Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 56

coordination pattern is not highly conducive to formation of an in-line
attack conformation. On the other hand, the RT-B-Mg simulation
shows a more rigid Mg 2 þ coordination with both the A9 and scissile
phosphate oxygens and sustains a considerable population of in-line
attack conformations. These results suggest that the coordination pattern
found in the RT-B-Mg simulation is able to stabilize in-line attack
conformations more readily than Mg 2 þ binding at the C-site as in the
RT-C-Mg simulation.
The dRT-Mg simulation is similar to the RT-B-Mg simulation with
regard to exhibiting rigid coordination with the A9 and scissile phosphate
oxygens and stabilization of in-line attack conformations. With the Mg 2 þ
ion at the bridging position (RT-B-Mg and dRT-Mg simulations), there
is considerably reduced interaction with G10.1:N7, which is compensated
by interactions with the C17:O2 0 that occur through two water molecules in
the inner sphere of the Mg 2 þ ion. This interaction is most pronounced in the
dRT-Mg simulation where the C17:O2 0 is deprotonated. In the ground-
state reactant simulations with Mg 2 þ (RT-C-Mg and RT-B-Mg), no
Na þ ions were observed to infiltrate the active site. In the activated precur-
sor simulation, dRT-Mg, a single Na ion was observed to be bound at

high occupancy to the deprotonated C17:O2 0 in a manner similar to the
M3 position in Fig. 2.6 .

þ

4.1.3 Na þ ions bind nonspecifically and exhibit different coordination
patters in the reactant and activated precursor states
In this section, we explore the monovalent metal ion-binding modes that are
correlated with formation of catalytically active in-line attack conforma-
tions. For the simulations with no Mg 2 þ ions in the active site (RT-Na
and dRT-Na), binding of Na þ ions to the coordination sites exhibits larger
variation and exchange events occur giving rise to a fairly broad array of
coordination patterns.
Simulation results 133 suggestthattwoNa þ ions are present in the
active site and bind to both A9:O2P and C1.1:O2P at the same time
in the RT-Na simulation. Hence, two Na þ ions collectively act like a
single bridging Mg 2 þ ion to hold the negatively charged A9 and scissile
phosphates together to maintain an in-line conformation. In the dRT-Na
simulation, we observe a high correlation between the Na þ ion coordi-
nation index and in-line conformation. When less than three Na þ ions
bind to the active site ligands, the in-line conformation is no longer held,