Fig. 3 Cooperativity and allosteric modulations in the assembly of RNA-ligand
complexes. (a) Schematic of alternative folding of the M-box riboswitch
[55]. Schematic depicts ligand-free active conformation of the riboswitch on
the left and ligand-bound, repressed conformation on the right. Several Mg
2+
cations predominantly bind RNA in core 2 and 3 regions and induce allosteric
transition that brings the RNA structure, depicted in blue, closer to the 5
0
end of
the RNA. This conformational change induces tertiary RNA interactions,
mediated by cations in the core 1 regions, and facilitates formation of the
transcription terminator. This aborts transcription elongation and switches the
gene off. Pairing interactions essential for switching the conformations are
shown with thin black lines. (b) Schematic of alternative folding of the THF
riboswitch. Cooperative binding of two ligands to the metabolite-sensing domain
RNA Cooperativity and Allostery
265