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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Penner-Hahn JE (2005) Characterization of "spectroscopically quiet" metals in biology. Coordin Chem Rev 249:161–177
Rigby K, Zhang L, Cobine PA et al (2007) Characterization of the cytochrome c oxidase assembly factor Cox19 of Saccharomyces cerevisiae. J Biol Chem 282:10233–10242
Coyne HJ 3rd, Ciofi-Baffoni S, Banci L et al (2007) The characterization and role of zinc binding in yeast Cox4. J Biol Chem 282:8926–8934
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 53:769–806
Teo BK (1986) Exafs: basic principles and data analysis. Springer-Verlag, New York
Koningsberger DC, Prins R (1988) X-ray absorption: principles, applications, techniques of EXAFS, SEXAFS, and XANES. John Wiley and Sons, New York, NY
Rehr JJ, Albers RC (2000) Theoretical approaches to X-ray absorption fine structure. Rev Mod Phys 72:621–654
Ascone I, Fourme R, Hasnain S et al (2005) Metallogenomics and biological X-ray absorption spectroscopy. J Synchrotron Radiat 12:1–3
George GN, Pickering IJ (2007) X-ray absorption spectroscopy in biology and chemistry. Nato Sec Sci B Phys:97–119
Newville M (2014) Fundamentals of XAFS. Rev Mineral Geochem 78:33–74
Lang ND, Williams AR (1978) Theory of atomic chemisorption on simple metals. Phys Rev B 18:616–636
Rehr JJ, Kas JJ, Vila FD et al (2010) Parameter-free calculations of X-ray spectra with FEFF9. Phys Chem Chem Phys 12:5503–5513
George GN (1997) X-ray absorption spectroscopy of molybdenum enzymes. J Biol Inorg Chem 2:790–796
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 45:493–495
Jiang DT, Chen N, Zhang L et al (2007) XAFS at the canadian light source. AIP Conf Proc 882:893–895
Winick H (1995) Synchrotron radiation sources — a primer. World Scientific, Singapore
Fontecilla-Camps JC, Nicolet Y (eds) (2014) Metalloproteins: methods and protocols. Humana Press, New York, pp 1–299
Mattle D, Zhang L, Sitsel O et al (2015) A sulfur-based transport pathway in Cu+-ATPases. EMBO Rep 16:728–740
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 278:23163–23170
Pickering IJ, Gumaelius L, Harris HH et al (2006) Localizing the biochemical transformations of arsenate in a hyperaccumulating fern. Environ Sci Technol 40:5010–5014
Bjornsson R, Delgado-Jaime MU, Lima FA et al (2015) Molybdenum L-edge XAS spectra of MoFe nitrogenase. Z Anorg Allg Chem 641:65–71
Liu T, Ramesh A, Ma Z et al (2007) CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator. Nat Chem Biol 3:60–68
Stern EA, Heald SM (1983) Basic principles and applications of EXAFS. In: Koch EE (ed) Handbook of Synchrotron Radiation. North-Holland, Amsterdam, New York, Oxford
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 27:1204
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, NY
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 34:1661–1668
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 281:4580–4588
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 19:875–886
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 20:9770–9783
Zhang L, Lichtmannegger J, Summer KH et al (2009) Tracing copper-thiomolybdate complexes in a prospective treatment for Wilson's disease. Biochemistry 48:891–897
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 37:6078–6083
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 129:2210–2211
Zhang L, Kaiser JT, Meloni G et al (2013) The sixteenth iron in the nitrogenase MoFe protein. Angew Chem Int Ed Engl 52:10529–10532
Spatzal T, Schlesier J, Burger EM et al (2016) Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement. Nat Commun 7:10902
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Zhang, L. (2019). X-Ray Absorption Spectroscopy of Metalloproteins. In: Hu, Y. (eds) Metalloproteins. Methods in Molecular Biology, vol 1876. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8864-8_12
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8864-8_12
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8863-1
Online ISBN: 978-1-4939-8864-8
eBook Packages: Springer Protocols