Solution structures of chicken parvalbumin 3 in the Ca 2+-free and Ca 2+-bound states

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 3, 2011, Pages 752-764

  Henzl, Michael T ^a   Tanner, John J ^a,b   Tan, Anmin ^a  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

Ca 2+ binding protein; EF hand protein; NMR; Protein structure; Protein ligand interaction

Indexed keywords

CALCIUM ION; PARVALBUMIN; PROTEIN CPV 3; UNCLASSIFIED DRUG;

ARTICLE; CHICKEN; HYDROPHOBICITY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; ANIMALS; CALCIUM; CHICKENS; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PARVALBUMINS; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID;

AVES; RATTUS;

EID: 79551480505     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22915     Document Type: Article

References (63)

1. Kretsinger RH. Structure and evolution of calcium-modulated proteins. CRC Crit Rev Biochem 1980; 8: 119-174.
2. Kawasaki H, Kretsinger RH. Calcium-binding proteins 1: EF-hands. Protein Profile 1995; 2: 297-490.
3. Celio MR, Pauls T, Schwaller B. Guidebook to the calcium-binding proteins. Oxford: Oxford University Press; 1996.
4. Kawasaki H, Nakayama S, Kretsinger RH. Classification and evolution of EF-hand proteins. Biometals 1998; 11: 277-295.
5. Kretsinger RH, Nockolds CE. Carp muscle calcium-binding protein. II. Structure determination and general description. J Biol Chem 1973; 248: 3313-3326.
6. 2+-binding proteins parvalbumin and oncomodulin and their genes: new structural and functional findings. Biochim Biophys Acta 1996; 1306: 39-54.
7. 2+ buffers. Cell Mol Life Sci 2009; 66: 275-300.
8. Goodman M, Pechere JF. The evolution of muscular parvalbumins investigated by the maximum parsimony method. J Mol Evol 1977; 9: 131-158.
9. Moncrief ND, Kretsinger RH, Goodman M. Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences. J Mol Evol 1990; 30: 522-562.
10. Swain AL, Kretsinger RH, Amma EL. 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 1989; 264: 16620-16628.
11. Roquet F, Declercq JP, Tinant B, Rambaud J, Parello J. Crystal structure of the unique parvalbumin component from muscle of the leopard shark (Triakis semifasciata). The first X-ray study of an alpha-parvalbumin J Mol Biol 1992; 223: 705-720.
12. Declercq JP, Evrard C, Lamzin V, Parello J. Crystal structure of the EF-hand parvalbumin at atomic resolution (0.91 Å) and at low temperature (100 K). Evidence for conformational multistates within the hydrophobic core. Protein Sci 2010; 8: 2194-2204.
13. McPhalen CA, Sielecki AR, Santarsiero BD, James MNG. Refined crystal structure of rat parvalbumin, a mammalian α-lineage parvalbumin, at 2.0 Å resolution. J Mol Biol 1994; 235: 718-732.
14. Bottoms CA, Schuermann JP, Agah S, Henzl MT, Tanner JJ. Crystal structure of rat α-parvalbumin at 1.05 Å resolution. Protein Sci 2004; 13: 1724-1734.
15. Ahmed FR, Rose DR, Evans SV, Pippy ME, To R. Refinement of recombinant oncomodulin at 1.30 Å resolution. J Mol Biol 1993; 230: 1216-1224.
16. 2+-free rat β-parvalbumin (oncomodulin). Protein Sci 2007; 16: 1914-1926.
17. 2+-free rat α-parvalbumin. Protein Sci 2008; 17: 431-438.
18. Hapak RC, Zhao H, Boschi JM, Henzl MT. Novel avian thymic parvalbumin displays high degree of sequence homology to oncomodulin. J Biol Chem 1994; 269: 5288-5296.
19. Gillen MF, Banville D, Rutledge RG, Narang S, Seligy VL, Whitfield JF, MacManus JP. A complete complementary DNA for the oncodevelopmental calcium-binding protein, oncomodulin. J Biol Chem 1987; 262: 5308-5312.
20. Barger B, Pace JL, Ragland WL. Purification and partial characterization of an avian thymic hormone. Thymus 1991; 17: 181-197.
21. Hapak RC, Stanley CM, Henzl MT. Intrathymic distribution of the two avian thymic parvalbumins. Exp Cell Res 1996; 222: 234-245.
22. Novak R, Henzl MT, Ragland WL. Receptor cells for the CPV3 parvalbumin of chicken thymus in spleen and caecal tonsils. J Allergy Clin Immunol 99: S202, 1997.
23. Novak R, Brewer JM, Ragland WL. Immunophenotype of splenic lymphocytes with receptors for avian thymic hormone. FASEB J 1996; 10: A1048.
24. Rada JA, Denis CS. Analysis of gene expression during the recovery from experimental myopia. Mol Biol Cell 2003; 14: 367a.
25. 2+ buffer in hair cells. J Assoc Res Otolaryngol 2002; 3: 488-498.
26. Henzl MT, Shibasaki O, Comegys TH, Thalmann I, Thalmann R. Oncomodulin is abundant in the organ of Corti. Hear Res 1997; 106: 105-111.
27. Sakaguchi N, Henzl MT, Thalmann I, Thalmann R, Schulte BA. Oncomodulin is expressed exclusively by outer hair cells in the organ of Corti. J Histochem Cytochem 1998; 46: 29-39.
28. Henzl MT, Agah S. Divalent ion-binding properties of the two avian β-parvalbumins. Proteins 2006; 62: 270-278.
29. Henzl MT, Larson JD, Agah S. Influence of monovalent cations on rat α- and β-parvalbumin stabilities. Biochemistry 2000; 39: 5859-5867.
30. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995; 6: 277-293.
31. Goddard TD, Kneller DG. Sparky 3, University of California, San Francisco. 2007.
32. 15N spectra of larger proteins: Heteronuclear triple-resonance three-dimensional NMR spectroscopy. Appl Calmodulin Biochem 1990; 29: 4659-4667.
33. 13C enriched proteins. J Biomol NMR 1991; 1: 99-104.
34. 2O saturation. J Magn Reson 1994; 109: 129-133.
35. Muhandiram DR, Kay LE. Gradient-enhanced triple-resonance three-dimensional NMR experiments with improved sensitivity. J Magn Reson 1994; 103: 203-216.
36. Grzesiek S, Bax A. Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 1992; 114: 6291-6293.
37. Lohr F, Ruterjans H. A new triple-resonance experiment for the sequential assignment of backbone resonances in proteins. J Biomol NMR 2005; 6: 189-197.
38. 15N-enriched proteins by isotropic mixing of carbon-13 magnetization. J Magn Reson 1993; 101: 114-119.
39. 15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1β. Biochemistry 1989; 28: 6150-6156.
40. Kay LE, Xu GY, Singer AU, Muhandiram DR, Forman-Kay JD. A gradient-enhanced HCCH-TOCSY experiment for recording side-chain proton and carbon-13 correlations in water samples of proteins. J Magn Reson 1993; B101: 333-337.
41. 13C-labeled proteins via scalar couplings. J Am Chem Soc 1993; 115: 11054-11055.
42. 13C labeling. Biochemistry 1989; 28: 7510-7516.
43. Marion D, Kay LE, Sparks SW, Torchia D, Bax A. Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins. J Am Chem Soc 1989; 111: 1515-1517.
44. Cornilescu G, Delaglio F, Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 1999; 13: 289-302.
45. Güntert P. Automated NMR structure calculation with CYANA. In: Downing AK, editor. Protein NMR techniques. Totowa, NJ: Humana Press; 2004. pp 353-378.
46. Herrmann T, Güntert P, Wüthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 2002; 319: 209-227.
47. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993; 26: 283-291.
48. Dosset P, Hus J-C, Blackledge M, Marion D. Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 2000; 16: 23-28.
49. 15N NMR relaxation. J Am Chem Soc 1995; 117: 12562-12566.
50. Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 1982; 104: 4546-4559.
51. Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results J Am Chem Soc 1982; 104: 4559-4570.
52. Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 1990; 112: 4989-4991.
53. 1H NMR spectroscopy. Biochemistry 1990; 29: 7387-7401.
54. Mandel AM, Akke M, Palmer IIIAG. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J Mol Biol 1995; 246: 144-163.
55. DeLano WL. The PyMOL molecular graphics system, Version 1.3, Schrödinger, LLC. 2002.
56. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998; 54: 905-921.
57. Hubbard SJ, Thornton JM. NACCESS. London: Department of Biochemistry and Molecular Biology, University College London; 1993.
58. Krishnan VV, Cosman M. An empirical relationship between rotational correlation time and solvent accessible surface area. J Biomol NMR 1998; 12: 177-182.
59. 15N nuclear magnetic resonance relaxation studies on rat β-parvalbumin and the pentacarboxylate variants, S55D and G98D. Protein Sci 2002; 11: 158-173.
60. Henzl MT, Davis ME, Tan A. Leucine-85 is an important determinant of divalent ion affinity in rat β-parvalbumin (oncomodulin). Biochemistry 2008; 47: 13635-13646.
61. 2+-bound states. J Mol Biol 2010; 397: 991-1002.
62. 2+-specific conformational change in avian thymic hormone, a high-affinity β-parvalbumin. Biochemistry 2009; 48: 3936-3945.
63. Henzl MT, Agah S, Larson JD. Association of the AB and CD-EF domains from rat α- and β-parvalbumin. Biochemistry 2004; 43: 10906-10917.