TABLE 4.

Comparison between computed and experimental double differences in binding free energies between mutant and wild-type PwTBP at 0.4 M salt concentration

PwTBP	ΔΔG (kcal mol−1)
ID*	ΔΔGelec†	ΔΔHvdW‡	Calculated§	Experimental¶
WT	0.0	0.0	0.0	0.0
E12A	−4.7	3.7	−1.0	−1.0
E42A	−5.7	4.3	−1.4	−0.3
D101A	2.6	0.2	2.8	−0.4
E128A	0.6	−3.2	−2.8	−0.5
E12AE128A	−2.9	1.5	−1.4	−1.3
E12AE42A	−9.7	9.4	−0.3	−1.1
3	−7.9	5.8	−2.1	−1.8
4	−8.2	−4.0	−12.2	−1.9

^*Wild-type and mutant PwTBPs. Labels 3 and 4 represent mutants E12AE41KE128A and E12AE41KE42KE128A, respectively.

^†The electrostatic energy difference between the mutant and the wild-type PwTBP, ΔΔG_elec, is computed from the nonlinear solution to the Poisson-Boltzmann equation.

^‡The vdW energy, ΔΔH_vdW, is the intermolecular DNA-TBP energy difference as computed from the empirical CHARMM 22/27 all-atom force field.

^§ΔΔG is approximated as ΔΔG_elec + ΔΔH_vdW for the mutant minus the wild-type.

^¶Experimental ΔΔG from previous works by Ladbury and co-workers (15,21).