Advertisement

Diffraction and Scattering by X-Rays and Neutrons

  • Ivan RaymentEmail author
Chapter
Part of the Biophysics for the Life Sciences book series (BIOPHYS, volume 6)

Abstract

X-ray and neutron scattering methods have played a historically pivotal role in the development of molecular biophysics and biochemistry. Today a large proportion of papers that address a question in macromolecular structure carry with them a pictorial representation based on structural features derived from scattering methods. These images are often compelling and yet it is often difficult to assess the presented information based on pictures alone. The purpose of this chapter is to allow the non-expert to develop a sense of how much can be accepted or what can be learned from the images derived from scattering methods.

Keywords

X-ray diffraction Neutron diffraction Small-angle scattering Molecular structure 

References

  1. 1.
    Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(pt 2):213–221. doi: 10.1107/S0907444909052925 PubMedCrossRefGoogle Scholar
  2. 2.
    Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M (2011) The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334(6062):1524–1529. doi: 10.1126/science.1212642 PubMedCrossRefGoogle Scholar
  3. 3.
    Blow DM (2002) Outline of crystallography for biologists. Oxford University Press, Oxford, New YorkGoogle Scholar
  4. 4.
    Brunger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355(6359):472–475PubMedCrossRefGoogle Scholar
  5. 5.
    Burke JE, Sashital DG, Zuo X, Wang YX, Butcher SE (2012) Structure of the yeast U2/U6 snRNA complex. RNA 18(4):673–683. doi: 10.1261/rna.031138.111 PubMedCrossRefGoogle Scholar
  6. 6.
    Chen VB, Arendall WB III, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(pt 1):12–21. doi: 10.1107/S0907444909042073 PubMedCrossRefGoogle Scholar
  7. 7.
    DeLano WL (2002) The PyMOL molecular graphics system. http://www.pymol.org
  8. 8.
    Dickinson M, Farman G, Frye M, Bekyarova T, Gore D, Maughan D, Irving T (2005) Molecular dynamics of cyclically contracting insect flight muscle in vivo. Nature 433(7023):330–334. doi: 10.1038/nature03230 PubMedCrossRefGoogle Scholar
  9. 9.
    Dodson E (2008) The befores and afters of molecular replacement. Acta Crystallogr D Biol Crystallogr 64(pt 1):17–24. doi: 10.1107/S0907444907049736 PubMedCrossRefGoogle Scholar
  10. 10.
    Eisenberg D (2003) The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins. Proc Natl Acad Sci U S A 100(20):11207–11210. doi: 10.1073/pnas.2034522100 PubMedCrossRefGoogle Scholar
  11. 11.
    Franklin RE, Gosling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171(4356):740–741PubMedCrossRefGoogle Scholar
  12. 12.
    Guinier A, Fournet G (1955) Small-angle scattering of X-rays. Structure of matter series. Wiley, New YorkGoogle Scholar
  13. 13.
    Hazemann I, Dauvergne MT, Blakeley MP, Meilleur F, Haertlein M, Van Dorsselaer A, Mitschler A, Myles DA, Podjarny A (2005) High-resolution neutron protein crystallography with radically small crystal volumes: application of perdeuteration to human aldose reductase. Acta Crystallogr D Biol Crystallogr 61(pt 10):1413–1417. doi: 10.1107/S0907444905024285 PubMedCrossRefGoogle Scholar
  14. 14.
    James RW (1962) The optical principles of the diffraction of X-rays. OxBow Press, WoodbridgeGoogle Scholar
  15. 15.
    Kleywegt GJ, Jones TA (1995) Where freedom is given, liberties are taken. Structure 3(6):535–540PubMedCrossRefGoogle Scholar
  16. 16.
    Koch MHJ, 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. doi: 10.1017/S0033583503003871 PubMedCrossRefGoogle Scholar
  17. 17.
    Kozin MB, Svergun DI (2001) Automated matching of high- and low-resolution structural models. J Appl Crystallogr 34:33–41CrossRefGoogle Scholar
  18. 18.
    Lattman E, Loll P (2008) Protein crystallography: a concise guide. Johns Hopkins University Press, BaltimoreGoogle Scholar
  19. 19.
    Lu Y, Jeffries CM, Trewhella J (2011) Invited review: probing the structures of muscle regulatory proteins using small-angle solution scattering. Biopolymers 95(8):505–516. doi: 10.1002/bip.21624 PubMedCrossRefGoogle Scholar
  20. 20.
    Mertens HD, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172(1):128–141. doi: 10.1016/j.jsb.2010.06.012 PubMedCrossRefGoogle Scholar
  21. 21.
  22. 22.
    Mouzakis KE, Burke JE, Butcher SE (2012) Investigating RNAs involved in translational control by NMR and SAXS. In: Dinman JD (ed) The biophysics of translational control of gene expression. Springer, New YorkGoogle Scholar
  23. 23.
    Munshi P, Chung SL, Blakeley MP, Weiss KL, Myles DA, Meilleur F (2012) Rapid visualization of hydrogen positions in protein neutron crystallographic structures. Acta Crystallogr D Biol Crystallogr 68(pt 1):35–41. doi: 10.1107/S0907444911048402 PubMedCrossRefGoogle Scholar
  24. 24.
    Myles DA (2006) Neutron protein crystallography: current status and a brighter future. Curr Opin Struct Biol 16(5):630–637. doi: 10.1016/j.sbi.2006.08.010 PubMedCrossRefGoogle Scholar
  25. 25.
    Namba K, Pattanayek R, Stubbs G (1989) Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction. J Mol Biol 208(2):307–325PubMedCrossRefGoogle Scholar
  26. 26.
    Pauling L, Corey RB (1951) Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc Natl Acad Sci U S A 37(11):729–740PubMedCrossRefGoogle Scholar
  27. 27.
    Pauling L, Corey RB, Branson HR (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 37(4):205–211PubMedCrossRefGoogle Scholar
  28. 28.
  29. 29.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612. doi: 10.1002/jcc.20084 PubMedCrossRefGoogle Scholar
  30. 30.
    Piazzesi G, Reconditi M, Linari M, Lucii L, Bianco P, Brunello E, Decostre V, Stewart A, Gore DB, Irving TC, Irving M, Lombardi V (2007) Skeletal muscle performance determined by modulation of number of myosin motors rather than motor force or stroke size. Cell 131(4):784–795. doi: 10.1016/j.cell.2007.09.045 PubMedCrossRefGoogle Scholar
  31. 31.
    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. doi: 10.1017/S0033583507004635 PubMedCrossRefGoogle Scholar
  32. 32.
    Rajagopal S, Kostov KS, Moffat K (2004) Analytical trapping: extraction of time-independent structures from time-dependent crystallographic data. J Struct Biol 147(3):211–222. doi: 10.1016/j.jsb.2004.04.007 PubMedCrossRefGoogle Scholar
  33. 33.
    Rambo RP, Tainer JA (2010) Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering. Curr Opin Struct Biol 20(1):128–137. doi: 10.1016/j.sbi.2009.12.015 PubMedCrossRefGoogle Scholar
  34. 34.
    Reconditi M (2006) Recent improvements in small angle X-ray diffraction for the study of muscle physiology. Rep Prog Phys 69(10):2709–2759. doi: 10.1088/0034-4885/69/10/R01 PubMedCrossRefGoogle Scholar
  35. 35.
    Rupp B (2010) Biomolecular crystallography: principles, practice, and application to structural biology. Garland Science, New YorkGoogle Scholar
  36. 36.
    Stubbs G (1999) Developments in fiber diffraction. Curr Opin Struct Biol 9(5):615–619PubMedCrossRefGoogle Scholar
  37. 37.
    Sunde M, Serpell LC, Bartlam M, Fraser PE, Pepys MB, Blake CC (1997) Common core structure of amyloid fibrils by synchrotron X-ray diffraction. J Mol Biol 273(3):729–739. doi: 10.1006/jmbi.1997.1348 PubMedCrossRefGoogle Scholar
  38. 38.
    Svergun DI (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys J 76(6):2879–2886PubMedCrossRefGoogle Scholar
  39. 39.
    Tamada T, Kinoshita T, Kurihara K, Adachi M, Ohhara T, Imai K, Kuroki R, Tada T (2009) Combined high-resolution neutron and X-ray analysis of inhibited elastase confirms the active-site oxyanion hole but rules against a low-barrier hydrogen bond. J Am Chem Soc 131(31):11033–11040. doi: 10.1021/ja9028846 PubMedCrossRefGoogle Scholar
  40. 40.
    The Protein Data Bank. http://www.pdb.org/
  41. 41.
    Toyama BH, Weissman JS (2011) Amyloid structure: conformational diversity and consequences. Annu Rev Biochem 80:557–585. doi: 10.1146/annurev-biochem-090908-120656 PubMedCrossRefGoogle Scholar
  42. 42.
    Tsuruta H, Irving TC (2008) Experimental approaches for solution X-ray scattering and fiber diffraction. Curr Opin Struct Biol 18(5):601–608. doi: 10.1016/j.sbi.2008.08.002 PubMedCrossRefGoogle Scholar
  43. 43.
    Wille H, Bian W, McDonald M, Kendall A, Colby DW, Bloch L, Ollesch J, Borovinskiy AL, Cohen FE, Prusiner SB, Stubbs G (2009) Natural and synthetic prion structure from X-ray fiber diffraction. Proc Natl Acad Sci U S A 106(40):16990–16995. doi: 10.1073/pnas.0909006106 PubMedCrossRefGoogle Scholar
  44. 44.
    Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AG, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67(pt 4):235–242. doi: 10.1107/S0907444910045749 PubMedCrossRefGoogle Scholar
  45. 45.
    Worldwide PDB. http://www.wwpdb.org/
  46. 46.
    Yamashita I, Suzuki H, Namba K (1998) Multiple-step method for making exceptionally well-oriented liquid-crystalline sols of macromolecular assemblies. J Mol Biol 278(3):609–615. doi: 10.1006/jmbi.1998.1710 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUSA

Personalised recommendations