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X-ray Structural Analysis of S100 Proteins

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Book cover Calcium-Binding Proteins and RAGE

Part of the book series: Methods in Molecular Biology ((MIMB,volume 963))

Abstract

X-ray crystallography is a potent and meanwhile fast technique to obtain detailed structural information of S100 proteins in their apo or metal ion-loaded state. S100 proteins crystallize in the absence or presence of Ca2+ and Zn2+ and the obtained crystals often diffract to high resolution yielding information on the ion-binding sites, conformation, and target interaction sites of the proteins. Here, I describe a general scheme to isolate and crystallize S100 proteins and the analysis of protein crystals using a modern synchrotron source.

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References

  1. Marenholz I, Heizmann CW, Fritz G (2004) S100 proteins in mouse and man: from evolution to function and pathology (including an update of the nomenclature). Biochem Biophys Res Commun 322:1111–1122

    Article  PubMed  CAS  Google Scholar 

  2. Marenholz I, Lovering RC, Heizmann CW (2006) An update of the S100 nomenclature. Biochim Biophys Acta 1763:1282–1283

    Article  PubMed  CAS  Google Scholar 

  3. Fritz G, Heizmann CW (2004) 3D structures of the calcium and zinc binding S100 proteins. In: Messerschmidt A, Bode W, Cygler M, Cygler M (eds) Handbook of metalloproteins, vol 3. Wiley, Chichester, pp 529–540

    Google Scholar 

  4. Santamaria-Kisiel L, Rintala-Dempsey AC, Shaw GS (2006) Calcium-dependent and -independent interactions of the S100 protein family. Biochem J 396:201–214

    Article  PubMed  CAS  Google Scholar 

  5. Kabsch W (2011) XDS. Acta Crystallogr D66:125–132

    Google Scholar 

  6. Battye TG, Kontogiannis L, Johnson O, Powell HR, Leslie AG (2011) iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr D67:271–281

    CAS  Google Scholar 

  7. Pflugrath JW (1999) The finer things in X-ray diffraction data collection. Acta Crystallogr D Biol Crystallogr 55:1718–1725

    Article  PubMed  CAS  Google Scholar 

  8. Vonrhein C, Flensburg C, Keller P, Sharff A, Smart O, Paciorek W, Womack T, Bricogne G (2011) Data processing and analysis with the autoPROC toolbox. Acta Crystallogr D Biol Crystallogr 67:293–302

    Article  PubMed  Google Scholar 

  9. Koch M, Diez J, Wagner A, Fritz G (2010) Crystallization and calcium/sulfur SAD phasing of the human EF-hand protein S100A2. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1032–1036

    Article  PubMed  Google Scholar 

  10. Koch M, Diez J, Fritz G (2008) Crystal structure of Ca2+ -free S100A2 at 1.6Å resolution. J Mol Biol 378:933–942

    Article  PubMed  Google Scholar 

  11. Otterbein LR, Kordowska J, Witte-Hoffmann C, Wang CL, Dominguez R (2002) Crystal structures of S100A6 in the Ca2+-free and Ca2+-bound states: the calcium sensor mechanism of S100 proteins revealed at atomic resolution. Structure 10:557–567

    Article  PubMed  CAS  Google Scholar 

  12. Drohat AC, Amburgey JC, Abildgaard F, Starich MR, Baldisseri D, Weber DJ (1996) Solution structure of rat apo-S100B(beta beta) as determined by NMR spectroscopy. Biochemistry 35:11577–11588

    Article  PubMed  CAS  Google Scholar 

  13. Potts BC, Smith J, Akke M, Macke TJ, Okazaki K, Hidaka H, Case DA, Chazin WJ (1995) The structure of calcyclin reveals a novel homodimeric fold for S100 Ca2+-binding proteins. Nat Struct Biol 2:790–796

    Article  PubMed  CAS  Google Scholar 

  14. Ostendorp T, Diez J, Heizmann CW, Fritz G (2011) The crystal structures of human S100B in the zinc- and calcium-loaded state at three pH values reveal zinc ligand swapping. Biochim Biophys Acta 1813:1083–1091

    Article  PubMed  CAS  Google Scholar 

  15. Moroz OV, Blagova EV, Wilkinson AJ, Wilson KS, Bronstein IB (2009) The crystal structures of human S100A12 in apo form and in complex with zinc: new insights into S100A12 oligomerisation. J Mol Biol 391:536–551

    Article  PubMed  CAS  Google Scholar 

  16. Wilder PT, Varney KM, Weiss MB, Gitti RK, Weber DJ (2005) Solution structure of zinc- and calcium-bound rat S100B as determined by nuclear magnetic resonance spectroscopy. Biochemistry 44:5690–5702

    Article  PubMed  CAS  Google Scholar 

  17. Sastry M, Ketchem RR, Crescenzi O, Weber C, Lubienski MJ, Hidaka H, Chazin WJ (1998) The three-dimensional structure of Ca2+-bound calcyclin: implications for Ca2+signal transduction by S100 proteins. Structure 6:223–231

    Article  PubMed  CAS  Google Scholar 

  18. Keegan RM, Winn MD (2007) Automated search-model discovery and preparation for structure solution by molecular replacement. Acta Crystallogr D Biol Crystallogr 63:447–457

    Article  PubMed  Google Scholar 

  19. McCoy AJ (2007) Solving structures of protein complexes by molecular replacement with Phaser. Acta Crystallogr D Biol Crystallogr 63:32–41

    Article  PubMed  Google Scholar 

  20. Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr D67:355–367

    Article  CAS  Google Scholar 

  21. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr D53:240–255

    Article  CAS  Google Scholar 

  22. Brunger AT, Adams PD, Clore GM, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges N, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D54:905–921

    CAS  Google Scholar 

  23. Brunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728–2733

    Article  PubMed  CAS  Google Scholar 

  24. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221

    Article  PubMed  Google Scholar 

  25. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr D60:2126–2132

    Article  CAS  Google Scholar 

  26. Ostendorp T, Heizmann CW, Kroneck PM, Fritz G (2005) Purification, crystallization and preliminary X-ray diffraction studies on human Ca2+-binding protein S100B. Acta Crystallogr F61:673–675

    CAS  Google Scholar 

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Acknowledgments

This work was supported by grants FR14488/3-1 and FR1488/5-1 from the Deutsche Forschungsgemeinschaft (DFG).

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Authors and Affiliations

  1. Department of Neuropathology, Neurozentrum, University of Freiburg, Freiburg, Germany

    Günter Fritz

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  1. Günter Fritz
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Correspondence to Günter Fritz .

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Editors and Affiliations

  1. Div of Clinical Chem & Biochem, Department of Pediatrics, University of Zürich, Steinwiesstrasse 75, Zürich, 8032, Switzerland

    Claus W. Heizmann

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Fritz, G. (2013). X-ray Structural Analysis of S100 Proteins. In: Heizmann, C. (eds) Calcium-Binding Proteins and RAGE. Methods in Molecular Biology, vol 963. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-230-8_6

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  • DOI: https://doi.org/10.1007/978-1-62703-230-8_6

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-229-2

  • Online ISBN: 978-1-62703-230-8

  • eBook Packages: Springer Protocols

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