Supplementary Information for “Coupling of Fast and Slow Modes in the Reaction
Pathway of the Minimal Hammerhead Ribozyme Cleavage” by R. Radhakrishnan
Figures
Figure S1: The eigenvalue spectrum resulting from PCA of 2 30 ns MD trajectories (purple
histograms and red dotted line). (Inset) Root-mean-square deviation (RMSD) of relative motion
between the 41 phosphorous backbone atoms (the correspondence between the numbers and the
hammerhead sequence is given in table S1) of the minimal hammerhead molecule recorded from
the aggregate 60 ns MD trajectory. The color scale is in Å. The numbers in the RMSD map
correspond to hammerhead backbone phosphorous atoms, see table S1 to identify with the
literature convention that is used throughout the main manuscript.
Figure S2: The pucker angle and pucker amplitude associated with the ribose sugars of four RNA
bases at the catalytic site resulting from 2 30 ns MD trajectories. The colored symbols represent
the distribution of pucker angles and amplitudes sampled from the trajectory for four bases in the
active-site, see legend. The first trajectory (top) shows no conformational rearrangement, whereas
the second (bottom) shows repuckering for bases A1.1 and C1.2.
Figure S3: (a) Geometry of the hammerhead active site. The snapshots depict key dihedral angles
(top) and distances (bottom).
Figure S3: (b) The time-evolution of key dihedral angle measures in the course of the 2 30 ns
classical MD trajectories (denoted MM 1,2) and two subsequent 2 ps QMMM MD trajectories
(denoted QM and QM2) are depicted.
MM1
MM2
QM GS
QM2 GS
A1.1 C5’:A1.1 O5’:A1.1 P:C17 O3’
Dihedral Angle (degrees)
A1.1 P:C17 O3’:C17 C3’:C17 C2’
C17 C3’:C17 O3’:A1.1 P:A1.1 O5’
A1.1 C4’:A1.1 C5’:A1.1 O5’:A1.1 P
Time (×1ns; ×0.1ps)
Figure S3: (c) The time-evolution of key distance measures in the course of the 2 30 ns classical
MD trajectories (denoted MM 1,2) and two subsequent 2 ps QMMM MD trajectories (denoted
QM and QM2) are depicted.
Distance (Å)
A1.1 P:C17 O2’
MM1
MM2
QM GS
QM2 GS
A1.1 P:A1.1 O5’
C17 O2’:A1.1 O5’
Time (×1ns for large symbols; ×0.1ps for small symbols)
Figure S4 (panels A-H): Landscape of ion diffusion. The evolution of distances of the specified
ions (in blue) from the cleavage site (ADE1.1 P) and the rescue site (GUA 10.1 N7) is provided
in panels A-N. Tight binding at the active site is apparent from A and tight binding at the rescue
site is apparent from E, N. The transient assembly of the two-metal-ion landscape at the cleavage
site is observed through a diffuse binding of a second Mg2+ ion in D, and through binding of a
surrogate Na+ ion in B,J.
A1.1P
G10.1 N7
SOD 28
SOD 33
MG 2
D
MG 5
Distance [Å]
A
B
E
SOD 1
SOD 3
C
SOD 12
SOD 13
F
G
H
Time [ns]
Figure S4 (panels I-N): Landscape of ion diffusion.
I
A1.1P
G10.1 N7
J
SOD 18
K
MG 5
Distance [Å]
SOD 7
SOD 22
L
SOD 1
M
Time [ns]
Mg 8
N
Figure S5: Two-dimensional free energy landscape of the hammerhead ribozyme cleavage
(phosphoryl transfer) reaction from umbrella sampling and QMMM MD simulations. The scale is
in units of kBT. Inset depicts the active site. The reaction was initiated from an equilibrated state
close to the minimal hammerhead crystal structure of Scott et. al. The reaction proceeds via a
trigonal bipyramidal geometry but not through an in-line attack (O2’-P-O5’ angle is 90º) resulting
in a stereo-isomer with retention configuration.
Tables
Table S1: Minimal hammerhead sequence
Number
Sequence
Convention
Number
Sequence
Convention
Number
Sequence
Convention
Number
Sequence
Convention
5'
1
G
2.5
11
G
8
21
G
12
31
A
2
U
2.4
12
A
9
22
A
13
32
G
16.4
3
G
2.3
13
G
10.1
23
A
14
33
A
16.3
4
G
2.2
14
G
10.2
24
A
15.1
34
G
16.2
5
U
2.1
15
C
10.3
25
C
15.2
35
U
6
C
3
16
C
10.4
26
U
15.3
36
C
17
7
U
4
17
G
11.4
27
C
15.4
37
A
1.1
8
G
5
18
G
11.3
28
G
9
A
6
19
C
11.2
29
U
10
U
7
20
C
11.1
30
A
38
C
1.2
39
C
1.3
40
A
1.4
41
C
1.5
3'