Christina Bergonzo, Thomas E. Cheatham Biophysical Journal

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Mg2+ Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction Christina Bergonzo, Thomas E. Cheatham Biophysical Journal Volume 113, Issue 2, Pages 313-320 (July 2017) DOI: 10.1016/j.bpj.2017.06.008 Copyright © 2017 Biophysical Society Terms and Conditions

Figure 1 SLI-SLV system. SLI is shown in blue and SLV in red, with SLI kissing loop junction residues highlighted in green and SLV kissing loop junction residues highlighted in orange. 3D coordinates from PDB: 2MI0 (19) shown left, and 2D sequence and numbering shown right. To see this figure in color, go online. Biophysical Journal 2017 113, 313-320DOI: (10.1016/j.bpj.2017.06.008) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 2 Calculated NMR restraint values versus experiment. Calculated numbers are the average and SD of back-calculated distances from NOE atom pairs sampled during 10 (a) −Mg2+ and (b) +Mg2+ simulations, colored by intra SLI (black), intra SLV (red) and inter SLI-SLV (blue) NOEs, and (c) RDC restraints calculated for 1000 frames per Mg2+ simulation colored by simulation. The linear fit and correlation coefficient for the combined data is presented. To see this figure in color, go online. Biophysical Journal 2017 113, 313-320DOI: (10.1016/j.bpj.2017.06.008) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 3 Deviation in the kissing loop junction conformation is a result of SLI conformational entropy and not SLV. Left: RMSD histograms of +Mg2+ simulations, average and SD of first and second microseconds of simulation. Top: Junction residues. Middle: junction residues contributed by SLI. Bottom: SLV. Right: Representative conformations from cluster analysis for SLV (purple) and SLI (multicolored). SLI structures are representative of cluster populations of (a) 69.1, (b) 8.3, (c) 6.6, and (d) 4.2%. To see this figure in color, go online. Biophysical Journal 2017 113, 313-320DOI: (10.1016/j.bpj.2017.06.008) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 4 RNA atoms with > 10% Mg2+ occupancy in any run. Stem residues are shown in blue, SLI loop residues are shown in green, and SLV loop residues are shown in yellow. Values represent the average over all 10 runs and error bars represent SD. Fig. S8 shows the average fraction occupancy between the first microsecond and second microsecond of simulation. To see this figure in color, go online. Biophysical Journal 2017 113, 313-320DOI: (10.1016/j.bpj.2017.06.008) Copyright © 2017 Biophysical Society Terms and Conditions

Figure 5 MM-GBSA binding free energy results of SLI to SLV in various ion conditions: −Mg2+ (blue), +Mg2+ (red), and +Mg2+ with explicit Mg2+ ions bound (orange) for each starting structure (runs 0–9). Values indicate average and error bars are SD over frames within each run. To see this figure in color, go online. Biophysical Journal 2017 113, 313-320DOI: (10.1016/j.bpj.2017.06.008) Copyright © 2017 Biophysical Society Terms and Conditions