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Protein Shape and Assembly Studied with X-Ray Solution Scattering: Fundaments and Practice

  • R.M. BueyEmail author
  • P. Chacón
  • J.M. Andreu
  • J. Fernando Díaz
Chapter
Part of the Lecture Notes in Physics book series (LNP, volume 776)

Abstract

Small-angle X-ray scattering (SAXS) is a widely used technique to study non-crystalline systems such as protein solutions. The experimental description of application of SAXS to protein solution has been described in the previous chapter. The size and shape of proteins can be determined from the scattering profile at low-medium resolution using computer simulations. The generated structural information perfectly complements high-resolution data resulting from other structural biology methodologies such as X-ray crystallography or nuclear magnetic resonance (NMR). In this chapter, the methods employed in a common protein SAXS experiment are briefly reviewed, covering diverse aspects ranging from data collection and analysis to computer modeling and docking procedures.

Keywords

Tubulin Polymerization SAXS Data Dummy Atom SAXS Experiment Bead Model 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Lipfert J., Doniach, S. Annu. Rev. Biophys. Biomol. Struct. 36, 307–327 (2007).CrossRefGoogle Scholar
  2. 2.
    Putnam C.D., Hammel M., Hura G.L., Tainer J.A. Q Rev. Biophys. 40, 191–285 (2007).CrossRefGoogle Scholar
  3. 3.
    Koch M.H., Vachette P., Svergun D.I. Q Rev. Biophys. 36, 147–227 (2003).CrossRefGoogle Scholar
  4. 4.
    Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., Svergun D.I. J. App. Cryst. 36, 1277–1282 (2003).CrossRefGoogle Scholar
  5. 5.
    Kuwamoto S., Akiyama S., Fujisawa T. J. Synchrotron Radiat. 11, 462–468 (2004).CrossRefGoogle Scholar
  6. 6.
    Guinier A., Fournet F. Small Angle Scattering of X-Rays. Wiley Interscience, New York (1955).Google Scholar
  7. 7.
    Svergun D. J. App. Cryst. 25, 495–503 (1992).CrossRefGoogle Scholar
  8. 8.
    Porod G. Kolloid Zeitschrift 124, 83–114 (1951).CrossRefGoogle Scholar
  9. 9.
    Heller W. J. App. Cryst. 39, 671–675 (2006).CrossRefMathSciNetGoogle Scholar
  10. 10.
    Svergun D.I., Volkov V.V., Kozin M.B., Stuhrmann H.B. Acta Cryst. A 52, 419–426 (1996).Google Scholar
  11. 11.
    Chacon P., Moran F., Diaz J.F., Pantos E., Andreu J.M. Biophys. J. 74, 2760–2775 (1998).Google Scholar
  12. 12.
    Chacon P., Diaz J.F., Moran F., Andreu J.M. J. Mol. Biol. 299, 1289–1302 (2000).CrossRefGoogle Scholar
  13. 13.
    Svergun D.I. Biophys. J. 76, 2879–2886 (1999).CrossRefADSGoogle Scholar
  14. 14.
    Walther D., Cohen F.E., Doniach S. J App. Cryst. 33, 350–363 (2000).CrossRefGoogle Scholar
  15. 15.
    Zipper P., Durchschlag H. J. App. Cryst. 36, 509–514 (2003).CrossRefGoogle Scholar
  16. 16.
    Durchschlag H., Zipper P., Krebs A. J. Appl. Crystall. 40, 1123–1134 (2007).CrossRefGoogle Scholar
  17. 17.
    Takahashi Y., Nishikawa Y., Fujisawa T. J. App. Cryst. 36, 549–552 (2003).CrossRefGoogle Scholar
  18. 18.
    Svergun D.I., Petoukhov M.V., Koch M.H. J. Biophys. J. 80, 2946–2953 (2001).CrossRefGoogle Scholar
  19. 19.
    Kozin M.B., Svergun D. J. App. Cryst. 34, 33–41 (2001).CrossRefGoogle Scholar
  20. 20.
    Volkov V.V., Svergun D. J. App. Cryst. 36, 860–864 (2003).CrossRefGoogle Scholar
  21. 21.
    Garcia de la Torre J., Navarro S., Lopez Martinez M.C., Diaz F.G., Lopez Cascales J.J. Biophys. J. 67, 530–531 (1994).Google Scholar
  22. 22.
    Garcia de la Torre J., del Rio Echenique G., Ortega A. J. Phys. Chem. B 111, 955–961 (2007).Google Scholar
  23. 23.
    Debye P. Zerstreeung von röntgenstrahlen. Ann. Phys. 46, 809–823 (1915).CrossRefGoogle Scholar
  24. 24.
    Pantos E., van Garderen H.A., Hilbers P.A.J., Beelen T.P.M., van Santen R.A. J. Mol. Struct. 383, 303–308 (1996).CrossRefADSGoogle Scholar
  25. 25.
    Svergun D.I., Barberato C., Koch M.H.J. J. App. Cryst. 28, 768–773 (1995).CrossRefGoogle Scholar
  26. 26.
    Davis L. Handbook of Genetic Algorithms. Van Nostrand Reinhold, New York (1991).Google Scholar
  27. 27.
    Buey R.M., Monterroso B., Menendez M., Diakun G., Chacon P., Hermoso J.A., Diaz J.F. J. Mol. Biol. 365, 411–424 (2007).CrossRefGoogle Scholar
  28. 28.
    de Groot B.L., van Aalten D.M., Scheek R.M., Amadei A., Vriend G., Berendsen H.J. Proteins 29, 240–251 (1997).CrossRefGoogle Scholar
  29. 29.
    Wriggers W., Birmanns S. J. Struct. Biol. 133, 193–202 (2001).CrossRefGoogle Scholar
  30. 30.
    Konarev P.V., Petoukhov M.V., Volkov V.V., Svergun D.I. J. App. Cryst. 39, 277–286 (2006).CrossRefGoogle Scholar
  31. 31.
    Konarev, P.V., Petoukhov, M.V., Svergun, D.I. J App Cryst 34, 527-532(2001)CrossRefGoogle Scholar
  32. 32.
    Kozin M.B., Volkov V.V., Svergun D.I. J. App. Cryst. 30, 811–815 (1997).CrossRefGoogle Scholar
  33. 33.
    Petoukhov M.V., Svergun D.I. Biophys. J. 89, 1237–1250 (2005).CrossRefGoogle Scholar
  34. 34.
    Andreu J.M., Garcia de Ancos J.G., Starling D., Hogkingson J.L., Bordas J. Biochemistry 28, 4036–4040 (1989).CrossRefGoogle Scholar
  35. 35.
    Andreu J.M., Bordas J., Diaz J.F., Garcia de Ancos J., Gil R., Medrano F.J., Nogales E., Towns-Andrews E. J. Mol. Biol. 226, 169–184 (1992).CrossRefGoogle Scholar
  36. 36.
    Andreu J.M., Diaz J.F., Gil R., de Pereda J.M., Garcia de Lacoba M., Peyrot V., Briand C., Towns-Andrews E., Bordas J. J. Biol. Chem. 269, 31785–31792 (1994).Google Scholar
  37. 37.
    Diaz J.F., Andreu J.M., Diakun G., Towns-Andrews E., Bordas J. Biophys. J. 70, 2408–2420 (1996).CrossRefADSGoogle Scholar
  38. 38.
    Diaz J.F., Pantos E., Bordas J., Andreu J.M. J. Mol. Biol. 238, 214–225 (1994).CrossRefGoogle Scholar
  39. 39.
    Diaz J.F., Valpuesta J.M., Chacon P., Diakun G., Andreu J.M. J. Biol. Chem. 273, 33803–33810 (1998).CrossRefGoogle Scholar
  40. 40.
    Bordas J., Mandelkow E.M., Mandelkow E. J. Mol. Biol. 164, 89–135 (1983).CrossRefGoogle Scholar
  41. 41.
    Klug A., Crick F.H.C., Wyckhoff H.W. Acta Crystallogr. 11, 199–213 (1958).CrossRefGoogle Scholar
  42. 42.
    Wang H.W., Nogales, E. Nature 435, 911–915 (2005).CrossRefADSGoogle Scholar
  43. 43.
    Nogales E., Wang H.W., Niederstrasser H. Curr. Opin. Struct. Biol. 13, 256–261 (2003).CrossRefGoogle Scholar
  44. 44.
    Chretien D., Fuller S.D., Karsenti E. J. Cell. Biol. 129, 1311–1328 (1995).CrossRefGoogle Scholar
  45. 45.
    Lopez R., Garcia E. FEMS Microbiol. Rev. 28, 553–580 (2004).CrossRefGoogle Scholar
  46. 46.
    Hermoso J.A., Monterroso B., Albert A., Galan B., Ahrazem O., Garcia P., Martinez-Ripoll M., Garcia J.L., Menendez M. Structure 11, 1239–1249 (2003).CrossRefGoogle Scholar
  47. 47.
    Hermoso J.A., Lagartera L., Gonzalez A., Stelter M., Garcia P., Martinez-Ripoll M., Garcia J.L., Menendez M. Nat. Struct. Mol. Biol. 12, 533–538 (2005).CrossRefGoogle Scholar
  48. 48.
    Fernandez-Tornero C., Lopez R., Garcia E., Gimenez-Gallego G., Romero A. Nat. Struct. Biol. 8, 1020–1024 (2001).CrossRefGoogle Scholar
  49. 49.
    Fernandez-Tornero C., Garcia E., Lopez R., Gimenez-Gallego G., Romero A. J. Mol. Biol. 321, 163–173 (2002).CrossRefGoogle Scholar
  50. 50.
    Varea J., Saiz J.L., Lopez-Zumel C., Monterroso B., Medrano F.J., Arrondo J.L., Iloro I., Laynez J., Garcia J.L., Menendez M. J. Biol. Chem. 275, 26842–26855 (2000).Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • R.M. Buey
    • 1
    Email author
  • P. Chacón
    • 2
  • J.M. Andreu
    • 2
  • J. Fernando Díaz
    • 2
  1. 1.Paul Scherrer Institute. Villigen PSISwitzerland
  2. 2.Centro de Investigaciones Biologicas CSIC.MadridSpain

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