. 2004 Feb 1;18(3):344–354. doi: 10.1101/gad.1167904

Table 1.

Parameters used in physicochemical modeling

Operator^a	ΔG (kcal/mole)	Operator	ΔG (kcal/mole)
O_r1	−13.2	O_l1	−13.8
O_r2	−10.7	O_l2	−12.1
O_r3	−10.2	O_l3	−12.4
O_r1-O_r2 coop	−3.0	O_l1-O_l2 coop	−2.5
O_r2-O_r3 coop	−3.0	O_l2-O_l3 coop	−2.5
O_r1-O_r3 coop	0	O_l1-O_l3 coop	0
O_r1-O_r2- O_r3 coop	−3.0	O_l1-O_l2- O_l3 coop	−2.5
O_r3 (c12)^b	−11.0	O_l3-4^c	−6.2
O_r3 (r1)^b	−7.3

Parameter	Value	Promoter	LacZ units^h
K_dim^d (M⁻¹)	6.7 × 10⁷ (ΔG_dim = −11.1)	P_r basal	1056
K_ns^e (M⁻¹)	2.5 × 10⁴ (ΔG_ns = −6.2)	P_r repressed	2
[NS]^f	6.76 × 10⁻³ M	P_rm basal	45
[CI]_lysogenic^g	3.7 × 10⁻⁷ M	P_rm activated	360 (265)
		P_rm repressed	0.5

O_r values from Koblan and Ackers (1992); O_l values from Senear et al. (1986).

Calculated from ΔΔG values of Sarai and Takeda (1989); see Dodd et al. (2001) for sequences.

Set as equal to nonspecific binding.

CI dimerization (Koblan and Ackers 1991).

Affinity for nonspecific DNA; see text for details. K_ns is a tool to align in vitro and in vivo repressor concentration scales, and we ascribe no particular significance to its value.

Concentration of nonspecific sites from E. coli genome size (4.6 × 10⁶ bp/cell) and 1 molecule/cell = 1.47 nM (Donachie and Robinson 1987).

Calculated from the data of Reichardt and Kaiser (1971) and 1 molecule/cell = 1.47 nM.

Wild-type values; value in parentheses for looped configuration. P_r values for mutants (basal/repressed): O_l3-4 998/2, no O_l 1164/2. P_rm values for mutants (basal/activated/repressed): c12 37/240(180)/0.5, r1 47/380(280)/0.5.