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Diffraction and Scattering by X-Rays and Neutrons

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Molecular Biophysics for the Life Sciences

Part of the book series: Biophysics for the Life Sciences ((BIOPHYS,volume 6))

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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.

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References

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  3. Blow DM (2002) Outline of crystallography for biologists. Oxford University Press, Oxford, New York

    Google Scholar 

  4. Brunger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355(6359):472–475

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  7. DeLano WL (2002) The PyMOL molecular graphics system. http://www.pymol.org

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  11. Franklin RE, Gosling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171(4356):740–741

    Article  PubMed  CAS  Google Scholar 

  12. Guinier A, Fournet G (1955) Small-angle scattering of X-rays. Structure of matter series. Wiley, New York

    Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  14. James RW (1962) The optical principles of the diffraction of X-rays. OxBow Press, Woodbridge

    Google Scholar 

  15. Kleywegt GJ, Jones TA (1995) Where freedom is given, liberties are taken. Structure 3(6):535–540

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  17. Kozin MB, Svergun DI (2001) Automated matching of high- and low-resolution structural models. J Appl Crystallogr 34:33–41

    Article  CAS  Google Scholar 

  18. Lattman E, Loll P (2008) Protein crystallography: a concise guide. Johns Hopkins University Press, Baltimore

    Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  21. Molprobity server. http://molprobity.biochem.duke.edu/

  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 York

    Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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):307–325

    Article  PubMed  CAS  Google Scholar 

  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):729–740

    Article  PubMed  CAS  Google Scholar 

  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):205–211

    Article  PubMed  CAS  Google Scholar 

  28. PDBsum server. http://www.ebi.ac.uk/pdbsum/

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  35. Rupp B (2010) Biomolecular crystallography: principles, practice, and application to structural biology. Garland Science, New York

    Google Scholar 

  36. Stubbs G (1999) Developments in fiber diffraction. Curr Opin Struct Biol 9(5):615–619

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  40. The Protein Data Bank. http://www.pdb.org/

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  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

    Article  PubMed  CAS  Google Scholar 

  45. Worldwide PDB. http://www.wwpdb.org/

  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

    Article  PubMed  CAS  Google Scholar 

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Rayment, I. (2013). Diffraction and Scattering by X-Rays and Neutrons. In: Allewell, N., Narhi, L., Rayment, I. (eds) Molecular Biophysics for the Life Sciences. Biophysics for the Life Sciences, vol 6. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8548-3_4

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