Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 33

2.3.1.2 Simulations performed
A total of eight classical force field MD simulations were performed that
involved different points along the catalytic reaction pathway including
the reactant state (RT), reactant state activated precursor where the
2 0 OH nucleophile is deprotonated (dRT), early transition state (ETS),
and late transition state (LTS) mimics. In addition, the presence and initial
position of the Mg 2 þ ion in the active site was also varied so as to include
Mg 2 þ ion bound at the C-site or in a bridging position (B-site) as described
above. The parameters for the Mg 2 þ ion and the reactive intermediates in
the simulations have been described in detail elsewhere, 75,102 and a sum-
mary of the different simulations and their abbreviations are provided
in Table 2.1 . All the simulations were performed with CHARMM 106
(version c32a2) using the all-atom CHARMM27 nucleic acid force
field 103,104 with extension to reactive intermediate models (e.g., transition
state mimics) 102 and TIP3P water model. 107

Table 2.1 Simulations performed in Section 2.3
Mg 2þ ion State Time (ns) Potential

RT-B B-site Reactant 12 CHARMM

RT-C C-site Reactant 12 CHARMM

dRT-C C-site Deprotonated

Reactant

12 CHARMM

ETS-B B-site ETS mimic 12 CHARMM

LTS-B B-site LTS mimic 12 CHARMM

ETS-C C-site ETS mimic 12 CHARMM

ETS-C C-site LTS mimic 12 CHARMM

QM-ETS-B B-site ETS 1 QM/MM

QM-LTS-B B-site LTS 1 QM/MM

Summary of simulations discussed in Section 2 . Simulations for eHHR differ by their initial placement of
the Mg 2 þ , protonation state of the 2 0 OH of C17, and progression along the reaction coordinate. A total
of eight 12-ns simulations were performed with the all-atomCHARMM27 nucleic acid force field 103,104
with extension to reactive intermediate models, 102 and two 1-ns simulations using a QM/MM potential
using the AM1/d-PhoTHamiltonian 105 for phosphoryl transfer. Initial Mg 2 þ placement was either in the
B-site (bridging position) 75 coordinated to the A9 and scissile phosphates, or the “C-site” position 74
coordinating the A9 phosphate and N7 of G10.1.