Skip to main content
SpringerLink
Log in

X-Ray Absorption Spectroscopy: Determination of Transition Metal Site Structures in Photosynthesis

  • Chapter
Book cover Biophysical Techniques in Photosynthesis

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 3))

  • 675 Accesses

Summary

This chapter gives a brief description of the theory and experimental methodology involved in X-ray absorption Spectroscopy, both X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS). The advantages and limitations of the methods are discussed. Several examples of applications of X-ray absorption Spectroscopy in the field of photosynthesis are presented.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Andrews JC, Cinco R, Dau H, Latimer MJ, Liang W, Roelofs TA, Rompel A, Sauer K, Yachandra VK and Klein MP (1994) Photosynthetic water oxidation: Structural insights to the catalytic manganese complex. Physica B 208: 657–659.

    Google Scholar 

  • Bertagnolli H and Ertel TS (1994) X-ray absorption spectroscopy of amorphous solids, liquids, and catalytic and biochemical systems — capabilities and limitations. Angew Chem Int Ed Engl 33: 45–66.

    Article  Google Scholar 

  • Bianconi A (1988) XANES spectroscopy. In: Koningsberger DC and Prins R (ed) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 573–662 John Wiley, New York.

    Google Scholar 

  • Blackburn NJ (1990) EXAFS studies of copper proteins. In: Hasnain SS (ed) Synchrotron Radiation in Biophysics, pp 63–103. Ellis Horwood, Chichester, UK.

    Google Scholar 

  • Britt RD, Sauer K, Klein MP, Knaff DB, Kriauciunas A, Yu C-A, Yu L and Malkin R (1991) Electron spin echo envelope modulation spectroscopy supports the suggested coordination of two histidine ligands to the Rieske Fe-S centers of the cytochrome b 6f complex of spinach and cytochrome bc 1 complexes of Rhodospirillum rubrum, Rhodobacter sphaeroides R-26, and bovine heart mitochondria. Biochemistry 30: 1892–1901.

    Article  PubMed  CAS  Google Scholar 

  • Bunker G, Stern EA, Blankenship RE and Parson WW (1982) An X-ray absorption study of the iron site in bacterial photosynthetic reaction centers. Biophys J 37: 539–551.

    PubMed  CAS  Google Scholar 

  • Carmelli C, Huang JY, Mills DM, Jagendorf AT and Lewis A (1986) Extended X-ray absorption fine structure of and Mn2+ and Mn2+-ATP complex bound to coupling factor 1 of the H+-ATPase from chloroplasts J Biol Chem 261: 16969–16975.

    Google Scholar 

  • Conradson SD, Burgess BK, Newton WE, Hodgson KO, McDonald JW, Rubinson JF, Gheller SF, Mortenson LE, Adams MWW, Mascharak PK, Armstrong WA and Holm RH (1985) Structural insights from the Mo K-edge X-ray absorption near edge structure of the iron-molybdenum protein of nitrogenase and its iron-molybdenum cofactor by comparison with synthetic Fe-Mo-S clusters. J Am Chem Soc 107: 7935–7940.

    Article  CAS  Google Scholar 

  • Cramer SP (1988) Biological applications of XAS, In: Koningsberger DC and Prins R (eds) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 257–320. John Wiley and Sons, New York.

    Google Scholar 

  • Cramer SP, Tench O, Yocum M and George GN (1988) A 13-element Ge detector for fluorescence EXAFS. Nucl Instrum Methods A266; 586–591.

    CAS  Google Scholar 

  • Debus R (1992) The manganese and calcium ions of photosynthetic oxygen evolution. Biochim Biophys Acta 110: 269–352.

    Google Scholar 

  • DeRose VJ, Mukerji I, Latimer MJ, Yachandra VK, Sauer K and Klein MP (1994) Comparison of the manganese oxygen-evolving complex in photosystem II of spinach and Synechococcus sp. with multinuclear manganese model compounds by X-ray absorption spectroscopy. J Am Chem Soc 116: 5239–5249.

    Article  Google Scholar 

  • Durham PJ (1988) Theory of XANES. In: Koningsberger DC and Prins R (eds) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 53–84. John Wiley and Sons, New York.

    Google Scholar 

  • Eisenberger P and Kincaid BM (1978) EXAFS: New horizons in structure determinations. Science 200: 1441–1447.

    PubMed  CAS  Google Scholar 

  • Eisenberger P, Okamura MY and Feher G (1982) The electronic structure of Fe2+ in reaction centers from Rhodopseudomonas sphaeroides II. Extended X-ray absorption fine structure. Biophys J 37: 523–538.

    Article  PubMed  CAS  Google Scholar 

  • George GN, Prince RC and Cramer SP (1989) The manganese site of the photosynthetic water-splitting enzyme. Science 243: 789–791.

    PubMed  CAS  Google Scholar 

  • Goodin DB (1983) The local structure of manganese in the photosynthetic apparatus and superoxide dismutase: An X-ray absorption study. Ph D Dissertation. Universtity of California, Berkeley, CA, USA Lawrence Berkeley Laboratory Report, LBL-16901.

    Google Scholar 

  • Goodin DB, Yachandra VK, Britt RD, Sauer K and Klein MP (1984) State of manganese in the photosynthetic apparatus. 3 Light-induced changes in X-ray absorption (K-edge) energies of manganese in photosynthetic membranes. Biochim Biophys Acta 767: 209–216.

    CAS  Google Scholar 

  • Guiles RD (1988) Structure and Function of the Manganese Complex Involved in Photosynthetic Oxygen Evolution Determined by X-ray Absorption Spectroscopy and Electron Paramagnetic Resonance Spectroscopy. Ph D Dissertation University of California, Berkeley, CA, USA, Lawrence Berkeley Laboratory Report, LBL-25186.

    Google Scholar 

  • Guiles RD, Yachandra VK, McDermott AE, Cole JL, Dexheimer SL, Britt RD, Sauer K and Klein MP (1990a) The S0 state of photosystem II induced by hydroxylamine: differences between the structure of the manganese complex in the S0 and S1 states determined by X-ray absorption spectroscopy. Biochemistry 29: 486–496.

    PubMed  CAS  Google Scholar 

  • Guiles RD, Zimmermann J-L, McDermott AE, Yachandra VK, Cole J, Dexheimer SL, Britt RD, Wieghardt K, Bossek U, Sauer K and Klein MP (1990b) The S3 state of photosystem II: differences between the structure of the manganese complex in the S2 and S3 states determined by X-ray absorption spectroscopy. Biochemistry 29: 471–485.

    PubMed  CAS  Google Scholar 

  • Gurbiel RJ, Ohnishi T, Robertson DE, Daldal F and Hoffman BM (1991) Q-band ENDOR spectra of the Rieske protein from Rhodobactor capsulatus ubiquinol-cytochrome c oxidoreductase show two histidines coordinated to the [2Fe-2S] cluster. Biochemistry 30: 11579–11584.

    Article  PubMed  CAS  Google Scholar 

  • Heald SM (1988a) Design of an EXAFS experiment. In: Koningsberger DC and Prins R (eds) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 87–118. John Wiley and Sons, New York.

    Google Scholar 

  • Heald SM (1988b) EXAFS with synchrotron radiation. In: Koningsberger DC and Prins R (eds) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 119–161. John Wiley and Sons, New York.

    Google Scholar 

  • Jaklevic J, Kirby JA, Klein MP, Robertson AS, Brown GS and Eisenberger P (1977) Fluorescence detection of EX-AFS-sensitivity enhancement for dilute species and thin films. Solid State Commun 23: 679–682.

    Article  CAS  Google Scholar 

  • Kirby JA, Goodin DB, Wydrzynski T, Robertson AC and Klein MP (1981) State of manganese in the photosynthetic apparatus. 2 X-ray absorption edge studies on manganese in photosynthetic membranes. J Am Chem Soc 103: 5537–5542.

    CAS  Google Scholar 

  • Klein MP, Sauer K and Yachandra VK (1993) Perspectives on the structure of the photosynthetic oxygen evolving manganese complex and its relation to the Kok cycle. Photosynth Res 38: 265–277.

    Article  CAS  Google Scholar 

  • Krauss N, Hinrichs W, Witt I, Fromme P, Pritzkow W, Dauter Z, Betzel C, Wilson KS, Witt H and Saenger W (1993) 3-Dimensional structure of system-I of photosynthesis at 6 angstrom resolution. Nature (London) 361: 326–331.

    Article  CAS  Google Scholar 

  • Kutzler FW, Natoli CR, Misemer DK, Doniach S and Hodgson KO (1980) Use of one-electron theory for the interpretation of near edge structure in K-shell X-ray absorption spectra of transition metal complexes. J Chem Phys 73: 3274–3288.

    Article  CAS  Google Scholar 

  • Latimer MJ, DeRose VJ, Mukerji I, Yachandra VK, Sauer K and Klein MP (1995) Evidence for the proximity of calcium to the manganese cluster of photosystem II: Determination by X-ray absorption spectroscopy. Biochemistry 34: 10898–10909.

    Article  PubMed  CAS  Google Scholar 

  • Lee PA, Citrin PH, Eisenberger P and Kincaid BM (1981) Extended X-ray absorption fine structure — Its strengths and limitations as a structural tool. Rev Mod Phys 53: 769–806.

    Article  CAS  Google Scholar 

  • MacLachlan DJ, Hallahan BJ, Ruffle SV, Nugent JHA, Evans MCW, Strange RW and Hasnain SS (1992) A EXAFS study of the manganese O2-evolving complex in purified photosystem II membrane fractions. Biochem J 285: 569–576.

    PubMed  CAS  Google Scholar 

  • McDermott AE, Yachandra VK, Guiles RD, Britt RD, Dexheimer SL, Sauer K and Klein MP (1988a) Low-potential iron-sulfur centers in photosystem I: An X-ray absorption spectroscopy study. Biochemistry 27: 4013–4020.

    PubMed  CAS  Google Scholar 

  • McDermott AE, Yachandra VK, Guiles RD, Cole JL, Britt RD, Dexheimer SL, Sauer K and Klein MP (1988b) Characterization of the manganese O2-evolving complex and the iron-quinone acceptor complex in photosystem II from a thermophilic cyanobacterium by electron paramagnetic resonance and X-ray absorption spectroscopy. Biochemistry 27: 4021–4031.

    PubMed  CAS  Google Scholar 

  • McDermott AE, Yachandra VK, Guiles RD, Sauer K, MP Klein, Parrett KG and Golbeck J (1989) EXAFS structural study of Fx the low potential Fe-S center in photosystem I Biochemistry 28: 8056–8059.

    Article  PubMed  CAS  Google Scholar 

  • McKale AG, Veal BW, Paulikas AP, Chan SK and Knapp GS (1988) Improved ab initio calculations of amplitude and phase functions for extended X-ray absorption fine structure spectroscopy. J Am Chem Soc 110: 3763–3768.

    Article  CAS  Google Scholar 

  • Mukerji I, Andrews JC, DeRose VJ, Latimer MJ, Yachandra VK, Sauer K and Klein MP (1994) Orientation of the oxygen-evolving manganese complex in a photosystem II membrane preparation: An X-ray absorption spectroscopy study. Biochemistry 33: 9712–9721.

    PubMed  CAS  Google Scholar 

  • Ono T-A, Noguchi T, Inoue Y, Kusunoki M, Matsushita T and Oyanagi H (1992) X-ray detection of the period-four cycling of the manganese cluster in the photosynthetic water oxidizing enzyme. Science 258:1335–1337.

    CAS  PubMed  Google Scholar 

  • Pecoraro VL (1992) Structurally diverse manganese coordination compounds. In: Pecoraro VL (ed) Manganese Redox Enzymes, pp 197–231, VCH Publishers, New York.

    Google Scholar 

  • Pendry JB (1983) The transition between XANES and EXAFS. In: Bianconi A, Incoccia L and Stipcich S (eds) EXAFS and Near Edge Structure, p 4. Springer-Verlag, Berlin.

    Google Scholar 

  • Penner-Hahn JE, Fronko RM, Pecoraro VL, Yocum CF, Betts SD and Bowlby NR (1990) Structural characterization of the manganese sites in the photosynthetic oxygenevolving complex using X-ray absorption spectroscopy. J Am Chem Soc 112: 2549–2557.

    Article  CAS  Google Scholar 

  • Powers L (1982) X-ray absorption spectroscopy: applications to biological molecules. Biochim Biophys Acta 683: 1–38.

    PubMed  CAS  Google Scholar 

  • Powers L, Schägger H, von Jagow G, Smith J, Chance B and Ohnishi T (1989) EXAFS studies of the isolated bovine heart Rieske [2Fe-2S]1+(1+,2+) cluster. Biochim Biophys Acta 975: 293–298.

    PubMed  CAS  Google Scholar 

  • Rehr JJ, de Leon JM, Zabinsky SI and Albers RC (1991) Theoretical X-ray absorption fine structure standards. J Am Chem Soc 113: 5135–5140.

    Article  CAS  Google Scholar 

  • Rehr JJ, Albers RC and Zabinsky SI (1992) High-order multiple-scattering calculations of X-ray absorption fine structure. Phys Rev Lett 69: 3397–3400.

    Article  PubMed  CAS  Google Scholar 

  • Roe AL, Schneider DJ, Mayer RJ, Pyrz JW, Widom J and Que L (1984) X-ray absorption spectroscopy of iron-tyrosinate proteins. J Am Chem Soc 106: 1676–1681.

    Article  CAS  Google Scholar 

  • Roelofs TA, Liang W, Latimer MJ, Cinco R, Rompel A, Andrews JC, Yachandra VK, Sauer K and Klein MP (1995) Manganese oxidation states of the flash-induced S-states of photosystem II. In: Mathis P (ed) Photosynthesis from Light to Biosphere, Vol. II, pp 459–462. Kluwer Academic Publishers, Dordrecht.

    Google Scholar 

  • Rutherford AW, Zimmermann, J-L and Boussac A (1992) Oxygen evolution. In: Barber J (ed) The Photosystems: Structure, Function and Molecular Biology, pp 179–229. Elsevier, Amsterdam.

    Google Scholar 

  • Rypniewski WR, Breiter DR, Benning MM, Wesenberg G, Oh B-H, Markley JL, Rayment I and Holden HM (1991) Crystallization and structure determination to 2.5 Å resolution of the oxidized [2Fe-2S] ferredoxin isolated from Anabaena 7120 Biochemistry 30: 4126–4131

    Article  PubMed  CAS  Google Scholar 

  • Sauer K, Yachandra VK, Britt RD and Klein MP (1992) The photosynthetic water oxidation complex studied by EPR and X-ray absorption spectroscopy. In: Pecoraro VL (ed) Manganese Redox Enzymes, pp 141–175. VCH Publishers, New York.

    Google Scholar 

  • Sayers DE and Bunker BA (1988) Data Analysis. In: Koningsberger DC and Prins R (eds) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 211–253. John Wiley and Sons, New York.

    Google Scholar 

  • Sayers DE, Stern EA and Lytle FW (1971) New technique for investigating noncrystalline structures: Fourier analysis of the extended X-ray absorption fine structure. Phys Rev Lett 27: 1204–1207.

    Article  CAS  Google Scholar 

  • Scott RA (1984) X-ray absorption spectroscopy. In: Rousseau RL (ed) Structural and Resonance Techniques in Biological Research, pp 295–362. Academic Press, Orlando, FL.

    Google Scholar 

  • Scott RA and Eidsness MK (1988) The use of X-ray absorption spectroscopy for detection of metal-metalinteractions. Applications to copper-containing enzymes. Comments Inorg Chem 7: 235–267.

    CAS  Google Scholar 

  • Shulman RG, Yafet Y, Eisenberger P and Blumberg, WE (1976) Observation and interpretation of X-ray absorption edges in iron compounds and proteins. Proc Natl Acad Sci USA, 73: 1384–1388.

    PubMed  CAS  Google Scholar 

  • Spiro TG (1982) Iron-Sulfur Proteins. John Wiley, New York

    Google Scholar 

  • Stern E (1988) Theory of EXAFS. In: Koningsberger DC and Prins R (ed) X-ray Absorption: Principles, Applications, Techniques of EXAFS, SEXAFS and XANES, pp 3–51. John Wiley and Sons, New York.

    Google Scholar 

  • Stöhr J (1992) NEXAFS Spectroscopy. Springer-Verlag, Berlin.

    Google Scholar 

  • Teo B-K (1986) EXAFS: Basic Principles and Data Analysis. Springer-Verlag, New York.

    Google Scholar 

  • Teo B-K and Shulman RG (1982) X-ray absorption studies of iron-sulfur proteins and related compounds. In: Spiro TG (ed,) pp 343–366. John Wiley and Sons, New York.

    Google Scholar 

  • Tsang H-T, Batie CJ, Ballou DP and Penner-Hahn JE (1989) X-ray absorption spectroscopy of the [2Fe-2S] Rieske cluster in Pseudomonas cepacia phthalate dioxygenase. Determination of core dimensions and iron ligation. Biochemistry 28: 7233–7240.

    Article  PubMed  CAS  Google Scholar 

  • Tsukihara T, Fukuyama K, Tahara H, Katsube Y, Matsuura Y, Tanaka N, Kakudo M, Wada K, and Matsubara H (1978) X-ray analysis of ferredoxin from Spirulina platensis. II Chelate structure of active center. J Biochem (Tokyo) 84: 1645–1647.

    CAS  Google Scholar 

  • Wieghardt K (1989) The active site in manganese-containing metalloproteins and inorganic model compounds. Angew Chem Int Ed Engl 28: 1153–1172.

    Article  Google Scholar 

  • Yachandra, VK (1995) X-ray absorptionspectroscopy and applications in structural biology. In: Sauer K (ed) Methods in Enzymology. Biochemical Spectroscopy Vol 246. pp 638–675. Academic Press, Orlando, FL.

    Google Scholar 

  • Yachandra VK, DeRose VJ, Latimer MJ, Mukerji I, Sauer K and Klein MP (1993) Where plants make oxygen: A structural model for the photosynthetic oxygen evolving manganese cluster. Science 260: 675–679.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Structural Biology Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, 94720, USA

    Vittal K. Yachandra & Melvin P. Klein

Authors
  1. Vittal K. Yachandra
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Melvin P. Klein
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Department of Biophysics Huygens Laboratory, University of Leiden, 2300 RA, Leiden, The Netherlands

    Jan Amesz  & Arnold J. Hoff  & 

Rights and permissions

Reprints and permissions

Copyright information

© 1996 Kluwer Academic Publishers

About this chapter

Cite this chapter

Yachandra, V.K., Klein, M.P. (1996). X-Ray Absorption Spectroscopy: Determination of Transition Metal Site Structures in Photosynthesis. In: Amesz, J., Hoff, A.J. (eds) Biophysical Techniques in Photosynthesis. Advances in Photosynthesis and Respiration, vol 3. Springer, Dordrecht. https://doi.org/10.1007/0-306-47960-5_21

Download citation

  • DOI: https://doi.org/10.1007/0-306-47960-5_21

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-0-7923-3642-6

  • Online ISBN: 978-0-306-47960-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation