The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch
Figure 2
Structure modeling, and pseudo-dihedral analysis.
(A) A secondary structure representation of the RNA switching intermediate which we chose to model for our starting structure is shown. The AT helix is assumed to be fully formed and two base pairs form in the P1 helix (in blue). The remaining P2, P3, and P4 helices and tertiary structures including a pseudoknot structure and a kink-turn motif (red box) are assumed to form and derived without change from the aptamer X-ray structure. The base triplet highlighted in purple: A4 (P1 helix, 5′ strand)-U110 (switching strand)-A136 (AT helix, 3′ strand) represents one base pairing position that involves the P1 helix and the AT helix competition. Three additional nucleotides (in green) in the 5′ strand of the P1 helix are modeled as single strand RNA. Thus, these three positions begin the simulation as AT base pairs. B). Schematic of the local switching region. The two arrows indicate the order for numbering the base pairs. C) Schematic of the pseudo-dihedral angle definition from reference [58] D) Histogram of pseudo-dihedral angles for 5′-AU-3′ dinucleotide (Left) and 5′-UA-3′ dinucleotide (Right) in known RNA structures. (Top) and for A109-U110 dinucleotide and U110-A111 dinucleotide sampled by MC-Sym (Bottom).
doi: https://doi.org/10.1371/journal.pcbi.1003069.g002