Figure 3.

The dependence of ribozyme activity on the concentration of divalent metal ion effector. Plots of the logarithm of the rate constant for ribozyme cleavage versus the logarithm of the concentration of divalent metal effector for the class II (A) and class IV (B) allosteric ribozymes. Each point represents a k_obs value calculated by conducting a time course for ribozyme activity and determining the negative slope of the line from a plot of the natural logarithm of the fraction of RNA remaining uncleaved versus time (min⁻¹). For the class II ribozyme, the dotted lines in the case of Cd²⁺, Co²⁺ and Ni²⁺ represent the expected plot for an ideal ribozyme with a k_max of 3 min⁻¹, a k_min of 4.8 × 10⁻⁵ min⁻¹ and two critical metal-binding sites each with an apparent K_D of 130 μM, as determined by a variation of the Henderson–Hasselbach equation. The apparent K_D, k_max and k_min parameters plotted for Mn²⁺ are 100 μM, 1.5 min⁻¹ and 6.7 × 10⁻⁵ min⁻¹ and for Zn²⁺ are 220 μM, 3 min⁻¹and 4.8 × 10⁻⁵ min⁻¹, respectively. For the class IV ribozyme, dotted lines in the case of Cd²⁺, Co²⁺ and Ni²⁺ represent the expected plots for and ideal ribozyme with an apparent K_D of 1 mM, a k_max of 1 min⁻¹ and one critical metal-binding site. The apparent K_D, k_max and k_min parameters plotted for Zn²⁺ are 5 × 10⁻⁴, 0.01 min⁻¹ and 2 × 10⁻⁴ min⁻¹ and for Mn²⁺ are 0.07, 0.7 min⁻¹ and 3.5 × 10⁻⁴ min⁻¹, respectively.