Measurement and modelling of sequence-specific pK(a) values of lysine residues in calbindin D(9k)

Journal of Molecular Biology

Volumn 259, Issue 4, 1996, Pages 828-839

  Kesvatera, Tönu ^a,b   Jönsson, Bo ^a   Thulin, Eva ^a   Linse, Sara ^a  

^a LUND UNIVERSITY   (Sweden)

^b ESTONIAN ACADEMY OF SCIENCES   (Estonia)

Author keywords

Calcium binding proteins; Electrostatic interactions; Monte Carlo simulations; Nuclear magnetic resonance; pK(a) of lysine residues

Indexed keywords

CALBINDIN; CALCIUM ION; CARBON 13; LYSINE;

ARTICLE; BINDING SITE; DIELECTRIC CONSTANT; IONIZATION; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PKA; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION; TITRIMETRY;

ALOCASIA MACRORRHIZOS; TRIXIS;

EID: 0030596490     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0361     Document Type: Article

References (44)

1. Abildgaard, F., Munk Jørgensen, A. M., Led, J. J., Christensen, T., Jensen, E. B., Junker, F. & Dalbøge, H. (1992). Characterization of tertiary interactions in a folded protein by NMR methods: studies of pH-induced structural changes in human growth hormone. Biochemistry, 31, 8587-8596.
2. Åkesson, T. & Jönsson, B. (1991). Monte Carlo simulations of colloidal stability - beyond the Poisson-Boltzmann approximation. Electrochim. Acta, 36, 1723-1727.
3. Akke, M. & Forsén, S. (1990). Protein stability and electrostatic interactions between solvent exposed charged side chains. Proteins: Struct. Funct. Genet. 8, 23-29.
4. Antosiewics, J., McCammon, J. A. & Gilson, M. K. (1994). Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238, 415-436.
5. 1H NMR. Biophys. J. 66, 1180-1184.
6. a's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry, 29, 5752-5761.
7. Bax, A., Ikura, M., Kay, L. E., Torchia, D. A. & Tscudin, R. (1990). Comparison of different models of two-dimensional reverse-correlation NMR for the study of proteins. J. Magn. Reson. 86, 304-318.
8. Braunschweiler, L. & Ernst, R. R. (1983). Coherence transfer by isotropic mixing: application to proton correlation spectroscopy J. Magn. Reson. 53, 521-528.
9. 1H NMR spectroscopy. Proc. Natl Acad. Sci. USA, 86, 2195-2198.
10. 1H NMR. Biochemistry, 28, 8646-8653.
11. Huque, E. & Vogel, H. J. (1993). Carbon-13 NMR studies of the lysine side chains of calmodulin and its proteolytic fragments. J. Protein Chem. 12, 693-705.
12. 9k modified in the pseudo EF-hand. Eur. J. Biochem. 187, 455-460.
13. 13C NMR study of the mode of interaction in solution of the B fragment of staphylococcal protein A and the Fc fragments of mouse immunoglobulin G. FEBS Letters, 328, 49-54.
14. Kokesh, F. C. & Westheimer, F. H. (1971). A reporter group at the active site of acetoacetate decarboxylase. II. Ionization constant of the amino group. J. Am. Chem. Soc. 93, 7270-7274.
15. 9k. Biochemistry, 28, 7065-7074.
16. 9k. J. Mol. Biol. 231, 711-734.
17. Lewis, S. D., Johnson, F. A. & Shafer, J. A. (1981). Effect of cysteine-25 on the ionization of histidine-159 in papain as determined by proton nuclear magnetic resonance spectroscopy. Evidence for a His-156-Cys-25 ion pair and its possible role in catalysis. Biochemistry, 20, 48-51.
18. Lin, Y., Fusek, M., Lin, X., Hartsuck, J. A., Kezdy F. C. & Tang, J. (1992). pH dependence of kinetic parameters of pepsin, rhizopuspepsin, and their active-site hydrogen bond mutants. J. Biol. Chem. 267, 18413-18418.
19. Linse, S., Jönsson, Bo & Chazin, W. J. (1995). The effect of protein concentration on ion binding. Proc. Natl Acad. Sci. USA, 92, 4748-4752.
20. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953). Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092.
21. 15N spectroscopy J. Magn. Reson. 87, 488-501.
22. Nozaki, Y. & Tanford, C. (1967). Examination of titration behavior. Methods Enzymol. 11, 715-734.
23. Oda, Y., Yamazaki, T., Nagayama, K., Kanaya, S., Kuroda, Y. & Nakamura, H. (1994). Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry, 33, 5275-5284.
24. a values of the denatured state are on average 0.4 units lower than those of model compounds. Biochemistry, 34, 9424-9433.
25. Ranee, M. (1987). Improved techniques for homonuclear rotating-frame and isotropic mixing experiments. J. Magn. Reson. 74, 557-564.
26. Schaller, W. & Robertson, A. D. (1995). pH, ionic strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain. Biochemistry, 34, 4714-4723.
27. Shaka, A. J., Barker, P. B. & Freeman, R. (1985). Computer-optimized decoupling scheme for wideband applications and low-level operation. J. Magn. Reson. 64, 547-552.
28. Shaka, A. J., Lee, C. J. & Pines, A. (1988). Iterative schemes for bilinear operators; application to spin decoupling. J. Magn. Reson. 77, 274-293.
29. 9k. Biochemistry, 29, 5752-5761.
30. 2+-binding proteins. Nature Struct. Biol. 1, 239-245.
31. 9k by NMR spectroscopy. J. Mol. Biol. 249, 441-462.
32. Smith, P. E., Brunne, R. M. Mark, A. E. & van Gunsteren, W. F. (1993). Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics. J. Phys. Chem. 97, 2009-2014.
33. Sørensen, M. D. & Led, J. J. (1994). Structural details of asp(B9) human insulin at low pH from two-dimensional NMR titration studies. Biochemistry, 33, 13727-13733.
34. Sternberg, M. J. E., Hayes, F. R. F., Russell, A. J., Thomas, P. G. & Fersht, A. R. (1987). Prediction of electrostatic effects on engineering of protein charges. Nature, 330, 86-88.
35. 9k: a Monte Carlo simulation study. Biochemistry, 30, 5209-5217.
36. 2+ to calmodulin and its tryptic fragments: theory and experiment. Biochemistry, 32, 2828-2834.
37. Szebenyi, D. M. E. & Moffat, K. (1986). The refined structure of vitamin D dependent calcium-binding protein from bovine intestine. Molecular details, ion binding, and implications for the structure of other calcium-binding preoteins. J. Biol. Chem. 261, 8671-8777.
38. Szyperski, T., Antuch, W., Schick, M., Betz, A., Stone, S. R. & Wütrich, K. (1994). Transient hydrogen bonds identified on the surface of the NMR solution structure of hirudin. Biochemistry, 33, 9303-9310.
39. Tanford, C. & Kirkwood, J. G. (1957). Theory of protein titration curves. I. General equations for impenetrable spheres. J. Am. Chem. Soc. 79, 5333-5339.
40. 9k. Eur. J. Biochem. 175, 435-445.
41. Widom, B. (1963). Some topics in the theory of fluids. J. Chem. Phys. 39, 2808-2812.
42. Yu, L. & Fesik, S. W. (1994). pH titration of the histidine residues of cyclophilin and FK506 binding protein in the absence and presence of immunosuppressant ligands. Biochim. Biophys. Acta, 1209, 24-32.
43. 9k. J. Biol. Chem. 268, 22420-22428.
44. 9k. J. Protein Chem. 13, 527-535.