Metal-ion affinity and specificity in EF-hand proteins: Coordination geometry and domain plasticity in parvalbumin

Structure

Volumn 7, Issue 10, 1999, Pages 1269-1278

  Cates, M Susan ^a   Berry, Michael B ^a   Ho, Emai Lynn ^a   Li, Qi ^b   Potter, James D ^b   Phillips Jr , George N ^a  

^a RICE UNIVERSITY   (United States)

^b UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

Ca2+ binding; EF hand proteins; Mg2+ binding; Parvalbumin; Protein plasticity

Indexed keywords

CALCIUM BINDING PROTEIN; PARVALBUMIN;

ARTICLE; BINDING AFFINITY; CRYSTAL STRUCTURE; GEOMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0033570025     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(00)80060-X     Document Type: Article

References (47)

1. 1. Chazin, W.J. (1995). Releasing the calcium trigger. Nat. Struct. Biol. 2, 707-710.
2. 2. da Silva, A.C.R. & Reinach, F.C. (1991). Calcium binding induces conformational changes in muscle regulatory proteins. Trends Biochem. Sci. 16, 53-57.
3. 3. Kawasaki, H. & Kretsinger, R. (1994). Calcium-binding proteins 1: EF-hands. Protein Profile 1, 343-391.
4. 4. Ikura, M. (1996). Calcium binding and conformational response in EF-hand proteins. Trends Biochem. Sci. 21, 14-17.
5. 5. Berchtold, M.W. (1996). Parvalbumin. In Guidebook to the Calcium-Binding Proteins. (Celio, M.R., Pauls, T. & Schwaller, B., eds), pp. 123-125, Oxford University Press, Oxford.
6. 6. Coffee, C.J. & Bradshaw, R.A. (1973). Carp muscle calcium-binding protein I. Characterization of the tryptic peptides and the complete amino acid sequence of component B. J. Biol. Chem. 248, 3305-3312.
7. 2+. In Metal Ions in Biological Systems. (Sigel, H. & Sigel, A., eds), 26, pp. 1-13, Marcel Dekker Inc., New York.
8. 8. Falke, J.J., Drake, S.K., Hazard, A.L. & Peersen, O.B. (1994). Molecular tuning of ion binding to calcium signaling proteins. Q. Rev. Biophys. 27, 219-290.
9. 9. Babu, Y.S., Bugg, C.E. & Cook, W.J. (1988). Structure of calmodulin refined at 2.2 angstrom resolution. J. Mol. Biol. 204, 191-204.
10. 10. Herzberg, O. & James, M. (1988). Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 A resolution. J. Mol. Biol. 203, 761-779.
11. 2+. Biophys. J. 34, 559-569.
12. 2+ binding sites in troponin C with circular dichroism and tyrosine fluorescence. J. Biol. Chem. 253, 3675-3677.
13. 13. Hutnik, C.M.L., MacManus, J.P., Banville, D. & Szabo, A.G. (1990). Comparison of metal ion-induced conformational changes in parvalbumin and oncomodulin as probed by the intrinsic fluorescence of tryptophan 102. J. Biol. Chem. 265, 11456-11464.
14. 14. Pauls, T.L., et al., & Berchtold, M.W. (1993). Metal binding properties of recombinant rat parvalbumin wild-type and F102W mutant. J. Biol. Chem. 268, 20897-20903.
15. 2+ affinity constants of troponin C from eel skeletal muscle and positioning of the single tryptophan in the primary structure. J. Muscle Res. Cell Motil. 14, 585-593.
16. 2+. J. Muscle Res. Cell Motil. 18, 323-334.
17. 17. Swain, A., Kretsinger, R. & Amma, E. (1989). Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6 Å resolution. J. Biol. Chem. 264, 16620-166208.
18. 18. Kretsinger, R. & Nockolds, C. (1973). Carp muscle calcium-binding protein II. Structure determination and general description. J. Biol. Chem. 248, 3313-3326.
19. 19. Szebenyi, D.M.E. & Moffat, K. (1986). The refined structure of vitamin D-dependent calcium-binding protein from bovine intestine. J. Biol. Chem. 261, 8761-8777.
20. 20. Lin, G., et al., & Narayana, S. (1997). Crystal structure of calcium bound domain VI of calpain at 1.9 Å resolution and its role in enzyme assembly, regulation and inhibitor binding. Nat. Struct. Biol. 4, 539-547.
21. 2+-induced conformational changes. Nat. Struct. Biol. 4, 532-538.
22. 22. Declercq, J., Tinant, B., Parello, J. & Rambaud, J. (1991). Ionic interactions with parvalbumins. Crystal structure determination of pike 4.10 parvalbumin in four different ionic environments. J. Mol. Biol. 220, 1017-1039.
23. 23. Houdusse, A. & Cohen, C. (1996). Structure of the regulatory domain of scallop myosin at 2 Å resolution: implications for regulation. Structure 4, 21-32.
24. 24. Strynadka, N.C. & James, M.N.G. (1991). Crystal structures of helix-loop-helix calcium-binding proteins. Annu. Rev. Biochem. 58, 951-998.
25. 25. da Silva, A.C.R., Kendrick-Jones, J. & Reinach, F. (1995). Determinants of ion specificity on EF-hand sites. J. Biol. Chem. 270, 6773-6778.
26. 26. Schleef, M., Zuhlke, C., Schoffl, F. & Jockusch, H. (1994). Subtractive cDNA cloning as a tool to analyse secondary effects of a muscle disease. Characterization of affected genes in the myotonic ADR mouse. Neuromuscul. Disord. 4, 205-217.
27. 27. Idrizbegovic, E., Bogdanovic, N. & Canlon, B. (1998). Modulating calbindin and parvalbumin immunoreactivity in the cochlear nucleus by moderate noise exposure in mice. Brain Res. 800, 86-96.
28. 2+-binding protein ALG-2 and Alzheimer's disease gene ALG-3. Science 271, 521-525.
29. 29. Krzywkowski, P., et al., & Yamamura, H. I. (1996). Synaptic mechanisms and calcium binding proteins in the aged rat brain. Life Sci. 59, 421-428.
30. 30. Zimmer, D.B., Cornwall, E.H., Landar, A. & Song, W. (1995). The S100 protein family: history, function and expression. Brain Res. Bull. 37, 417-429.
31. 31. Calabretta, B., et al., & Baserga, R. (1985). Cell-cycle-specific genes differentially expressed in human leukemias. Proc. Natl Acad. Sci. USA 82, 4463-4467.
32. 32. Polans, A.S., et al., & Adamus, G. (1995). Recoverin, a photoreceptor-specific calcium-binding protein, is expressed by the tumor of a patient with cancer-associated retinopathy. Proc. Natl. Acad. Sci. USA 92, 9176-9180.
33. 33. Blum, J.K. & Berchtold, M.W. (1994). Calmodulin-like effect of oncomodulin on cell proliferation. J. Cell. Physiol. 160, 455-462.
34. 34. Ausubel, F.M., et al., & Struhl, K. (1987). Current Protocols in Molecular Biology I. Suppl. 15, 8.5.5. John Wiley & Sons, Inc., Toronto, Canada.
35. 35. Pauls, T.L. & Berchtold, M.W. (1993). Efficient complementary DNA amplification and expression using polymerase chain reaction technology. Methods Enzymol. 217, 102-122.
36. 36. Kretsinger, R.H., Dangelat, D. & Bryan, R.F. (1971). Crystal data for low molecular weight albumins of carp. J. Mol. Biol. 59, 213-214.
37. 37. Otwinowski, Z. (1993). Oscillation and data reduction program. In Proceedings of the CCP4 Study Weekend: Data Collection and Processing. (Sawyer, L., Isaacs, N. & Bailey, S., eds), pp. 56-62, Daresbury Laboratory, Warrington, UK.
38. 38. Brünger, A.T. (1992). X-PLOR Version 3.1: A System for X-ray Crystallography and NMR. Yale University Press, New Haven.
39. 39. Brünger, A., et al., & Warren, G. (1998). Crystallography and NMR system: a new software system for macromolecular structure determination. Acta Crystallogr. D 54, 905-921.
40. 40. Sheldrick, G.M. & Schneider, T.R. (1997). SHELXL: high-resolution refinement. Methods Enzymol. 276, 319-343.
41. 41. Sack, J.S. (1988). CHAIN-A crystallographic modeling program. J. Mol. Graphics 6, 244-245.
42. 42. Jones, T., Zou, J., Cowan, S. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. 47, 110-119.
43. 43. Kabsch, W. (1978). A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 34, 827-828.
44. 44. Molecular Simulations, Inc. (1998). Quanta97. San Diego, CA.
45. 45. Carson, M. (1987). Ribbon models of macromolecules. J. Mol. Graphics 5, 103-106.
46. 46. The Math Works, Inc. (1994). Matlab®. (4.2a edn). Natick, MA.
47. 47. Schwartz, A. (1984). The regulation of calcium in the regulation of the skeletal muscle contraction-relaxation cycle. Methods Pharmacol. 5, 63-75.