Crystallization and Structural Details of Ca2+-Induced Conformational Changes in the EF-Hand Domain VI of Calpain

  • Miroslaw Cygler
  • Pawel Grochulski
  • Helen Blanchard
Part of the Methods in Molecular Biology™ book series (MIMB, volume 172)


Calpains are calcium-regulated neutral cysteine proteases that include ubiquitous, as well as tissue-specific, isoforms. The ubiquitous isoforms, μ- and m-calpains are intracellular, nonlysosomal proteases (1). The tissue-specific isoforms include calpain 3, which is found in skeletal muscle, and stomach-specific nCL-2 (2). The calpains catalyze limited proteolysis of substrates involved in cytoskeletal remodeling and signal transduction, although definitive physiological roles are not yet ascertained. They are also thought to contribute to the tissue damage that follows ischemia and reperfusion in conditions such as stroke and cardiac infarct (3 4), stimulating a search for specific and clinically acceptable inhibitors aimed at both the active site and also the Ca2+-binding domains (5). The calpains are heterodimers that consist of an 80-kDa catalytic subunit (the large subunit), and a 30-kDa regulatory subunit (the small subunit)


Reservoir Solution Cys146Ser Mutant Interhelical Angle Interresidue Contact Heterodimer Interface 
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  1. 1.
    Sorimachi, H., Ishiura, S., and Suzuki, K. (1997) Structure and physiological function of calpains. Biochem. J. 328, 721–732.PubMedGoogle Scholar
  2. 2.
    Sorimachi, H., Saido, T. C., and Suzuki, K. (1994) New era of calpain research. Discovery of tissue-specific calpains. FEBS Lett. 343, 1–5.CrossRefPubMedGoogle Scholar
  3. 3.
    Bartus, R. T., Elliott, P. J., Hayward, N. J., Dean, R. L., Harbeson, S., Straub, J. A., et al. (1995) Calpain as a novel target for treating acute neurodegenerative disorders. Neurol. Res. 17, 249–258.PubMedGoogle Scholar
  4. 4.
    Iwamoto, H., Miura, T., Okamura, T., Shirakawa, K., Iwatate, M., Kawamura, S., et al. (1999) Calpain inhibitor-1 reduces infarct size and DNA fragmentation of myocardium in ischemic/reperfused rat heart. J. Cardiovasc. Pharmacol. 33, 580–586.CrossRefGoogle Scholar
  5. 5.
    Wang, K. K. and Yuen, P. W. (1994) Calpain inhibition: an overview of its therapeutic potential. Trends. Pharmacol. Sci. 15, 412–419.CrossRefPubMedGoogle Scholar
  6. 6.
    Ohno, S., Emori, Y., Imajoh, S., Kawasaki, H., Kisaragi, M., and Suzuki, K. (1984) Evolutionary origin of a calcium-dependent protease by fusion of genes for a thiol protease and a calcium-binding protein? Nature 312, 566–570.CrossRefPubMedGoogle Scholar
  7. 7.
    Berti, P. J. and Storer, A. C. (1995) Alignment/phylogeny of the papain superfamily of cysteine proteases. JMol. Biol. 246, 273–283.CrossRefGoogle Scholar
  8. 8.
    Minami, Y., Emori, Y., Imajoh-Ohmi, S., Kawasaki, H., and Suzuki, K. (1988) Carboxyl-terminal truncation and site-directed mutagenesis of the EF hand struc-258 ture-domain of the small subunit of rabbit calcium-dependent protease. J.Biochem. (Tokyo) 104, 927–933.Google Scholar
  9. 9.
    Nakayama, S. and Kretsinger, R. H. (1994) Evolution of the EF-hand family of proteins. Annu. Rev. Biophys. Biomol. Struct. 23, 473–507.CrossRefPubMedGoogle Scholar
  10. 10.
    Mellgren, R. L. (1997) Specificities of cell permeant peptidyl inhibitors for the proteinase activities of mu-calpain and the 20 S proteasome. J.Biol. Chem. 272, 29,899–29,903.CrossRefPubMedGoogle Scholar
  11. 11.
    Croall, D. E. and DeMartino, G. N. (1991) Calcium-activated neutral protease (calpain) system: structure, function, and regulation. Physiol. Rev. 71, 813–847.PubMedGoogle Scholar
  12. 12.
    Goll, D. E., Thompson, V. F., Taylor, R. G., and Zalewska, T. (1992) Is calpain activity regulated by membranes and autolysis or by calcium and calpastatin? Bioessays 14, 549–556.CrossRefPubMedGoogle Scholar
  13. 13.
    Crawford, C., Brown, N. R., and Willis, A. C. (1993) Studies of the active site of m-calpain and the interaction with calpastatin. Biochem. J. 296, 135–142.PubMedGoogle Scholar
  14. 14.
    Saido, T. C., Nagao, S., Shiramine, M., Tsukaguchi, M., Yoshizawa, T., Sorimachi, H., et al. (1994) Distinct kinetics of subunit autolysis in mammalian m-calpain activation. FEBS Lett. 346, 263–267.CrossRefPubMedGoogle Scholar
  15. 15.
    Elce, J. S., Davies, P. L., Hegadorn, C., Maurice, D. H., and Arthur, J. S. (1997) The effects of truncations of the small subunit on m-calpain activity and heterodimer formation. Biochem. J. 326, 31–38.PubMedGoogle Scholar
  16. 16.
    Blanchard, H., Li, Y., Cygler, M., Kay, C. M., Arthur, J. S. C., Davies, P. L., and Elce, J. S. (1996) Ca2+binding domain vi of rat calpain is a homodimer in solution: Hydrodynamic, crystallization and preliminary x ray diffraction studies. Protein Sci. 5, 535–537.CrossRefPubMedGoogle Scholar
  17. 17.
    Blanchard, H., Grochulski, P., Li, Y., Arthur, J. S. C., Davies, P. L., Elce, J. S., and Cygler, M. (1997) Structure of a calpain Ca(2+)-binding domain reveals a novel EF-hand and Ca(2+)-induced conformational changes. Nat. Struct. Biol. 4, 532–538.CrossRefPubMedGoogle Scholar
  18. 18a.
    Lin, G. D., Chattopadhyay, D., Maki, M., Wang, K. K., Carson, M., Jin, L., et al. (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.CrossRefPubMedGoogle Scholar
  19. 18b.
    Dutt, P., Arthur, J. S. C., Grochulski, P., Cygler, M., and Elce, J. S. (2000) The roles of individual calcium-binding EF-hands in the activation of m-calpain. J Biochem. 15, 37–43.Google Scholar
  20. 19.
    Graham-Siegenthaler, K., Gauthier, S., Davies, P. L., and Elce, J. S. (1994) Active recombinant rat calpain II. Bacterially produced large and small subunits associate both in vivo and in vitro. J.Biol. Chem. 269, 30,457–30,460.PubMedGoogle Scholar
  21. 20.
    Jancarik, J. and Kim, S.-H. (1999) Sparse matrix sampling: a screening method for crystallization of proteins. J Appl. Cryst. 24, 409–414.CrossRefGoogle Scholar
  22. 21.
    Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326.CrossRefGoogle Scholar
  23. 22.
    Ramakrishnan, V. and Biou, V. (1999) Treatment of multiwavelength anomalous diffraction data as a special case of multiple isomorphous replacement, in Macro-molecular Crystallography Part A (Carter, C. W., Jr. and Sweet, R. M., eds.), Academic, San Diego, CA, pp. 538–557.Google Scholar
  24. 23.
    CCP4 (1998) Collaborative Computational Project Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760–763.Google Scholar
  25. 24.
    Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgoard, M. (1991) Improved methods for building models in electron density maps and the location of errors in these models. Acta. Crystallogr. A47, 110–119.Google Scholar
  26. 25.
    Brünger, A. T. (1993) X-Plor Version 3.1. Yale UniversityGoogle Scholar
  27. 26a.
    Akke, M., Forsen, S., and Chazin, W. J. (1995) Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo—>(Ca2+)II1—>(Ca2+)I,II2 binding pathway. J Mol. Biol. 252, 102–121.CrossRefPubMedGoogle Scholar
  28. 26b.
    Brooks, B. R., Bruccoleri, R. E., Olafson, B.D., States, D. J., Swaminthan, S., and Karplus, M. (1983) CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput. Chem. 4, 187–217.CrossRefGoogle Scholar
  29. 27.
    Flaherty, K. M., Zozulya, S., Stryer, L., and McKay, D. B. (1993) Three-dimensional structure of recoverin, a calcium sensor in vision. Cell 75, 709–716.CrossRefPubMedGoogle Scholar
  30. 28.
    Kawasaki, H. and Kretsinger, R. H. (1995) Calcium-binding proteins 1: EF-hands. Protein Profile 2, 297–490.PubMedGoogle Scholar
  31. 29.
    Strynadka, N. C. and James, M. N. (1989) Crystal structures of the helix-loop-helix calcium-binding proteins. Annu. Rev. Biochem. 58, 951–998.CrossRefPubMedGoogle Scholar
  32. 30.
    McPhalen, C. A., Strynadka, N. C., and James, M. N. (1991) Calcium-binding sites in proteins: a structural perspective. Adv. Protein Chem. 42, 77-144.Google Scholar
  33. 31.
    Nelson, M. R. and Chazin, W. J. (1998) An interaction-based analysis of calcium-induced conformational changes in Ca2+sensor proteins. Protein Sci. 7, 270–282.CrossRefPubMedGoogle Scholar
  34. 32.
    Ikura, M. (1996) Calcium binding and conformational response in EF-hand proteins. Trends Biochem. Sci. 21, 14–17.PubMedGoogle Scholar
  35. 33.
    Spyracopoulos, L., Li, M. X., Sia, S. K., Gagne, S. M., Chandra, M., Solaro, R. J. and Sykes, B. D. (1997) Calcium-induced structural transition in the regulatory domain of human cardiac troponin C. Biochemistry 36, 12,138–12,146.CrossRefPubMedGoogle Scholar
  36. 34.
    Wang, K. K., Nath, R., Posner, A., Raser, K. J., Buroker-Kilgore, M., Hajimohammadreza, I., et al. (1996) An alpha-mercaptoacrylic acid derivative is a selective nonpeptide cell-permeable calpain inhibitor and is neuroprotective. Proc. Natl. Acad. Sci. USA 93, 6687–6692.CrossRefPubMedGoogle Scholar
  37. 35.
    Nishimura, T. and Goll, D. E. (1991) Binding of calpain fragments to calpastatin. J Biol. Chem. 266, 11,842–11,850.PubMedGoogle Scholar
  38. 36.
    Babu, Y. S., Bugg, C. E., and Cook, W. J. (1988) Structure of calmodulin refined at 2.2 Å resolution. J Mol. Biol. 204, 191–204.CrossRefPubMedGoogle Scholar
  39. 37.
    Herzberg, O. and James, M. N. (1988) Refined crystal structure of troponin C from turkey skeletal muscle at 2.0 Å resolution. J Mol. Biol. 203, 761–779.CrossRefPubMedGoogle Scholar
  40. 38.
    Vijay-Kumar, S. and Cook, W. J. (1992) Structure of a sarcoplasmic calcium-binding protein from Nereis diversicolor refined at 2.0 Å resolution. J Mol. Biol. 224, 413–426.CrossRefPubMedGoogle Scholar
  41. 39.
    Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J Mol. Biol. 233, 123–138.CrossRefPubMedGoogle Scholar
  42. 40.
    Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M. (1997) CATH — a hierarchic classification of protein domain structures. Structure 5, 1093–1108.CrossRefPubMedGoogle Scholar
  43. 41.
    Maki, M., Narayana, S. V., and Hitomi, K. (1997) A growing family of the Ca2+-binding proteins with five EF-hand motifs. Biochem. J. 328, 718–720.PubMedGoogle Scholar
  44. 42.
    Kraulis, P. J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl. Crystallogr. 24, 946–950.CrossRefGoogle Scholar
  45. 43.
    Merritt, E. A. and Bacon, D. J. (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol. 277, 505–524.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press Inc. 2002

Authors and Affiliations

  • Miroslaw Cygler
    • 1
    • 2
  • Pawel Grochulski
    • 3
  • Helen Blanchard
    • 4
  1. 1.National Research CouncilMontreal
  2. 2.Biotechnology Research InstituteQuebecCanada
  3. 3.BioMep Inc., Department of BiochemistryUniversity of MontrealQuebecCanada
  4. 4.Biochemisches InstitütUniversität ZürichZürichSwitzerland

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