Design Principles for Riboswitch Function (original) (raw)
Figure 3
Rate competition dictates riboswitch performance.
The relative values of the reversible and irreversible rate constants generally establish three operating regimes: thermodynamically-driven (▪) when reversible rate constants dominate, kinetically-driven (▪) when the rate constants are balanced, and non-functional (□) when irreversible rate constants dominate. Regimes are qualitatively marked for dynamic range and basal and ligand-saturating levels according the ratio of the rate constants for terminator stem formation (kM) and the progression from conformation A to conformation B (k1). Effect of varying kM on (A) dynamic range, (B) basal protein levels and ligand-saturating protein levels, and (C) EC50 for riboswitches functioning through transcriptional termination. In (B), colored pairs show basal (light) and ligand-saturating (dark) protein levels for complete (red), balanced (black), and negligible (blue) transcriptional folding into conformation B. Parameter values for all curves in (A) and (B) and the red curve in (C): k1 = 10−1/s;k1′ = 10/s; k2 = 106/M·s; k2′ = 10−1/s; KA = kP·kMA/kM = 10−3/s; KB = kP·kMB/kM = 10−2/s; kf = 10−11 M/s; kdP = 10−3/s.