Appendix 1—table 2.

Kinetic model determination for Mbo holo+RbpA on the Cy3-AP3 promoter.

DOI: http://dx.doi.org/10.7554/eLife.22520.025

	Mbo holo+RbpA**
Model*	1-step	2-step	3-step	4-step
k1 (M−1s−1)	(6.4 ± 0.3) x 106	(1.2 ± 0.1) x 107	(1.5 ± 0.1) x 107	(1.6 ± 0.1) x 107
k-1 (s−1)	(6.5 ± 1.1) x 10−3	0.80 ± 0.07	1.1 ± 0.1	0.88 ± 0.09
K1 (M−1)	(9.9 ± 1.7) x 108	(1.5 ± 0.2) x 107	(1.4 ± 0.2) x 107	(1.8 ± 0.2) x 107
k2 (s−1)		1.1 ± 0.1	1.4 ± 0.1	0.81 ± 0.08
k-2 (s−1)		0.017 ± 0.002	0.090 ± 0.020	0.062 ± 0.030
K2		65 ± 10	16 ± 4	13 ± 6
k3 (s−1)			0.046 ± 0.015	0.59 ± 0.75
k-3 (s−1)			0.011 ± 0.004	1.6 ± 0.7
K3			4.2 ± 2.0	0.37 ± 0.50
k4 (s−1)				0.091 ± 0.193
k-4 (s−1)				(9.9 ± 14) x 10−3
K4				4.1 ± 10.2
χ2/DOF	1.47786	1.24241	1.11268	1.10116
kd†	6.4 × 10−3	0.016	6.4 × 10−3	3.6 × 10−3
t1/2 (min)	1.8	0.71	1.8	3.2
t1/2exp (min)‡	~1.5
a	0.099	0.038	0.16	0.65
b	1.2	0.70	0.68	0.83
c		1.1	1.3	1.8
d			1.3	0.026
e				1.5
bkg	0.81	0.86	0.74	0.064

*Appendix 1—figure 1.

^**The errors listed are the standard errors from the global fit as reported by Kintek Global Kinetic Explorer (Johnson et al., 2009a).

^†TT For the 1-step, 2-step, and 3-step models, the value for k_d, the dissociation rate for RPo, was calculated using equation (17) of (Tsodikov and Record, 1999):.

$${\displaystyle \frac{1}{k_{\text{d}}}=\frac{1}{k_{-3}}+\frac{1+{\text{K}}_3}{k_{-2}}+\frac{{\text{K}}_2+{\text{K}}_2{\text{K}}_3}{k_{-1}}+\frac{1}{k_{-1}}}$$ (2)

.

For the 1-step model, K₂ = K₃ = 0, k_-2 = k_-3 = ∞; for the 2-step model, K₃ = 0, k_-3 = ∞. For the 4-step model, dissociation was simulated and the result was fit to a single exponential decay to derive k_d. The value for t_1/2 was calculated as t_1/2 = ln(2)/k_d.

^‡The experimental half-life (t_1/2^exp) was determined from promoter lifetime experiments (Figure 2C).