Concurrent interactions contribute to the raised pK(a) of His18 in barnase

Journal of Molecular Biology

Volumn 260, Issue 1, 1996, Pages 99-110

  Prévost, Martine ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

Barnase; Free energy simulations; Helix capping interactions; pK(a); Protein stability

Indexed keywords

HISTIDINE; PROTEIN;

AMINO ACID ANALYSIS; ARTICLE; CARBOXY TERMINAL SEQUENCE; DIPOLE; ELECTRICITY; ENZYME STABILITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STABILITY;

EID: 0030570519     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0384     Document Type: Article

References (50)

1. Antosiewicz, J., McCammon, J. A. & Gilson, M. K. (1994). Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436.
2. Åqvist, J. (1990). Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94, 8021-8024.
3. Åqvist, J., Luecke, H., Quiocho, F. A. & Warshel, A. (1991). Dipoles localized at helix termini of proteins stabilize charges. Proc. Natl. Acad. Sci. USA, 88, 2026-2030.
4. Armstrong, K. & Baldwin, R. L. (1993). Charged histidine affects α-helix stability at all positions in the helix by interacting with the backbone charges. Proc. Natl Acad. Sci. USA, 90, 11337-11340.
5. Amstrong, K. M., Fairman, R. & Baldwin, R. L. (1993). The (i, i + 4) Phe-His interaction studied in an alanine-based α-helix. J. Mol. Biol. 230, 284-291.
6. Bashford, D. (1991). Electrostatic effects in biological molecules. Curr. Opin. Struct. Biol. 1, 175-184.
7. Bashford, D. & Karplus, M. (1990). pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry, 29, 10219-10225.
8. Bodkin, M. J. & Goodfellow, J. M. (1995). Competing interactions contributing to α-helical stability in aqueous solution. Protein Sci. 4, 603-612.
9. Born, M. (1920). Volumen und hydrationwärme der ionen. Z. Phys. 1, 45-48.
10. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983). CHARMM: a program for macromolecular energy minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217.
11. Brooks, C. L., III & Karplus, M. (1983). Deformable stochastic boundaries in molecular dynamics. J. Chem. Phys. 79, 6312-6325.
12. Brooks, C. L., III, Brünger, A. & Karplus, M. (1985). Active site dynamics in protein molecules: A stochastic boundary molecular - dynamics approach. Biopolymers, 24, 843-865.
13. Brunne, R. M., Liepinsh, E., Otting, G., Wüthrich, K. & van Gunsteren, W. F. (1993). Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231, 1040-1048.
14. + or α-COO-group on helix stability. Proteins: Struct Funct. Genet. 5, 1-7.
15. Hol, W. G. J., van Duijnen, P. T. & Berendsen, H. J. C. (1978). The α-helix dipole and the properties of proteins. Nature, 273, 443-446.
16. Jorgensen, W. L. (1989). Free energy calculations: a breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 22, 184-189.
17. Jorgensen, W. L. & Briggs, J. M. (1989). A priori pKa calculations and the hydration of organic anions. J. Am. Chem. Soc. 111, 4190-4197.
18. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
19. Jorgensen, W. L., Briggs, J. M. & Gao, J. (1987). A priori calculations of pKa's for organic compounds in water. The pKa of ethane. J. Am. Chem. Soc. 109, 6857-6858.
20. Kirkwood, J. G. (1935). Statistical mechanics of fluid mixtures. J. Chem. Phys. 3, 300-313.
21. Levitt, M. & Park, B. H. (1993). Water: now you see it, now you don't. Structure, 1, 223-226.
22. Levitt, M. & Perutz, M. F. (1988). Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 201, 751-754.
23. Lockhart, D. J. & Kim, P. S. (1992). Internal stark effect measurement of the electric field at the amino terminus of an α-helix. Science, 257, 947-951.
24. Lockhart, D. J. & Kim, P. S. (1993). Electrostatic screening of charge and dipole interactions with the helix backbone. Science, 260, 198-202.
25. Loewenthal, R., Sancho, J. & Fersht, A. R. (1991). Fluorescence spectrum of barnase: contributions of three tryptophan residues and a histidine-related pH dependence. Biochemistry, 30, 6775-6779.
26. Loewenthal, R., Sancho, J. & Fersht, A. R. (1992). Histidine-aromatic interactions in barnase. Elevation of histidine pKa and contribution to protein stability. J. Mol. Biol. 224, 759-770.
27. Loewenthal, R., Sancho, J., Reinikainen, T. & Fersht, A. R. (1993). Long-range surface charge-charge interactions in proteins. Comparison of experimental results with calculations from a theoretical method. J. Mol. Biol. 232, 574-583.
28. Mauguen, Y., Hartley, R. W., Dodson, E. J., Dodson, G. G., Bricogne, G., Chothia, C. & Jack A. (1982). Molecular structure of a new family of ribonucleases. Nature, 297, 162-164.
29. Nicholson, H., Becktel, W. J. & Matthews, B. W. (1988). Enhanced protein thermostability from designed mutations that interact with α-helix dipoles. Nature, 336, 651-656.
30. Nicholson, H., Anderson, D. E., Dao-pin, S. & Matthews, B. W. (1991). Analysis of the interaction between charged side-chains and the α-helix dipole using designed thermostable mutants of phage T4 lysozyme. Biochemistry, 30, 9816-9828.
31. Otting, G., Liepinsh, E. & Wüthrich, K. (1991). Protein hydration in aqueous solution. Science, 254, 974-980.
32. a values of two histidine residues in human haemoglobin, the Bohr effect, and the dipole moments of α-helices. J. Mol. Biol. 183, 491-498.
33. Presta, L. G. & Rose, G. D. (1988). Helix signals in proteins. Science, 240, 1632-1641.
34. Prévost, M., Wodak, S. J., Tidor, B. & Karplus, M. (1991). Contribution of the hydrophobic effect to protein stability: Analysis based on simulations of the Ile → Ala mutation in barnase. Proc. Natl Acad. Sci. USA, 88, 10880-10884.
35. Reynolds, W. F., Peat, I. R., Freedman, M. H. & Lyerla, J. R., Jr (1973). Determination of the tautomeric form of the imidazole ring of L-histidine in basic solution by carbon-13 magnetic resonance spectroscopy. J. Am. Chem. Soc. 95, 328-331.
36. Richardson, J. S. & Richardson, D. C. (1988). Amino acid preferences for specific locations at the ends of α-helices. Science, 240, 1648-1652.
37. Sali, D., Bycroft, M. & Fersht, A. R. (1988). Stabilization of protein structure by interaction of α-helix dipole with a charged side-chain. Nature, 335, 740-743.
38. Sancho, J., Serrano, L. & Fersht, A. R. (1992). Histidine residues at the N-and C-termini of α-helices: perturbed pKas and protein stability. Biochemistry, 31, 2253-2258.
39. Serrano, L. & Fersht, A. R. (1989). Capping and α-helix stability. Nature, 342, 296-299.
40. Sharp, K. A. & Honig, B. (1990). Electrostatic interactions in macromolecules: theory and application. Annu. Rev. Biophys. Chem. 19, 301-332.
41. Shoemaker, K. R., Kim, P. S., York, E. J., Stewart, J. M. & Baldwin, R. L. (1987). Tests of the helix dipole model for the stabilization of α-helices. Nature, 26, 563-567.
42. Swope, W. C., Andersen, H. C., Berens, P. H. & Wilson, K. R. (1982). A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: application to small water clusters. J. Chem. Phys. 76, 637-649.
43. Tanford, C. & Kirkwood, J. G. (1957). Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79, 3333-5339.
44. 1H-NMR study on the tautomerism of the imidazole ring of histidine residues. I. Microscopic pK values and molar ratios of tautomers in histidine-containing peptides. Biochim. Biophys. Acta, 742, 576-585.
45. Tembe, B. L. & McCammon, J. A. (1984). Ligand-receptor interactions. Comput. Chem. 8, 281-283.
46. Tidor, B. (1994). Helix-capping interaction in λ, Cro protein: a free energy simulation analysis. Proteins: Struct. Funct. Genet. 19, 310-323.
47. Tidor, B. & Karplus, M. (1991). Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry, 30, 3217-3228.
48. Wada, A. (1976). The α-helix as an electric macro-dipole. Advan. Biophys. 9, 1-63.
49. Yang, A.-S., Gunner, M. R., Sampogna, R., Sharp, K. & Honig, B. (1993). On the calculation of pKas in proteins. Proteins: Struct. Funct. Genet. 15, 252-265.
50. Zwanzig, R. W. (1954). High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys. 22, 1420-1426.