Bridging the Gap Between Theory and Experiment to Derive a Detailed Understanding of Hammerhead Ribozyme Catalysis - Progress in Molecular Biology and Translational Science - page 72

Table 2.11 Characterization of the active site structure and fluctuations for the G5
mutants in activated precursor states
d-WT d-U7C d-G5I d-G5A d-G5D

r Nu 3.59 (0.17) 3.64 (0.17) 3.63 (0.15) 4.15 (0.11) 3.58 (0.24)

y inl 156.8 (7.9) 153.6 (8.7) 156.5 (7.6) 128.6 (5.8) 139.7 (9.8)

F 0.49 (0.09) 0.46 (0.09) 0.47 (0.08) 0.24 (0.03) 0.43 (0.11)

d 0

2.94 (0.13) 2.93 (0.12) 3 (0.13) 2.9 (0.12) 2.88 (0.12)

r HB 2.03 (0.37) 1.94 (0.14) 1.93 (0.13) 1.92 (0.15) 2.62 (0.96)

y HB 154.6 (11.9) 155.8 (9.4) 155.2 (9.4) 153.6 (8.9) 152.5 (11.9)

% 95 100 100 100 79

% 72 73 72 67 52

r HA 2.61 (0.77) 2.5 (0.79) 3.6 (0.3) 3.67 (1.09) 2.66 (0.6)

y HA 131.8 (34.5) 135.5 (35.2) 62.2 (11.4) 74.2 (55.6) 128.1 (34)

%69 75 0 30 62

%35 44 0 12 24

r 4 1.97 (0.14) 1.97 (0.15) 1.99 (0.16) 2.11 (0.30) 2.66 (0.97)

y 4 160.0 (10.5) 159.3 (9.8) 158.1 (10.2) 148.1 (13.7) 155.4 (14.8)

r 5 2.56 (0.46) 2.56 (0.49) - - 2.91 (0.87)

y 5 135.3 (12.7) 135.6 (13.4) - - 130.7 (18.0)

r 6 2.12 (0.20) 2.09 (0.17) - - 2.09 (0.21)

y 6 148.8 (10.5) 149.9 (10.8) - - 150.2 (13.0)

This table lists key structural indexes fluctuations for the G5 mutants, along with the control mutant U7C
in activated precursor states. Data analysis was performed over the last 65 ns of each simulation with
a 10 ps sampling frequency. Distance and angles ( Fig. 2.10 ) are in ˚ and degrees, respectively. SDs
are listed in parentheses. Boldface font is used to highlight key quantities that are significantly altered
with respect to the WT simulation upon mutation and that are discussed in the text. F is the in-line fitness
index. 150 r HB and y HB are the hydrogen bond length and angle for the general base step; defined by G12:
N1 d C17:HO2 0 d C17:O2 0 . r HA and y HA are the hydrogen bond length and angle for the general
acid step; defined by C1.1:O5 0 d G8:HO2 0 d G8:O2 0 . The hydrogen bond contact percentage for
the above entries, defined as the percentage of the snapshots in which r 3.0 ˚ and y 120 . The hydro-
gen bond contact percentage for the above entries, defined as the percentage of the snapshots in which
r 2.5 ˚ and y 150 .

5.1.2.1 C3U mutation disrupts the active site in the reactant
The C3Umutation reduces the catalytic rate by a factor

10 4 . 148 Sim-
ulation results indicate this mutation disrupts the normal Watson-Crick
hydrogen bonding with G8 ( Fig. 2.11 and Table 2.8 ), causing a base shift
that disrupts the active site structure in the reactant state. The average

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