Advertisement

Biological Small-Angle X-Ray Scattering (SAXS)

  • Tomáš Klumpler
Chapter

Abstract

Small angle X-ray scattering (SAXS) method for studies of biological macromolecules in solution is briefly described. A short introduction to the basic physical principles is followed by the description of SAXS experiment and an overview of modeling approaches used in scattering data analysis. Practical aspects, advantages, and limitations of the method are discussed.

References

  1. Berman HM (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242CrossRefPubMedPubMedCentralGoogle Scholar
  2. Bernadó 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 129:5656–5664CrossRefPubMedGoogle Scholar
  3. Debye PZ v R (1915) Ann Phys 351:809–823CrossRefGoogle Scholar
  4. Glatter O, Kratky O (1982) Structure analysis by small-angle X-ray and neutron scattering. Academic Press, New YorkGoogle Scholar
  5. Grishaev A, Guo L, Irving T, Bax A (2010) Improved fitting of solution X-ray scattering data to macromolecular structures and structural ensembles by explicit water modeling. J Am Chem Soc 132:15484–15486CrossRefPubMedPubMedCentralGoogle Scholar
  6. Guinier A (1939) La diffraction des rayons X aux très petits angles : application à l’étude de phénomènes ultramicroscopiques. Ann Phys 11:161–237CrossRefGoogle Scholar
  7. Jeffries CM et al (2016) Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 11:2122–2153CrossRefPubMedPubMedCentralGoogle Scholar
  8. Konarev PV, Volkov VV, Sokolova AV, Koch MHJ, Svergun DI (2003) PRIMUS: a windows PC-based system for small-angle scattering data analysis. J Appl Crystallogr 36:1277–1282CrossRefGoogle Scholar
  9. 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–s249CrossRefGoogle Scholar
  10. Ozenne V et al (2012) Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables. Bioinformatics 28:1463–1470CrossRefPubMedGoogle Scholar
  11. Panjkovich A, Svergun DI (2016) Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis. Phys Chem Chem Phys 18:5707–5719CrossRefPubMedGoogle Scholar
  12. Petoukhov MV, Svergun DI (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89:1237–1250CrossRefPubMedPubMedCentralGoogle Scholar
  13. Petoukhov MV et al (2012) New developments in the ATSAS program package for small-angle scattering data analysis. J Appl Crystallogr 45:342–350CrossRefPubMedPubMedCentralGoogle Scholar
  14. Porod G (1951) Die Röntgenkleinwinkelstreuung von dichtgepackten kolloiden Systemen: I. Teil. Kolloid-Z 124:83–114CrossRefGoogle Scholar
  15. Rambo RP, Tainer JA (2013) Accurate assessment of mass, models and resolution by small-angle scattering. Nature 496:477–481CrossRefPubMedPubMedCentralGoogle Scholar
  16. Schneidman-Duhovny D, Hammel M, Sali A (2010) FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res 38:W540–W544CrossRefPubMedPubMedCentralGoogle Scholar
  17. Svergun DI (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J Appl Crystallogr 25:495–503CrossRefGoogle Scholar
  18. Svergun D, Barberato C, Koch MHJ (1995) CRYSOL – a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J Appl Crystallogr 28:768–773CrossRefGoogle Scholar
  19. Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76:2879–2886CrossRefPubMedPubMedCentralGoogle Scholar
  20. Svergun DI, Petoukhov MV, Koch MHJ (2001) Determination of domain structure of proteins from X-ray solution scattering. Biophys J 80:2946–2953CrossRefPubMedPubMedCentralGoogle Scholar
  21. Svergun DI, Koch MHJ, Timmins PA, May RP (2013) Small angle x-ray and neutron scattering from solutions of biological macromolecules. Oxford University PressGoogle Scholar
  22. Trewhella J et al (2017) 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr Sect Struct Biol 73:710–728CrossRefGoogle Scholar
  23. Tuukkanen AT, Kleywegt GJ, Svergun DI (2016) Resolution of ab initio shapes determined from small-angle scattering. IUCrJ 3:440–447CrossRefPubMedPubMedCentralGoogle Scholar
  24. Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI (2015) SASBDB, a repository for biological small-angle scattering data. Nucleic Acids Res 43:D357–D363CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Central European Institute of Technology, Masaryk UniversityBrnoCzech Republic

Personalised recommendations