Supporting Information
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1 Supporting Information Isom et al /pnas of6
2 Fig. S1. Graphs of ph dependence of thermodynamic stability of Glu-containing variants. Unfolding free energies (ΔG o ) for the ΔþPHS reference protein (circle) and for each Glu-containing variant (solid circle) determined at several ph values by chemical denaturation with guanidinium chloride at 298 K. The dotted lines are meant to guide the eye. The uncertainty in each measured value is represented by the size of the data points. ΔΔG ph is the difference in the unfolding free energy of the Glu-containing variant and of the ΔþPHS reference protein. The error bars in each ΔΔG ph value represent the combined error of the individual ΔG o measurements. The solid line in the ΔΔG ph vs. ph data represents the fit of Eq. 2 in 1, used to determine the pk a values of each Glu residue. 1 Karp DA, et al. (2007) High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp. Biophys J 92: of6
3 Table S1. Thermodynamic stability (ΔG o H 2 O ) measured for the reference protein (ΔþPHS nuclease) and for Glucontaining variants of ΔþPHS nuclease. PROTEINS ph C m [M]* m (kcal mol 1 M 1 ) ΔG o H 2 O (kcal mol) ΔΔG o H 2 O (kcal mol) Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS Δ+PHS/G20E (0.1) 4.7 (0.1) 6.3 (0.1) 3.2 (0.2) Δ+PHS/G20E (0.1) 5.1 (0.1) 8.2 (0.1) 3.5 (0.2) Δ+PHS/G20E (0.1) 5.2 (0.1) 8.0 (0.1) 3.7 (0.2) Δ+PHS/G20E (0.1) 5.1 (0.1) 7.6 (0.2) 4.3 (0.2) Δ+PHS/G20E (0.1) 5.1 (0.1) 7.8 (0.2) 4.1 (0.2) Δ+PHS/G20E (0.1) 5.2 (0.1) 7.8 (0.1) 3.8 (0.2) Δ+PHS/G20E (0.1) 5.5 (0.1) 7.0 (0.1) 3.3 (0.2) Δ+PHS/V23E (0.1) 5.0 (0.1) 5.0 (0.1) 4.4 (0.2) Δ+PHS/V23E (0.1) 5.7 (0.1) 6.7 (0.1) 5.1 (0.2) Δ+PHS/V23E (0.1) 5.6 (0.1) 5.7 (0.1) 6.0 (0.2) Δ+PHS/V23E (0.1) 6.0 (0.2) 4.9 (0.2) 7.0 (0.2) Δ+PHS/V23E (0.1) 5.9 (0.1) 4.4 (0.1) 7.5 (0.2) Δ+PHS/V23E (0.1) 6.0 (0.2) 4.0 (0.1) 7.5 (0.2) Δ+PHS/V23E (0.1) 6.4 (0.2) 2.6 (0.1) 7.7 (0.2) Δ+PHS/L25E (0.1) 5.0 (0.1) 3.5 (0.1) 5.9 (0.2) Δ+PHS/L25E (0.1) 5.8 (0.1) 5.4 (0.1) 6.4 (0.2) Δ+PHS/L25E (0.1) 5.5 (0.2) 4.1 (0.2) 7.6 (0.2) Δ+PHS/L25E (0.1) 5.4 (0.3) 3.1 (0.2) 8.8 (0.2) Δ+PHS/L25E (0.1) 4.3 (0.2) 2.1 (0.2) 9.8 (0.2) Δ+PHS/L25E (0.1) 4.4 (0.1) 2.1 (0.2) 9.5 (0.2) Δ+PHS/F34E (0.1) 4.9 (0.1) 5.6 (0.1) 3.9 (0.2) Δ+PHS/F34E (0.1) 5.6 (0.1) 6.4 (0.2) 5.4 (0.3) Δ+PHS/F34E (0.1) 5.7 (0.1) 5.2 (0.1) 6.5 (0.2) Δ+PHS/F34E (0.1) 6.3 (0.1) 4.4 (0.1) 7.5 (0.2) Δ+PHS/F34E (0.1) 5.6 (0.1) 3.8 (0.1) 8.1 (0.2) Δ+PHS/F34E (0.1) 5.8 (0.1) 3.7 (0.1) 7.9 (0.2) Δ+PHS/L36E (0.1) 4.9 (0.1) 4.8 (0.1) 4.7 (0.2) Δ+PHS/L36E (0.1) 5.2 (0.1) 6.9 (0.1) 4.2 (0.2) Δ+PHS/L36E (0.1) 5.4 (0.1) 7.2 (0.1) 4.6 (0.2) Δ+PHS/L36E (0.1) 5.7 (0.1) 6.4 (0.1) 5.3 (0.2) Δ+PHS/L36E (0.1) 5.9 (0.1) 5.5 (0.1) 6.4 (0.2) Δ+PHS/L36E (0.1) 6.1 (0.1) 4.4 (0.1) 7.5 (0.2) Δ+PHS/L36E (0.1) 6.4 (0.1) 3.2 (0.1) 8.4 (0.2) Δ+PHS/L36E (0.1) 7.7 (0.1) 1.5 (0.1) 8.8 (0.2) Δ+PHS/L37E (0.1) 4.6 (0.1) 7.4 (0.1) 2.1 (0.2) Δ+PHS/L37E (0.1) 5.1 (0.1) 9.1 (0.2) 2.7 (0.3) Δ+PHS/L37E (0.1) 5.0 (0.1) 8.5 (0.1) 3.2 (0.2) Δ+PHS/L37E (0.1) 5.1 (0.1) 8.9 (0.1) 3.0 (0.2) Δ+PHS/L37E (0.1) 5.1 (0.1) 8.8 (0.2) 3.1 (0.2) Δ+PHS/L38E (0.1) 4.6 (0.1) 8.3 (0.2) 1.2 (0.2) Δ+PHS/L38E (0.1) 4.7 (0.1) 9.3 (0.1) 2.0 (0.2) Δ+PHS/L38E (0.1) 5.0 (0.1) 9.5 (0.2) 2.3 (0.3) Δ+PHS/L38E (0.1) 4.9 (0.1) 8.3 (0.1) 3.4 (0.2) Δ+PHS/L38E (0.1) 4.9 (0.3) 7.3 (0.4) 4.6 (0.4) Δ+PHS/L38E (0.1) 5.0 (0.2) 6.9 (0.3) 5.0 (0.3) Δ+PHS/L38E (0.1) 5.3 (0.1) 6.9 (0.1) 4.6 (0.2) Δ+PHS/L38E (0.1) 5.3 (0.2) 5.9 (0.2) 4.4 (0.2) Δ+PHS/V39E (0.1) 4.9 (0.1) 5.6 (0.1) 3.9 (0.2) Δ+PHS/V39E (0.1) 5.3 (0.1) 7.5 (0.2) 4.2 (0.2) Δ+PHS/V39E (0.1) 5.6 (0.2) 7.0 (0.2) 4.7 (0.2) Δ+PHS/V39E (0.1) 6.0 (0.2) 6.5 (0.2) 5.4 (0.2) Δ+PHS/V39E (0.1) 5.9 (0.1) 5.3 (0.1) 6.6 (0.2) Δ+PHS/V39E (0.1) 5.8 (0.1) 4.4 (0.1) 7.2 (0.2) 3of6
4 PROTEINS ph C m [M]* m (kcal mol 1 M 1 ) ΔG o H 2 O (kcal mol) ΔΔG o H 2 O (kcal mol) Δ+PHS/V39E (0.1) 6.1 (0.1) 3.2 (0.1) 7.1 (0.2) Δ+PHS/T41E (0.1) 4.6 (0.1) 7.3 (0.1) 2.1 (0.2) Δ+PHS/T41E (0.1) 5.2 (0.1) 9.2 (0.1) 2.6 (0.2) Δ+PHS/T41E (0.1) 5.3 (0.1) 8.7 (0.2) 3.0 (0.2) Δ+PHS/T41E (0.1) 5.4 (0.1) 8.2 (0.1) 3.7 (0.2) Δ+PHS/T41E (0.1) 5.2 (0.1) 7.6 (0.1) 4.3 (0.2) Δ+PHS/T41E (0.1) 5.3 (0.1) 7.6 (0.1) 4.0 (0.2) Δ+PHS/A58E (0.1) 4.6 (0.1) 5.7 (0.1) 3.8 (0.2) Δ+PHS/A58E (0.1) 5.3 (0.1) 7.5 (0.1) 4.2 (0.2) Δ+PHS/A58E (0.1) 5.5 (0.1) 6.9 (0.1) 4.8 (0.2) Δ+PHS/A58E (0.1) 5.6 (0.1) 6.1 (0.1) 5.8 (0.2) Δ+PHS/A58E (0.1) 5.3 (0.1) 5.0 (0.1) 6.9 (0.2) Δ+PHS/A58E (0.1) 5.4 (0.1) 4.7 (0.1) 6.9 (0.2) Δ+PHS/A58E (0.1) 5.6 (0.1) 3.9 (0.1) 6.4 (0.2) Δ+PHS/T62E (0.1) 4.6 (0.1) 7.0 (0.1) 2.5 (0.2) Δ+PHS/T62E (0.1) 5.2 (0.1) 8.6 (0.2) 3.2 (0.3) Δ+PHS/T62E (0.1) 5.3 (0.1) 7.5 (0.1) 4.2 (0.2) Δ+PHS/T62E (0.1) 5.7 (0.1) 6.5 (0.1) 5.4 (0.2) Δ+PHS/T62E (0.1) 5.5 (0.1) 5.6 (0.1) 6.3 (0.2) Δ+PHS/T62E (0.1) 5.5 (0.1) 4.9 (0.1) 6.7 (0.2) Δ+PHS/T62E (0.1) 5.9 (0.1) 3.8 (0.1) 6.5 (0.2) Δ+PHS/I72E (0.1) 4.9 (0.1) 4.8 (0.1) 4.7 (0.2) Δ+PHS/I72E (0.1) 5.1 (0.1) 6.3 (0.2) 5.4 (0.2) Δ+PHS/I72E (0.1) 5.5 (0.2) 5.2 (0.2) 6.5 (0.2) Δ+PHS/I72E (0.1) 5.7 (0.1) 4.6 (0.1) 7.3 (0.2) Δ+PHS/I72E (0.1) 5.8 (0.1) 3.7 (0.1) 8.2 (0.2) Δ+PHS/I72E (0.1) 5.6 (0.1) 3.1 (0.1) 8.5 (0.2) Δ+PHS/I72E (0.1) 6.0 (0.1) 2.1 (0.1) 8.0 (0.2) Δ+PHS/V74E (0.1) 4.7 (0.1) 4.1 (0.1) 5.4 (0.2) Δ+PHS/V74E (0.1) 5.5 (0.1) 5.7 (0.1) 6.1 (0.2) Δ+PHS/V74E (0.1) 5.8 (0.1) 4.9 (0.1) 6.8 (0.2) Δ+PHS/V74E (0.1) 6.4 (0.1) 4.0 (0.1) 7.9 (0.2) Δ+PHS/V74E (0.1) 5.5 (0.1) 2.7 (0.1) 9.2 (0.2) Δ+PHS/V74E (0.1) 5.2 (0.1) 2.1 (0.1) 9.4 (0.2) Δ+PHS/V74E (0.1) 5.4 (0.1) 1.2 (0.1) 9.1 (0.2) Δ+PHS/A90E (0.1) 4.3 (0.1) 1.9 (0.1) 7.5 (0.2) Δ+PHS/A90E (0.1) 5.7 (0.2) 4.7 (0.1) 7.1 (0.2) Δ+PHS/A90E (0.1) 5.7 (0.2) 4.0 (0.1) 7.7 (0.2) Δ+PHS/A90E (0.1) 6.0 (0.1) 3.8 (0.1) 8.1 (0.2) Δ+PHS/A90E (0.1) 5.4 (0.2) 3.3 (0.2) 8.6 (0.2) Δ+PHS/A90E (0.1) 5.7 (0.1) 3.3 (0.1) 8.2 (0.2) Δ+PHS/A90E (0.1) 5.8 (0.1) 2.2 (0.1) 8.1 (0.2) Δ+PHS/Y91E (0.1) 4.7 (0.1) 4.5 (0.1) 5.0 (0.2) Δ+PHS/Y91E (0.1) 5.3 (0.1) 6.3 (0.1) 5.4 (0.2) Δ+PHS/Y91E (0.1) 5.0 (0.4) 4.4 (0.4) 7.3 (0.4) Δ+PHS/Y91E (0.1) 5.3 (0.1) 3.7 (0.1) 8.2 (0.2) Δ+PHS/Y91E (0.1) 5.2 (0.3) 3.2 (0.2) 8.7 (0.2) Δ+PHS/Y91E (0.1) 5.4 (0.1) 3.0 (0.1) 8.6 (0.2) Δ+PHS/Y91E (0.1) 5.4 (0.1) 2.1 (0.1) 8.2 (0.2) Δ+PHS/I92E (0.1) 5.0 (0.1) 3.9 (0.1) 5.6 (0.2) Δ+PHS/I92E (0.1) 5.9 (0.1) 5.9 (0.1) 5.8 (0.2) Δ+PHS/I92E (0.1) 6.2 (0.1) 5.0 (0.1) 6.7 (0.2) Δ+PHS/I92E (0.1) 6.3 (0.1) 4.0 (0.1) 7.9 (0.2) Δ+PHS/I92E (0.1) 6.4 (0.1) 2.7 (0.1) 9.2 (0.2) Δ+PHS/I92E (0.1) 6.7 (0.1) 1.4 (0.1) 10.1 (0.2) Δ+PHS/V99E (0.1) 5.1 (0.1) 4.7 (0.1) 4.8 (0.2) Δ+PHS/V99E (0.1) 5.4 (0.1) 6.2 (0.1) 5.5 (0.2) Δ+PHS/V99E (0.1) 5.6 (0.2) 5.3 (0.2) 6.4 (0.2) Δ+PHS/V99E (0.1) 5.6 (0.2) 4.4 (0.1) 7.5 (0.2) Δ+PHS/V99E (0.1) 6.0 (0.1) 3.2 (0.1) 8.7 (0.2) Δ+PHS/V99E (0.1) 6.4 (0.1) 2.1 (0.1) 9.5 (0.2) Δ+PHS/N100E (0.1) 4.7 (0.1) 9.5 (0.2) 0.1 (0.2) Δ+PHS/N100E (0.1) 5.0 (0.1) 10.6 (0.3) 1.2 (0.3) Δ+PHS/N100E (0.1) 5.0 (0.1) 9.3 (0.2) 2.4 (0.2) Δ+PHS/N100E (0.1) 5.3 (0.1) 8.5 (0.2) 3.4 (0.2) Δ+PHS/N100E (0.1) 5.2 (0.2) 7.4 (0.2) 4.4 (0.2) Δ+PHS/N100E (0.1) 5.6 (0.1) 7.1 (0.2) 4.5 (0.2) Δ+PHSL103E (0.1) 4.8 (0.1) 5.7 (0.1) 3.8 (0.2) Δ+PHSL103E (0.1) 5.5 (0.1) 7.6 (0.1) 4.2 (0.2) Δ+PHSL103E (0.1) 5.6 (0.1) 6.6 (0.1) 5.1 (0.2) Δ+PHSL103E (0.1) 5.8 (0.1) 5.7 (0.1) 6.2 (0.2) Δ+PHSL103E (0.1) 5.9 (0.1) 4.7 (0.1) 7.2 (0.2) 4of6
5 PROTEINS ph C m [M]* m (kcal mol 1 M 1 ) ΔG o H 2 O (kcal mol) ΔΔG o H 2 O (kcal mol) Δ+PHSL103E (0.1) 6.1 (0.1) 3.4 (0.1) 8.2 (0.2) Δ+PHSL103E (0.1) 6.6 (0.1) 1.2 (0.1) 8.9 (0.2) Δ+PHS/V104E (0.1) 5.0 (0.1) 7.5 (0.2) 2.0 (0.2) Δ+PHS/V104E (0.1) 5.3 (0.1) 8.9 (0.2) 2.8 (0.2) Δ+PHS/V104E (0.1) 5.3 (0.1) 8.5 (0.2) 3.2 (0.2) Δ+PHS/V104E (0.1) 5.3 (0.2) 7.6 (0.2) 4.1 (0.2) Δ+PHS/V104E (0.1) 5.6 (0.1) 6.6 (0.1) 5.3 (0.1) Δ+PHS/V104E (0.1) 5.7 (0.1) 5.4 (0.1) 6.5 (0.2) Δ+PHS/V104E (0.1) 5.9 (0.1) 4.2 (0.1) 7.4 (0.1) Δ+PHS/V104E (0.1) 6.3 (0.1) 1.8 (0.1) 8.5 (0.1) Δ+PHS/A109E (0.1) 4.5 (0.1) 5.1 (0.1) 4.4 (0.2) Δ+PHS/A109E (0.1) 5.2 (0.1) 6.8 (0.1) 5.0 (0.2) Δ+PHS/A109E (0.1) 5.4 (0.1) 6.2 (0.1) 5.5 (0.2) Δ+PHS/A109E (0.1) 5.6 (0.1) 5.4 (0.1) 6.5 (0.2) Δ+PHS/A109E (0.1) 5.4 (0.1) 4.2 (0.1) 7.7 (0.2) Δ+PHS/A109E (0.1) 5.1 (0.1) 3.4 (0.1) 8.1 (0.2) Δ+PHS/A109E (0.1) 5.2 (0.1) 2.3 (0.1) 8.0 (0.2) Δ+PHS/N118E (0.1) 4.9 (0.1) 9.9 (0.2) 1.9 (0.2) Δ+PHS/N118E (0.1) 5.1 (0.1) 9.7 (0.1) 2.2 (0.2) Δ+PHS/N118E (0.1) 4.9 (0.2) 9.7 (0.3) 1.9 (0.3) Δ+PHS/L125E (0.1) 4.8 (0.1) 5.5 (0.1) 4.0 (0.2) Δ+PHS/L125E (0.1) 5.3 (0.1) 7.2 (0.1) 4.6 (0.2) Δ+PHS/L125E (0.1) 5.4 (0.1) 5.9 (0.1) 5.8 (0.2) Δ+PHS/L125E (0.1) 5.6 (0.1) 5.2 (0.1) 6.7 (0.2) Δ+PHS/L125E (0.1) 5.3 (0.2) 3.7 (0.1) 8.2 (0.2) Δ+PHS/L125E (0.1) 5.2 (0.1) 2.5 (0.1) 9.1 (0.2) Δ+PHS/L125E (0.1) 4.7 (0.2) 0.5 (0.1) 9.8 (0.2) Δ+PHS/A132E (0.1) 5.2 (0.1) 6.0 (0.2) 5.8 (0.2) Δ+PHS/A132E (0.1) 5.2 (0.1) 4.9 (0.1) 6.8 (0.2) Δ+PHS/A132E (0.1) 4.4 (0.2) 3.7 (0.2) 8.2 (0.3) Δ+PHS/A132E (0.1) 4.4 (0.2) 3.7 (0.2) 8.2 (0.2) Δ+PHS/A132E (0.1) 3.9 (0.2) 3.0 (0.3) 8.5 (0.3) Δ+PHS/A132E (0.1) 3.4 (0.3) 2.3 (0.2) 8.1 (0.2) The data for ΔþPHS and its V66E variant were published previously (refs. 1, 2, 3, and 4). The data at ph 7 and 10 for the Glu-containing variant was published previously (1). 1 Isom DG, et al. (2008) High tolerance for ionizable residues in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 105: Dwyer J, et al. (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophysical Journal 79: Fitch CA, et al. (2002) Experimental pka values of buried residues: analysis with continuum methods and role of water penetration.biophysical Journal 82: Karp DA, Stahley MR, García-Moreno E.B (2010) Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease. Biochemistry 49: *Midpoint of the GdnHCl denaturation curve analyzed with a two-state model. GdnHCl dependence of the equilibrium constant between native and denatured states. Stability of the protein at 298 K obtained by analysis of GndHCl denaturation curves using a two-state model and the linear extrapolation model. Difference in stability calculated at each ph value as: ΔΔG o H ¼ 2O ΔGo H ðglu-containing variantþ 2O ΔGo H ðδþphsþ. 2O 5of6
6 Table S2. Equilibrium thermodynamic parameters for base unfolding for 25 variants of SNase with internal Glu residues Position pk a * ph mid FL ph mid CD V104E L125E I92E L103E L36E V66E V99E V39E A109E V74E A58E T62E N100E L25E F34E I72E V23E Y91E A132E 7.0 NA 10.8 L38E T41E A90E L37E G20E N118E *Apparent pk a values. Estimated error was 0.2 pk a units for all but Glu-37 and Glu-90, which have an estimated error of 0.5 pk a units. Midpoint of the major base unfolding transition monitored by Trp fluorescence or by CD. In all cases, the experimental uncertainty is 0.1 ph units 6of6
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