Skip to main content
SpringerLink
Log in

Structure Analysis of Biological Macromolecules by Small-Angle X-ray Scattering

  • Conference paper
  • First Online:
Macromolecular Crystallography

  • 1368 Accesses

Abstract

Small-angle X-ray scattering (SAXS) is a low resolution (1–2 nm) structural method, which is applicable to macromolecules in solution providing information about the overall structure and structural transitions. The method covers an extremely broad range of sizes (from a few kDa to hundreds MDa) and experimental conditions (temperature, pH, salinity, ligand addition etc.). Recent progress in instrumentation and novel data analysis methods significantly enhanced resolution and reliability of structural models provided by the technique and made SAXS a useful complementary tool to high resolution methods. In particular, SAXS allows for rapid validation of high resolution crystallographic or theoretically predicted models, identification of biologically active oligomers and visualization of missing fragments. Quaternary structure of complexes can be analyzed by rigid body movements/rotations of high resolution models of the individual subunits of domains. The basics of SAXS will be presented and illustrated by advanced applications to macromolecular solutions.

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 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Aloy P, Russell RB (2006) Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 7(3):188–197

    Article  Google Scholar 

  2. Bada M, Walther D, Arcangioli B, Doniach S, Delarue M (2000) Solution structural studies and low-resolution model of the Schizosaccharomyces pombe sap1 protein. J Mol Biol 300(3):563–574

    Article  Google Scholar 

  3. Bernado P, Blanchard L, Timmins P, Marion D, Ruigrok RW, Blackledge M (2005) A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. Proc Natl Acad Sci USA 102(47):17002–17007

    Article  ADS  Google Scholar 

  4. Bernado P, Mylonas E, Petoukhov MV, Blackledge M, Svergun DI (2007) Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc 129(17):5656–5664

    Article  Google Scholar 

  5. Bertini I, Calderone V, Fragai M, Jaiswal R, Luchinat C, Melikian M, Mylonas E, Svergun DI (2008) Evidence of reciprocal reorientation of the catalytic and hemopexin-like domains of full-length MMP-12. J Am Chem Soc 130(22):7011–7021

    Article  Google Scholar 

  6. Blobel J, Bernado P, Svergun DI, Tauler R, Pons M (2009) Low-resolution structures of transient protein-protein complexes using small-angle X-ray scattering. J Am Chem Soc 131(12):4378–4386

    Article  Google Scholar 

  7. Chacon P, Moran F, Diaz JF, Pantos E, Andreu JM (1998) Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm. Biophys J 74(6):2760–2775

    Article  Google Scholar 

  8. Chacon P, Diaz JF, Moran F, Andreu JM (2000) Reconstruction of protein form with X-ray solution scattering and a genetic algorithm. J Mol Biol 299(5):1289–1302

    Article  Google Scholar 

  9. Doniach S (2001) Changes in biomolecular conformation seen by small angle X-ray scattering. Chem Rev 101(6):1763–1778

    Article  Google Scholar 

  10. Edwards AM, Arrowsmith CH, Christendat D, Dharamsi A, Friesen JD, Greenblatt JF, Vedadi M (2000) Protein production: feeding the crystallographers and NMR spectroscopists. Nat Struct Biol 7(Suppl):970–972

    Article  Google Scholar 

  11. Feigin LA, Svergun DI (1987) Structure analysis by small-angle x-ray and neutron scattering. Plenum Press, New York, pp. xiii, 335

    Google Scholar 

  12. Gerstein M, Edwards A, Arrowsmith CH, Montelione GT (2003) Structural genomics: current progress. Science 299(5613):1663

    Article  Google Scholar 

  13. Glatter O (1977) A new method for the evaluation of small-angle scattering data. J Appl Crystallogr 10:415–421

    Article  Google Scholar 

  14. Glatter O, Kratky O (1982) Small Angle X-ray Scattering. Academic, London, p 515

    Google Scholar 

  15. Golub G, Reinsh C (1970) Singular value decomposition and least squares solution. Numerische mathematik 14(5):403–420

    Google Scholar 

  16. Guinier A (1939) La diffraction des rayons X aux tres petits angles; application a l’etude de phenomenes ultramicroscopiques. Ann Phys (Paris) 12:161–237

    Google Scholar 

  17. Hamiaux C, Perez J, Prange T, Veesler S, Ries-Kautt M, Vachette P (2000) The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution. J Mol Biol 297(3):697–712

    Article  Google Scholar 

  18. Heller WT, Abusamhadneh E, Finley N, Rosevear PR, Trewhella J (2002) The solution structure of a cardiac troponin C-troponin I-troponin T complex shows a somewhat compact troponin C interacting with an extended troponin I-troponin T component. Biochemistry 41(52):15654–15663

    Article  Google Scholar 

  19. Heller WT, Finley NL, Dong WJ, Timmins P, Cheung HC, Rosevear PR, Trewhella J (2003) Small-angle neutron scattering with contrast variation reveals spatial relationships between the three subunits in the ternary cardiac troponin complex and the effects of troponin I phosphorylation. Biochemistry 42(25):7790–7800

    Article  Google Scholar 

  20. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL 2nd, Tsutakawa SE, Jenney FE Jr, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, Tainer JA (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6(8):606–612

    Article  Google Scholar 

  21. King WA, Stone DB, Timmins PA, Narayanan T, von Brasch AA, Mendelson RA, Curmi PM (2005) Solution structure of the chicken skeletal muscle troponin complex via small-angle neutron and X-ray scattering. J Mol Biol 345(4):797–815

    Article  Google Scholar 

  22. Koch MH, Vachette P, Svergun DI (2003) Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution. Q Rev Biophys 36(2):147–227

    Article  Google Scholar 

  23. Konarev PV, Petoukhov MV, Volkov VV, Svergun DI (2006) ATSAS 2.1, a program package for small-angle scattering data analysis. J Appl Crystallogr 39:277–286

    Article  Google Scholar 

  24. Levitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104(9):3183–3188

    Article  ADS  Google Scholar 

  25. Moore PB (1980) Small-angle scattering: Information content and error analysis. J Appl Crystallogr 13:168–175

    Article  Google Scholar 

  26. Mylonas E, Hascher A, Bernado P, Blackledge M, Mandelkow E, Svergun DI (2008) Domain conformation of tau protein studied by solution small-angle X-ray scattering. Biochemistry 47(39):10345–10353

    Article  Google Scholar 

  27. Mylonas E, Svergun DI (2007) Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. J Appl Crystallogr 40:s245–s249

    Article  Google Scholar 

  28. Nollmann M, He J, Byron O, Stark WM (2004) Solution structure of the Tn3 resolvase-crossover site synaptic complex. Mol Cell 16(1):127–137

    Article  Google Scholar 

  29. Okorokov AL, Sherman MB, Plisson C, Grinkevich V, Sigmundsson K, Selivanova G, Milner J, Orlova EV (2006) The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity. EMBO J 25(21):5191–5200

    Article  Google Scholar 

  30. Perez J, Vachette P, Russo D, Desmadril M, Durand D (2001) Heat-induced unfolding of neocarzinostatin, a small all-beta protein investigated by small-angle X-ray scattering. J Mol Biol 308(4):721–743

    Article  Google Scholar 

  31. Petoukhov MV, Svergun DI (2005) Global rigid body modelling of macromolecular complexes against small-angle scattering data. Biophys J 89(2):1237–1250

    Article  Google Scholar 

  32. Petoukhov MV, Svergun DI (2006) Joint use of small-angle X-ray and neutron scattering to study biological macromolecules in solution. Eur Biophys J 35:567–576

    Article  Google Scholar 

  33. Petoukhov MV, Svergun DI (2007) Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr Opin Struct Biol 17(5):562–571

    Article  Google Scholar 

  34. Petoukhov MV, Eady NA, Brown KA, Svergun DI (2002) Addition of missing loops and domains to protein models by x-ray solution scattering. Biophys J 83(6):3113–3125

    Article  Google Scholar 

  35. Petoukhov MV, Konarev PV, Kikhney AG, Svergun DI (2007) ATSAS 2.1 – towards automated and web-supported small-angle scattering data analysis. J Appl Crystallogr 40(s1):s223–s228

    Article  Google Scholar 

  36. Porod G (1982) General theory. In: Glatter O, Kratky O (eds) Small-angle X-ray scattering. Academic, London, pp 17–51

    Google Scholar 

  37. Putnam CD, Hammel M, Hura GL, Tainer JA (2007) X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution. Q Rev Biophys 40(3):191–285

    Article  Google Scholar 

  38. Round AR, Franke D, Moritz S, Huchler R, Fritsche M, Malthan D, Klaering R, Svergun DI, Roessle M (2008) Automated sample-changing robot for solution scattering experiments at the EMBL Hamburg SAXS station X33. J Appl Crystallogr 41:913–917

    Article  Google Scholar 

  39. Sali A, Glaeser R, Earnest T, Baumeister W (2003) From words to literature in structural proteomics. Nature 422(6928):216–225

    Article  ADS  Google Scholar 

  40. Svergun DI (1991) Mathematical methods in small-angle scattering data analysis. J Appl Crystallogr 24:485–492

    Article  Google Scholar 

  41. Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503

    Article  Google Scholar 

  42. Svergun DI (1994) Solution scattering from biopolymers: advanced contrast variation data analysis. Acta Crystallogr A50:391–402

    Google Scholar 

  43. Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76(6):2879–2886

    Article  Google Scholar 

  44. Svergun DI, Koch MHJ (2003) Small angle scattering studies of biological macromolecules in solution. Rep Prog Phys 66:1735–1782

    Article  ADS  Google Scholar 

  45. Svergun DI, Barberato C, Koch MHJ (1995) CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768–773

    Article  Google Scholar 

  46. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80(6):2946–2953

    Article  Google Scholar 

  47. Tidow H, Melero R, Mylonas E, Freund SM, Grossmann JG, Carazo JM, Svergun DI, Valle M, Fersht AR (2007) From the Cover: Quaternary structures of tumor suppressor p53 and a specific p53 DNA complex. Proc Natl Acad Sci USA 104(30):12324–12329

    Article  ADS  Google Scholar 

  48. Toft KN, Vestergaard B, Nielsen SS, Snakenborg D, Jeppesen MG, Jacobsen JK, Arleth L, Kutter JP (2008) High-throughput Small Angle X-ray Scattering from proteins in solution using a microfluidic front-end. Anal Chem 80(10):3648–3654

    Article  Google Scholar 

  49. Vestergaard B, Groenning M, Roessle M, Kastrup JS, van de Weert M, Flink JM, Frokjaer S, Gajhede M, Svergun DI (2007) A helical structural nucleus is the primary elongating unit of insulin amyloid fibrils. PLoS Biol 5(5):e134

    Article  Google Scholar 

  50. Volkov VV, Svergun DI (2003) Uniqueness of ab initio shape determination in small angle scattering. J Appl Crystallogr 36:860–864

    Article  Google Scholar 

  51. Whitten AE, Trewhella J (2009) Small-angle scattering and neutron contrast variation for studying bio-molecular complexes. Methods Mol Biol 544:307–323

    Article  Google Scholar 

  52. Xu XF, Reinle WG, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M (2008) Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy. J Am Chem Soc 130(20):6395–6403

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. European Molecular Biology Laboratory, Hamburg Outstation, Notkestraße 85, D-22603, Hamburg, Germany

    Dmitri I. Svergun

Authors
  1. Dmitri I. Svergun
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dmitri I. Svergun .

Editor information

Editors and Affiliations

  1. , Instit.de Technologia Química e Biológia, Universidade Nova de Lisboa, Rua da Quinta Grande , Apartado 127 6, Oeiras, 2781-901, Portugal

    Maria Armenia Carrondo

  2. Dipto. Scienze Chimiche, Università di Padova, Via F. Marzolo 1, Padova, 35131, Italy

    Paola Spadon

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this paper

Cite this paper

Svergun, D.I. (2012). Structure Analysis of Biological Macromolecules by Small-Angle X-ray Scattering. In: Carrondo, M., Spadon, P. (eds) Macromolecular Crystallography. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2530-0_15

Download citation

Publish with us

Policies and ethics

Search

Navigation