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Protein Sci. 1999 Feb; 8(2): 418–425.
PMCID: PMC2144253

Simplified methods for pKa and acid pH-dependent stability estimation in proteins: removing dielectric and counterion boundaries.

Abstract

Much computational research aimed at understanding ionizable group interactions in proteins has focused on numerical solutions of the Poisson-Boltzmann (PB) equation, incorporating protein exclusion zones for solvent and counterions in a continuum model. Poor agreement with measured pKas and pH-dependent stabilities for a (protein, solvent) relative dielectric boundary of (4,80) has lead to the adoption of an intermediate (20,80) boundary. It is now shown that a simple Debye-Huckel (DH) calculation, removing both the low dielectric and counterion exclusion regions associated with protein, is equally effective in general pKa calculations. However, a broad-based discrepancy to measured pH-dependent stabilities is maintained in the absence of ionizable group interactions in the unfolded state. A simple model is introduced for these interactions, with a significantly improved match to experiment that suggests a potential utility in predicting and analyzing the acid pH-dependence of protein stability. The methods are applied to the relative pH-dependent stabilities of the pore-forming domains of colicins A and N. The results relate generally to the well-known preponderance of surface ionizable groups with solvent-mediated interactions. Although numerical PB solutions do not currently have a significant advantage for overall pKa estimations, development based on consideration of microscopic solvation energetics in tandem with the continuum model could combine the large deltapKas of a subset of ionizable groups with the overall robustness of the DH model.

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Selected References

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  • Antosiewicz J, McCammon JA, Gilson MK. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 6;238(3):415–436. [PubMed]
  • Antosiewicz J, McCammon JA, Gilson MK. The determinants of pKas in proteins. Biochemistry. 1996 Jun 18;35(24):7819–7833. [PubMed]
  • Bashford D, Karplus M. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry. 1990 Nov 6;29(44):10219–10225. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Beroza P, Fredkin DR, Okamura MY, Feher G. Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc Natl Acad Sci U S A. 1991 Jul 1;88(13):5804–5808. [PMC free article] [PubMed]
  • Evans LJ, Goble ML, Hales KA, Lakey JH. Different sensitivities to acid denaturation within a family of proteins: implications for acid unfolding and membrane translocation. Biochemistry. 1996 Oct 8;35(40):13180–13185. [PubMed]
  • Fink AL, Calciano LJ, Goto Y, Kurotsu T, Palleros DR. Classification of acid denaturation of proteins: intermediates and unfolded states. Biochemistry. 1994 Oct 18;33(41):12504–12511. [PubMed]
  • Gilson MK, Honig BH. The dielectric constant of a folded protein. Biopolymers. 1986 Nov;25(11):2097–2119. [PubMed]
  • Karshikov A, Duerring M, Huber R. Role of electrostatic interaction in the stability of the hexamer of constitutive phycocyanin from Fremyella diplosiphon. Protein Eng. 1991 Aug;4(6):681–690. [PubMed]
  • Kesvatera T, Jönsson B, Thulin E, Linse S. Binding of Ca2+ to calbindin D9k: structural stability and function at high salt concentration. Biochemistry. 1994 Nov 29;33(47):14170–14176. [PubMed]
  • Kesvatera T, Jönsson B, Thulin E, Linse S. Measurement and modelling of sequence-specific pKa values of lysine residues in calbindin D9k. J Mol Biol. 1996 Jun 21;259(4):828–839. [PubMed]
  • Klapper I, Hagstrom R, Fine R, Sharp K, Honig B. Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins. 1986 Sep;1(1):47–59. [PubMed]
  • Kuramitsu S, Hamaguchi K. Analysis of the acid-base titration curve of hen lysozyme. J Biochem. 1980 Apr;87(4):1215–1219. [PubMed]
  • Lakey JH, Parker MW, González-Mañas JM, Duché D, Vriend G, Baty D, Pattus F. The role of electrostatic charge in the membrane insertion of colicin A. Calculation and mutation. Eur J Biochem. 1994 Feb 15;220(1):155–163. [PubMed]
  • Loewenthal R, Sancho J, Fersht AR. Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability. J Mol Biol. 1992 Apr 5;224(3):759–770. [PubMed]
  • Oliveberg M, Arcus VL, Fersht AR. pKA values of carboxyl groups in the native and denatured states of barnase: the pKA values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry. 1995 Jul 25;34(29):9424–9433. [PubMed]
  • Parker MW, Pattus F, Tucker AD, Tsernoglou D. Structure of the membrane-pore-forming fragment of colicin A. Nature. 1989 Jan 5;337(6202):93–96. [PubMed]
  • Parker MW, Postma JP, Pattus F, Tucker AD, Tsernoglou D. Refined structure of the pore-forming domain of colicin A at 2.4 A resolution. J Mol Biol. 1992 Apr 5;224(3):639–657. [PubMed]
  • Sham YY, Muegge I, Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys J. 1998 Apr;74(4):1744–1753. [PMC free article] [PubMed]
  • Warwicker J. Continuum dielectric modelling of the protein-solvent system, and calculation of the long-range electrostatic field of the enzyme phosphoglycerate mutase. J Theor Biol. 1986 Jul 21;121(2):199–210. [PubMed]
  • Warwicker J. Improving pKa calculations with consideration of hydration entropy. Protein Eng. 1997 Jul;10(7):809–814. [PubMed]
  • Warwicker J. Modeling charge interactions and redox properties in DsbA. J Biol Chem. 1998 Jan 30;273(5):2501–2504. [PubMed]
  • Warwicker J, Engelman BP, Steitz TA. Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent. Proteins. 1987;2(4):283–289. [PubMed]
  • Warwicker J, Watson HC. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J Mol Biol. 1982 Jun 5;157(4):671–679. [PubMed]
  • Yang AS, Honig B. On the pH dependence of protein stability. J Mol Biol. 1993 May 20;231(2):459–474. [PubMed]
  • You TJ, Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J. 1995 Nov;69(5):1721–1733. [PMC free article] [PubMed]
  • Zhou HX, Vijayakumar M. Modeling of protein conformational fluctuations in pKa predictions. J Mol Biol. 1997 Apr 11;267(4):1002–1011. [PubMed]

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