Advertisement

X-Ray Absorption Spectroscopy of Metalloproteins

  • Limei Zhang
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1876)

Abstract

X-ray absorption spectroscopy (XAS) has been widely used as a powerful local structural tool for studying the metal binding sites in metalloproteins, owing to its element specificity, chemical sensitivity, and minimum requirement for sample preparation. The principle subject of this chapter is to provide a general introduction of this technique to molecular biologists and biochemists, with the intention to fill the knowledge gaps in interdisciplinary communication and collaboration. An update of the XAS-based technique applied recently to metalloproteins is also briefly introduced at the end of the chapter.

Key words

X-ray absorption spectroscopy (XAS) X-ray absorption near edge spectrum (XANES) Extended X-ray absorption fine structure (EXAFS) Metalloproteins Metalloclusters 

Notes

Acknowledgments

The data presented in this chapter were collected at the Stanford Synchrotron Radiation Lightsource and Canadian Light Source. EXAFSPAK and IFFEFIT were used for analyzing data and generating figures in this chapter. The author thanks Dr. De-Tong Jiang at the Guelph University and Dr. Graham George at the University of Saskatchewan for invaluable discussions and contributions to the figures.

References

  1. 1.
    Penner-Hahn JE (2005) Characterization of "spectroscopically quiet" metals in biology. Coordin Chem Rev 249:161–177CrossRefGoogle Scholar
  2. 2.
    Rigby K, Zhang L, Cobine PA et al (2007) Characterization of the cytochrome c oxidase assembly factor Cox19 of Saccharomyces cerevisiae. J Biol Chem 282:10233–10242CrossRefGoogle Scholar
  3. 3.
    Coyne HJ 3rd, Ciofi-Baffoni S, Banci L et al (2007) The characterization and role of zinc binding in yeast Cox4. J Biol Chem 282:8926–8934CrossRefGoogle Scholar
  4. 4.
    Lee PA, Citrin PH, Eisenberger P et al (1981) Extended X-ray absorption fine-structure - its strengths and limitations as a structural tool. Rev Mod Phys 53:769–806CrossRefGoogle Scholar
  5. 5.
    Teo BK (1986) Exafs: basic principles and data analysis. Springer-Verlag, New YorkCrossRefGoogle Scholar
  6. 6.
    Koningsberger DC, Prins R (1988) X-ray absorption: principles, applications, techniques of EXAFS, SEXAFS, and XANES. John Wiley and Sons, New York, NYGoogle Scholar
  7. 7.
    Rehr JJ, Albers RC (2000) Theoretical approaches to X-ray absorption fine structure. Rev Mod Phys 72:621–654CrossRefGoogle Scholar
  8. 8.
    Ascone I, Fourme R, Hasnain S et al (2005) Metallogenomics and biological X-ray absorption spectroscopy. J Synchrotron Radiat 12:1–3CrossRefGoogle Scholar
  9. 9.
    George GN, Pickering IJ (2007) X-ray absorption spectroscopy in biology and chemistry. Nato Sec Sci B Phys:97–119Google Scholar
  10. 10.
    Newville M (2014) Fundamentals of XAFS. Rev Mineral Geochem 78:33–74CrossRefGoogle Scholar
  11. 11.
    Lang ND, Williams AR (1978) Theory of atomic chemisorption on simple metals. Phys Rev B 18:616–636CrossRefGoogle Scholar
  12. 12.
    Rehr JJ, Kas JJ, Vila FD et al (2010) Parameter-free calculations of X-ray spectra with FEFF9. Phys Chem Chem Phys 12:5503–5513CrossRefGoogle Scholar
  13. 13.
    George GN (1997) X-ray absorption spectroscopy of molybdenum enzymes. J Biol Inorg Chem 2:790–796CrossRefGoogle Scholar
  14. 14.
    Harris HH, George GN, Rajagopalan KV (2006) High-resolution EXAFS of the active site of human sulfite oxidase: Comparison with density functional theory and X-ray crystallographic results. Inorg Chem 45:493–495CrossRefGoogle Scholar
  15. 15.
    Jiang DT, Chen N, Zhang L et al (2007) XAFS at the canadian light source. AIP Conf Proc 882:893–895CrossRefGoogle Scholar
  16. 16.
    Winick H (1995) Synchrotron radiation sources — a primer. World Scientific, SingaporeCrossRefGoogle Scholar
  17. 17.
    Fontecilla-Camps JC, Nicolet Y (eds) (2014) Metalloproteins: methods and protocols. Humana Press, New York, pp 1–299Google Scholar
  18. 18.
    Mattle D, Zhang L, Sitsel O et al (2015) A sulfur-based transport pathway in Cu+-ATPases. EMBO Rep 16:728–740CrossRefGoogle Scholar
  19. 19.
    Ralle M, Lutsenko S, Blackburn NJ (2003) X-ray absorption spectroscopy of the copper chaperone Hah1 reveals a linear two-coordinate Cu(I) center capable of adduct formation with exogenous thiols and phosphines. J Biol Chem 278:23163–23170CrossRefGoogle Scholar
  20. 20.
    Pickering IJ, Gumaelius L, Harris HH et al (2006) Localizing the biochemical transformations of arsenate in a hyperaccumulating fern. Environ Sci Technol 40:5010–5014CrossRefGoogle Scholar
  21. 21.
    Bjornsson R, Delgado-Jaime MU, Lima FA et al (2015) Molybdenum L-edge XAS spectra of MoFe nitrogenase. Z Anorg Allg Chem 641:65–71CrossRefGoogle Scholar
  22. 22.
    Liu T, Ramesh A, Ma Z et al (2007) CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol 3:60–68CrossRefGoogle Scholar
  23. 23.
    Stern EA, Heald SM (1983) Basic principles and applications of EXAFS. In: Koch EE (ed) Handbook of Synchrotron Radiation. North-Holland, Amsterdam, New York, OxfordGoogle Scholar
  24. 24.
    Sayers DE, Stern EA, Lytle FW (1971) New technique for investigating noncrystalline structures: Fourier analysis of the extended X-ray absorption fine structure. Physl Rev Lett 27:1204CrossRefGoogle Scholar
  25. 25.
    Stern EA (1988) Theory of EXAFS. In: Koningsberger DC, Prins R (eds) X-ray absorption: principles, applications, techniques of EXAFS, SEXAFS, and XANES. John Wiley and Sons, New York, NYGoogle Scholar
  26. 26.
    Tierney DL, Fee JA, Ludwig ML et al (1995) X-ray absorption spectroscopy of the iron site in Escherichia coli Fe(III) superoxide dismutase. Biochemistry 34:1661–1668CrossRefGoogle Scholar
  27. 27.
    Grabolle M, Haumann M, Muller C et al (2006) Rapid loss of structural motifs in the manganese complex of oxygenic photosynthesis by X-ray irradiation at 10-300 k. J Biol Chem 281:4580–4588CrossRefGoogle Scholar
  28. 28.
    George GN, Pickering IJ, Pushie MJ et al (2012) X-ray-induced photo-chemistry and X-ray absorption spectroscopy of biological samples. J Synchrotron Radiat 19:875–886CrossRefGoogle Scholar
  29. 29.
    Pushie MJ, Nienaber KH, McDonald A et al (2014) Combined EXAFS and DFT structure calculations provide structural insights into the 1:1 multi-histidine complexes of Cu(II), Cu(I), and Zn(II) with the tandem octarepeats of the mammalian prion protein. Chemistry 20:9770–9783CrossRefGoogle Scholar
  30. 30.
    Zhang L, Lichtmannegger J, Summer KH et al (2009) Tracing copper-thiomolybdate complexes in a prospective treatment for Wilson's disease. Biochemistry 48:891–897CrossRefGoogle Scholar
  31. 31.
    Wu G, Zhang Y, Ribaud L et al (1998) Multitemperature resonance-diffraction and structural study of the mixed-valence complex [Fe3O(OOCC(CH3)3)6(C5H5N)3]. Inorg Chem 37:6078–6083CrossRefGoogle Scholar
  32. 32.
    Einsle O, Andrade SL, Dobbek H et al (2007) Assignment of individual metal redox states in a metalloprotein by crystallographic refinement at multiple X-ray wavelengths. J Am Chem Soc 129:2210–2211CrossRefGoogle Scholar
  33. 33.
    Zhang L, Kaiser JT, Meloni G et al (2013) The sixteenth iron in the nitrogenase MoFe protein. Angew Chem Int Ed Engl 52:10529–10532CrossRefGoogle Scholar
  34. 34.
    Spatzal T, Schlesier J, Burger EM et al (2016) Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement. Nat Commun 7:10902CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of Nebraska-LincolnLincolnUSA
  2. 2.Redox Biology CenterUniversity of Nebraska-LincolnLincolnUSA
  3. 3.Nebraska Center for Integrated Biomolecular CommunicationUniversity of Nebraska-LincolnLincolnUSA

Personalised recommendations