Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 81

catalysis ( Table 2.12 ). In recent studies on various HHRs, it has been shown
that the tolerance of mutations at C3 and G8 is dependent on the identities of
surrounding nucleotides, including C1.1 and G2.1. Residues C1.1 and G2.1
are not conserved, 69,83,153 and hence it may be possible to exploit variations
in C1.1 and G2.1, along with correlated mutations at G8 and C3, to design
new HHR motifs with modified activity.

5.2.5 Long-time simulations are required to understand some
mutational effects
The current study reports 100 ns simulations for a series of HHR mutants in
the reactant and activated precursor states. As previously discussed, 77,133
long-time simulations are necessary to relax the mutations and sufficiently
sample the conformational space required to observe the mutational effects.
As shown in Fig. 2.13 , the simulation of the activated precursor state of G8A
reaches a stable relaxed state after 30 ns. However, on this timescale, we do

Figure 2.13 The time series of general acid hydrogen bond indexes, r HA and

y HA , as well
as the hydrogen bond distance r 3 (see Figs. 2.10 and 2.11 ), from wild type and G8A acti-
vated precursor state simulations. The distances are in Å and the angles are in degrees.
These results indicate that the timescale for equilibration and stable fluctuation in some
cases exceed 30 ns (shown by vertical dashed line).