Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 36

were used for the analysis. The motions and relaxation of solvent and
counter-ions are notoriously slow to converge in nucleic acid simulations, 115
and careful equilibration is critical for reliable simulations. In summary, for
each simulation, a total of 3 ns of equilibration (1 ns of solvent relaxation and
2 ns of solvent and structure relaxation) was carried out before 10 ns of data
sampling.

2.3.2.2.1 QM/MM simulation setup QM/MM simulations on the
ETS and LTS mimics were set up as follows. Initial structures were taken
from snapshots of the classical MD simulations after 2 ns production
simulation, and the C17:O2 0 -P and P d C1.1:O5 0 distances of the scissile
phosphatewereharmonicalyre rainedw thaforcecon tantof
1000 kcal/mol/ ˚ 2 and equilibrium distances of 2.010 and 1.850 ˚ ,
respectively, for the ETS mimic and 1.856 and 2.382 ˚ , respectively,
for the LTS mimic. The system is partitioned into a QM region consti-
tuting the active site that is represented by the AM1/d-PhoT Hamilto-
nian 105 and the modified AM1 magnesium parameters of Hutter and
coworkers.

116

The total number of solute and solvent atoms, setup of
periodic boundary conditions, etc. were identical to the classical simula-
tions. The QM subsystem was defined as the 43 atoms around the active
site, and included the scissile and A9 phosphates, parts of the nucleophilic
and leaving ribose rings, and Mg 2 þ ion and coordinated waters. The gen-
eralized hybrid orbital method 117 is used to cut a covalent bond to divide
the system into the QM and MM region. Full electrostatic interactions
were calculated using a recently introduced linear-scaling QM/MM-
Ewald method. 118

2.4. Results
2.4.1 A diverse set of Mg 2þ -binding modes along the reaction
coordinate
The key heavy-atom distances around the active site are listed in Table 2.2
for the simulations with Mg 2 þ placed at the bridging position (B-site) and in
Table 2.3 for the simulations with Mg 2 þ initially placed at the C-site posi-
tion. In both tables, a comparison with the crystallographic values is pro-
vided. Figure 2.3 shows a series of snapshots that illustrate the migration
of the Mg 2 þ . The Mg 2 þ ion clearly migrates from the C-site to the bridging
position between the A9 and scissile phosphates (i.e., directly coordinating
A9:O2P and C1.1:O2P) in both ETS and LTS mimic simulations (ETS-C