithm25.
Trajectory analyses, like root mean
square deviation (RMSD) fluctuations and conformation distributions,
were performed via the cpptraj module26 of
AMBER 18.
For epimerization, the deprotonation distance
d(H1901Nε-LSubHα) was constrained
between 3.00 Å and 3.50 Å using a harmonic vibrational potential with a
force constant of 200 kcal/(mol·Å2) in the
equilibration step for NocTE-LSub system, catching the critical
pre-reaction structure for epimerization. Then the system was
re-equilibrated without constraints and six replicas of 100 ns MD
simulation trajectories were obtained. According to the distribution of
the deprotonation distance and angle, two optimal trajectories md2 and
md6 were selected and lengthened to 310 ns for the following mechanism
investigations.