Skip to main content
SpringerLink
Log in

Techniques for Functional and Structural Modeling of Nitrogenase

  • Protocol
  • First Online:
Nitrogen Fixation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 766))

Abstract

Synthetic compounds play an important role in developing our understanding of nitrogenase enzymes, and over the years, a multitude of new metal-containing compounds have been created using nitrogenase as an inspiration. The techniques for handling coordination compounds in organic solvents are different than those commonly encountered in a biochemistry or molecular biology laboratory. This chapter describes the precautions that are essential for successful synthesis of air- and moisture-sensitive synthetic compounds and gives details of the synthesis of some coordinatively unsaturated iron-dinitrogen and iron-sulfide compounds of interest in nitrogenase research.

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

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
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

References

  1. Ibers JA, Holm RH (1980) Modeling Coordination Sites in Metallobiomolecules. Science 209:223–235

    Article  PubMed  CAS  Google Scholar 

  2. Holm RH, Solomon EI (2004) Preface: Biomimetic Inorganic Chemistry. Chem Rev 104:347–348

    Article  PubMed  CAS  Google Scholar 

  3. Holland PL (2004) Nitrogen Fixation. In: McCleverty J, Meyer TJ (eds) Comprehensive Coordination Chemistry II, pp. 569–599. Elsevier, Oxford

    Google Scholar 

  4. Watt GD, Reddy KRN (1994) Formation of an all Ferrous Fe4S4 Cluster in the Iron Protein Component of Azotobacter vinelandii Nitrogenase. J Inorg Biochem 53:281–294

    Article  CAS  Google Scholar 

  5. Yoo SJ, Angove HC, Burgess BK et al (1999) Mössbauer and Integer-Spin EPR Studies and Spin-Coupling Analysis of the [4Fe-4S]0 Cluster of the Fe Protein from Azotobacter vinelandii Nitrogenase. J Am Chem Soc 121:2534–2545

    Article  CAS  Google Scholar 

  6. Scott TA, Berlinguette CP, Holm RH et al (2005) Initial Synthesis and Structure of an All-Ferrous Analogue of the Fully Reduced [Fe4S4]0 Cluster of the Nitrogenase Iron Protein. Proc Natl Acad Sci USA 102:9741–9744

    Article  PubMed  CAS  Google Scholar 

  7. Deng L, Holm RH (2008) Stabilization of Fully Reduced Iron-Sulfur Clusters by Carbene Ligation: The [Fe n S n ]0 Oxidation Levels (n = 4, 8). J Am Chem Soc 130:9878–9886

    Article  PubMed  CAS  Google Scholar 

  8. Howard JB, Rees DC (1996) Structural Basis of Biological Nitrogen Fixation. Chem Rev 96:2965–2982

    Article  PubMed  CAS  Google Scholar 

  9. Zhang Y, Zuo JL, Zhou HC, Holm RH (2002) Rearrangement of Symmetrical Dicubane Clusters into Topological Analogues of the P Cluster of Nitrogenase: Nature’s Choice? J Am Chem Soc 124:14292–14293

    Article  PubMed  CAS  Google Scholar 

  10. Ohki Y, Sunada Y, Honda M et al (2003) Synthesis of the P-Cluster Inorganic Core of Nitrogenases. J Am Chem Soc 125:4052–4053

    Article  PubMed  CAS  Google Scholar 

  11. Burgess BK, Lowe DJ (1996) Mechanism of Molybdenum Nitrogenase. Chem Rev 96:2983–3011

    Article  PubMed  CAS  Google Scholar 

  12. Eady RR (1996) Structure-Function Relationships of Alternative Nitrogenases. Chem Rev 96:3013–3030

    Article  PubMed  CAS  Google Scholar 

  13. Krahn E, Weiss BJR, Kröckel M et al (2002) The Fe-Only Nitrogenase from Rhodobacter capsulatus: Identification of the Cofactor, an Unusual, High-Nuclearity Iron-Sulfur Cluster, by Fe K-Edge EXAFS and Iron-57 Mössbauer Spectroscopy. J Biol Inorg Chem 7:37–45

    Article  PubMed  CAS  Google Scholar 

  14. Einsle O, Tezcan FA, Andrade SLA et al (2002) Nitrogenase MoFe-Protein at 1.16 Å resolution: A Central Ligand in the FeMo-Cofactor. Science 297:1696–1700

    Article  PubMed  CAS  Google Scholar 

  15. Xiao Y, Fisher K, Smith MC et al (2006) How Nitrogenase Shakes - Initial Information About P-Cluster and FeMo-Cofactor Normal Modes from Nuclear Resonance Vibrational Spectroscopy (NRVS). J Am Chem Soc 128:7608–7612

    Article  PubMed  CAS  Google Scholar 

  16. Lovell T, Liu T, Case DA et al (2003) Structural, Spectroscopic, and Redox Consequences of a Central Ligand in the FeMoco of Nitrogenase: A Density Functional Theoretical Study. J Am Chem Soc 125:8377–8383

    Article  PubMed  CAS  Google Scholar 

  17. Lukoyanov D, Pelmenschikov V, Maeser N et al (2007) Testing if the Interstitial Atom, X, of the Nitrogenase Molybdenum-Iron Cofactor Is N or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 Resting State in Multiple Environments. Inorg Chem 46:11437–11449

    Article  PubMed  CAS  Google Scholar 

  18. Lee SC, Holm RH (2003) Speculative Synthetic Chemistry and the Nitrogenase Problem. Proc Natl Acad Sci USA 100:3595–3600

    Article  PubMed  CAS  Google Scholar 

  19. Corbett MC, Hu Y, Fay AW et al (2006) Structural Insights into a Protein-Bound Iron-Molybdenum Cofactor Precursor. Proc Natl Acad Sci USA 103:1238–1243

    Article  PubMed  CAS  Google Scholar 

  20. Stack TDP, Holm RH (1988) Subsite-Differentiated Analogs of Biological [4Fe-4S]2+ Clusters: Synthesis, Solution and Solid-State Structures, and Subsite-Specific Reactions. J Am Chem Soc 110:2484–2494

    Article  CAS  Google Scholar 

  21. Thorneley RNF, Lowe DJ (1985) Kinetics and Mechanism of the Nitrogenase Enzyme System. Met Ions Biol 7:221–284

    CAS  Google Scholar 

  22. Seefeldt LC, Dance IG, Dean DR (2004) Substrate Interactions with Nitrogenase: Fe Versus Mo. Biochemistry 43:1401–1409

    Article  PubMed  CAS  Google Scholar 

  23. Holland PL (2008) Electronic Structure and Reactivity of Three-Coordinate Iron Complexes. Acc Chem Res 41:905–914

    Article  PubMed  CAS  Google Scholar 

  24. Smith JM, Sadique AR, Cundari TR et al (2006) Studies of Low-Coordinate Iron Dinitrogen Complexes. J Am Chem Soc 128:756–769

    Article  PubMed  CAS  Google Scholar 

  25. Vela J, Stoian S, Flaschenriem CJ et al (2004) A Sulfido-Bridged Diiron(II) Compound and Its Reactions with Nitrogenase-Relevant Substrates. J Am Chem Soc 126:4522–4523

    Article  PubMed  CAS  Google Scholar 

  26. Shah VK, Brill WJ (1977) Isolation of an Iron-Molybdenum Cofactor from Nitrogenase. Proc Natl Acad Sci USA 74:3249–3253

    Article  PubMed  CAS  Google Scholar 

  27. Shriver DF, Drezdzon MA (1986) The Manipulation of Air Sensitive Compounds. Wiley, New York, NY

    Google Scholar 

  28. Peters JC, Mehn MP (2006) Bio-organometallic Approaches to Nitrogen Fixation Chemistry. In: Tolman WB (ed) Activation of Small Molecules, pp. 81–119. VCH, Weinheim

    Google Scholar 

  29. Coucouvanis D (1991) Use of Preassembled Iron/Sulfur and Iron/Molybdenum/Sulfur Clusters in the Stepwise Synthesis of Potential Analogs for the Fe/Mo/S Site in Nitrogenase. Acc Chem Res 24:1–8

    Article  CAS  Google Scholar 

  30. Burfield DR, Lee K-H, Smithers RH (1977) Desiccant Efficiency in Solvent Drying. A Reappraisal by Application of a Novel Method for Solvent Water Assay. J Org Chem 42:3060–3065

    Article  CAS  Google Scholar 

  31. Seed B (2000) Silanizing Glassware. Current Protocols in Cell Biology, Appendix 3E, A.3E.1–A.3E.2. See also http://www.currentprotocols.com/protocol/cba03e. Accessed 15 February 2010

  32. Massa W (2000) Crystal Structure Determination, 2nd edn. Springer, New York, NY

    Google Scholar 

  33. Münck E (2000) Aspects of Iron-57 Mossbauer Spectroscopy. In: Que L (ed) Physical Methods in Bioinorganic Chemistry, pp. 287–319. University Science Books, New York, NY

    Google Scholar 

  34. Andres H, Bominaar E, Smith JM et al (2002) Planar Three-Coordinate High-Spin Fe(II) Complexes with Large Orbital Angular Momentum: Mössbauer, Electron Paramagnetic Resonance, and Electronic Structure Studies. J Am Chem Soc 124:3012–3025

    Article  PubMed  CAS  Google Scholar 

  35. Schubert EM (1992) Utilizing the Evans Method with a Superconducting NMR Spectrometer in the Undergraduate Laboratory. J Chem Educ 69:62

    Article  CAS  Google Scholar 

  36. Drago RS (1992) Physical Methods for Chemists. Surfside, Gainesville, FL

    Google Scholar 

  37. Feldman J, McLain SJ, Parthasarathy A et al (1997) Electrophilic Metal Precursors and a Beta-Diimine Ligand for Nickel(II)- and Palladium(II)Catalyzed Ethylene Polymerizations. Organometallics 16:1514–1516

    Article  CAS  Google Scholar 

  38. Kern RJ (1962) Tetrahydrofuran Complexes of Transition Metal Chlorides. J Inorg Nucl Chem 24:1105–1109

    Article  CAS  Google Scholar 

  39. Winter G (1973) Iron(II) Halides. Inorg Synth 14:101–104

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Research on nitrogenase-relevant compounds in the Holland laboratory is funded by the National Institutes of Health (grant GM065313). Most of all, I thank the hardworking students and postdoctoral researchers at Rochester who have braved the difficulties of handling these sensitive yet interesting iron complexes. I also thank our spectroscopic collaborators, who have often struggled with issues of air and moisture sensitivity alongside us. In particular, Eckard Münck (and his students Hanspeter Andres and Sebastian Stoian) and Eckhard Bill (and his technician Bernd Mienert) designed and used cells that enabled Mössbauer analysis of these compounds.

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Rochester, 14618, Rochester, NY, USA

    Patrick L. Holland

Authors
  1. Patrick L. Holland
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Patrick L. Holland .

Editor information

Editors and Affiliations

  1. , Dept Molecular Biology & Biochemistry, University of California, Irvine, Irvine, 92697, California, USA

    Markus W. Ribbe

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Holland, P.L. (2011). Techniques for Functional and Structural Modeling of Nitrogenase. In: Ribbe, M. (eds) Nitrogen Fixation. Methods in Molecular Biology, vol 766. Humana Press. https://doi.org/10.1007/978-1-61779-194-9_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-194-9_17

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-193-2

  • Online ISBN: 978-1-61779-194-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation