TABLE 8.

pK_a shifts with the “standard” PB protocol

		εp = 2*	εp = 4	εp = 20	MDFE†	Experiment
	ΔGs, protonated state‡	−8	−8	−8	−19	–
	ΔGs, ionized state‡	143	144	144	145	–
Model	ΔGr	−78	−79	−79	−82§	–
	ΔG	70/65¶	71/65	71/65	61	–
	ΔGs, protonated state‡	11	2	−6	−17	–
	ΔGs, ionized state‡	117	130	141	124	–
Thioredoxin	ΔGr	−46	−61	−75	−70§	–
Asp-26	ΔG	57/71	63/69	69/66	49	–
	ΔΔG‖	−13/6	−8/4	−2/1	−11	−4.8
	ΔpKa	9.6/−4.3	5.8/−2.8	1.4/−0.7	8	3.5
	ΔpKa**	–	3.5/−3.7	0.0/−1.4	8	3.5
	ΔGs, protonated state‡	0	−4	−7	−18	–
	ΔGs, ionized state‡	136	138	140	142	–
RNase A	ΔGr	−60	−68	−75	−80§	–
Asp-14	ΔG	60/76	64/70	68/65	59	–
	ΔΔG‖	−10/11	−7/5	−3/0	0	>2.7
	ΔpKa	7.2/−8.0	5.0/−3.6	2.2/0	0.0	<−2.0
	ΔpKa**	–	0.4/−5.6	−0.7/−2.0	0.0	<−2.0
	ΔGs, protonated state‡	−10	−9	−9	−19	–
	ΔGs, ionized state‡	137	138	140	144	–
Thioredoxin	ΔGr	−75	−76	−77	−81§	–
Asp-20	ΔG	65/62	67/62	68/63	60	–
	ΔΔG‖	−5/−3	−4/−3	−3/−2	−1	0.0
	ΔpKa	3.6/2.2	2.9/2.2	2.2/1.4	0.7	0.0
	ΔpKa**	–	1.7/1.2	0.8/0.7	0.7	0.0

^*Free energies in kcal/mol. The signs correspond to the direction ASP → ASPH (protonation).

^†From Simonson et al. (2004).

^‡Results averaged over 50–60 structures, taken from MD trajectories (with explicit solvent) of the corresponding state.

^§From Eq. 10.

^¶Throughout the table, x/y denote results using structures from the protonated/ionized state.

^‖The double differences were calculated using the same states (e.g., subtracting the protonated model/compound from the protonated protein value).

^**The side chain is embedded directly in the protein medium; there is no side-chain cavity (see text).