Biophysical Reviews

, Volume 10, Issue 5, pp 1295–1310 | Cite as

The role of small-angle scattering in structure-based screening applications

  • Po-chia ChenEmail author
  • Janosch HennigEmail author


In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.


Small-angle scattering Screening Structural biology 


Author Contributions

P.C. and J.H. co-wrote the article.

Funding information

P.C. was supported by the EIPOD postdoctoral programme cofunded by the European Molecular Biology Laboratory (EMBL) and the Marie Curie Actions Cofund grant MSCACOFUND-FP no. 664726. J.H. gratefully acknowledges the EMBL and the German Research Council (Deutsche Forschungsgemeinschaft, DFG) for support via an Emmy-Noether Fellowship and the Priority Programme SPP1935.

Compliance with Ethical Standards

Conflict of interest

P.C. declares that he has no conflict of interest. J.H. declares that he has no conflict of interest.


  1. Acerbo AS, Cook MJ, Gillilan RE (2015) Upgrade of MacCHESS facility for x-ray scattering of biological macromolecules in solution. J Synchrotron Radiat 22(1):180–186. PubMedPubMedCentralGoogle Scholar
  2. Adamo M, Poulos AS, Miller RM, Lopez CG, Martel A, Porcar L, Cabral JaT (2017) Rapid contrast matching by microfluidic SANS. Lab Chip 17(9):1559–1569. PubMedGoogle Scholar
  3. Ando N, Kung Y, Can M, Bender G, Ragsdale SW, Drennan CL (2012) Transient B12-dependent methyltransferase complexes revealed by small-angle x-ray scattering. J Am Chem Soc 134(43):17945–17954. PubMedPubMedCentralGoogle Scholar
  4. Ando N, Li H, Brignole EJ, Thompson S, McLaughlin MI, Page JE, Asturias FJ, Stubbe J, Drennan CL (2016) Allosteric inhibition of human ribonucleotide reductase by dATP entails the stabilization of a Hexamer. Biochemistry 55(2):373–381. PubMedGoogle Scholar
  5. Arkin MR, Tang Y, Wells JA (2014) Small-molecule inhibitors of protein–protein interactions: progressing toward the reality. Chem Biol 21(9):1102–1114. PubMedPubMedCentralGoogle Scholar
  6. Barile E, Pellecchia M (2014) NMR-based approaches for the identification and optimization of inhibitors of protein–protein interactions. Chem Rev 114(9):4749–4763. PubMedPubMedCentralGoogle Scholar
  7. Bayburt TH, Sligar SG (2010) Membrane protein assembly into Nanodiscs. FEBS Lett 584(9):1721–1727. PubMedGoogle Scholar
  8. Bernadó P, Svergun DI (2011) Structural analysis of intrinsically disordered proteins by small-angle x-ray scattering. Mol BioSyst 8(1):151–167. PubMedGoogle Scholar
  9. 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(17):5656–5664. PubMedGoogle Scholar
  10. Bernadó P, Shimizu N, Zaccai G, Kamikubo H, Sugiyama M (2017) Solution scattering approaches to dynamical ordering in biomolecular systems. Biochim Biophys Acta Gen Subj. Google Scholar
  11. Berthaud A, Manzi J, Pérez J, Mangenot S (2012) Modeling detergent organization around Aquaporin-0 using small-angle x-ray scattering. J Am Chem Soc 134(24):10080–10088. PubMedGoogle Scholar
  12. Björling A, Niebling S, Marcellini M, van der Spoel D, Westenhoff S (2015) Deciphering solution scattering data with experimentally guided molecular dynamics simulations. J Chem Theory Comput 11(2):780–787. PubMedPubMedCentralGoogle Scholar
  13. Cala O, Guillière F, Krimm I (2014) NMR-based analysis of protein–ligand interactions. Anal Bioanal Chem 406(4):943–956. PubMedGoogle Scholar
  14. Cammarata M, Levantino M, Schotte F, Anfinrud PA, Ewald F, Choi J, Cupane A, Wulff M, Ihee H (2008) Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering. Nat Methods 5(10):881–886. PubMedPubMedCentralGoogle Scholar
  15. Cardia JP, Eldo J, Xia J, O’Day EM, Tsuruta H, Gryncel KR, Kantrowitz ER (2008) Use of L-asparagine and N-phosphonacetyl-L-asparagine to investigate the linkage of catalysis and homotropic cooperativity in E. coli aspartate transcarbomoylase. Proteins 71(3):1088–1096. PubMedGoogle Scholar
  16. Carlomagno T (2014) Present and future of NMR for RNA–protein complexes: a perspective of integrated structural biology. J Magn Reson 241:126–136. PubMedGoogle Scholar
  17. Chavanieu A, Pugnière M (2016) Developments in SPR fragment screening. Expert Opin Drug Discovery 11(5):489–499. Google Scholar
  18. Chen Pc, Hub JS (2015a) Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics. Biophys J 108(10):2573–2584. PubMedPubMedCentralGoogle Scholar
  19. Chen Pc, Hub JS (2015b) Structural properties of protein–detergent complexes from SAXS and MD simulations. J Phys Chem Lett 624:5116–5121. PubMedGoogle Scholar
  20. Chen Pc, Masiewicz P, Rybin V, Svergun D, Hennig J (2018) A general small-angle x-ray scattering-based screening protocol validated for protein–RNA interactions. ACS Comb Sci 20(4):197–202. PubMedGoogle Scholar
  21. Ciulli A (2013) Biophysical screening for the discovery of small-molecule ligands. In: Protein-ligand interactions, methods in molecular biology, Humana Press, Totowa, NJ, pp 357–388. Google Scholar
  22. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA (2013) Implementation and performance of SIBYLS: a dual endstation small-angle x-ray scattering and macromolecular crystallography beamline at the advanced light source. J Appl Crystallogr 46 (Pt 1):1–1. PubMedPubMedCentralGoogle Scholar
  23. Collins KM, Oregioni A, Robertson LE, Kelly G, Ramos A (2015) Protein–RNA specificity by high-throughput principal component analysis of NMR spectra. Nucl Acids Res 43(6):e41–e41. PubMedGoogle Scholar
  24. Congreve M, Rich RL, Myszka DG, Figaroa F, Siegal G, Marshall FH (2011) Chapter five - fragment screening of stabilized g-protein-coupled receptors using biophysical methods. In: Kuo LC (ed) Methods in enzymology, fragment-based drug design, vol 493, Academic Press, pp 115–136. Google Scholar
  25. Cordeiro TN, Chen PC, De Biasio A, Sibille N, Blanco FJ, Hub JS, Crehuet R, Bernadó P (2017) Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly. Nucl Acids Res 45(3):1501–1515. PubMedGoogle Scholar
  26. Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P (2017) Structural characterization of highly flexible proteins by small-angle scattering. In: Biological small angle scattering: techniques, strategies and tips, advances in experimental medicine and biology. Springer, Singapore, pp 107–129. Google Scholar
  27. Cusack S, Ruigrok RWH, Krygsman PCJ, Mellemam JE (1985) Structure and composition of influenza virus: a small-angle neutron scattering study. J Mol Biol 186(3):565–582. PubMedGoogle Scholar
  28. Daghestani HN, Day BW (2010) Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors. Sensors 10(11):9630–9646. PubMedGoogle Scholar
  29. Dalvit C, Pevarello P, Tatò M, Veronesi M, Vulpetti A, Sundström M (2000) Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water*. J Biomol NMR 18(1):65–68. PubMedGoogle Scholar
  30. Dalvit C, Fogliatto G, Stewart A, Veronesi M, Stockman B (2001) WaterLOGSY as a method for primary NMR screening: practical aspects and range of applicability. J Biomol NMR 21(4):349–359. PubMedGoogle Scholar
  31. Das A, Zhao J, Schatz GC, Sligar SG, Van Duyne RP (2009) Screening of type I and II drug binding to human cytochrome P450-3A4 in Nanodiscs by localized surface plasmon resonance spectroscopy. Anal Chem 81 (10):3754–3759. PubMedPubMedCentralGoogle Scholar
  32. David G, Pérez J (2009) Combined sampler robot and high-performance liquid chromatography: a fully automated system for biological small-angle x-ray scattering experiments at the synchrotron SOLEIL SWING beamline. J Appl Crystallogr 42(5):892–900. Google Scholar
  33. Davies TG, Tickle IJ (2011) Fragment screening using x-ray crystallography. In: Fragment-based drug discovery and x-ray crystallography, topics in current chemistry. Springer, Berlin, pp 33–59. Google Scholar
  34. Dias DM, Ciulli A (2014) NMR approaches in structure-based lead discovery: recent developments and new frontiers for targeting multi-protein complexes. Prog Biophys Mol Biol 116(2-3):101–112. PubMedPubMedCentralGoogle Scholar
  35. van Dongen M, Weigelt J, Uppenberg J, Schultz J, Wikström M (2002) Structure-based screening and design in drug discovery. Drug Discov Today 7(8):471–478. PubMedGoogle Scholar
  36. Erlanson DA, Fesik SW, Hubbard RE, Jahnke W, Jhoti H (2016) Twenty years on: the impact of fragments on drug discovery. Nat Rev Drug Discovery 15(9):605. PubMedGoogle Scholar
  37. Felli IC, Brutscher B (2009) Recent advances in solution NMR: fast methods and heteronuclear direct detection. ChemPhysChem 10(9-10):1356–1368. PubMedGoogle Scholar
  38. Franke D, Jeffries CM, Svergun DI (2015) Correlation map, a goodness-of-fit test for one-dimensional x-ray scattering spectra. Nat Methods 12(5):419–422. PubMedGoogle Scholar
  39. Franke D, Petoukhov MV, Konarev PV, Panjkovich A, Tuukkanen A, Mertens HDT, Kikhney AG, Hajizadeh NR, Franklin JM, Jeffries CM, Svergun DI (2017) ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions. J Appl Crystallogr 50(4):1212–1225. PubMedPubMedCentralGoogle Scholar
  40. Freiburger L, Sonntag M, Hennig J, Li J, Zou P, Sattler M (2015) Efficient segmental isotope labeling of multi-domain proteins using Sortase A. J Biomol NMR 63(1):1–8. PubMedGoogle Scholar
  41. Friberg A, Vigil D, Zhao B, Daniels RN, Burke JP, Garcia-Barrantes PM, Camper D, Chauder BA, Lee T, Olejniczak ET, Fesik SW (2013) Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design. J Med Chem 56(1):15–30. PubMedGoogle Scholar
  42. Fukuda M, Watanabe A, Hayasaka A, Muraoka M, Hori Y, Yamazaki T, Imaeda Y, Koga A (2017) Small-scale screening method for low-viscosity antibody solutions using small-angle x-ray scattering. Eur J Pharm Biopharm 112:132–137. PubMedGoogle Scholar
  43. Gabel F (2015) Chapter thirteen - small-angle neutron scattering for structural biology of protein–RNA complexes. In: Allain S (ed) Methods in enzymology, structures of large RNA molecules and their complexes, vol 558, Academic Press, pp 391-415Google Scholar
  44. Gorba C, Miyashita O, Tama F (2008) Normal-mode flexible fitting of high-resolution structure of biological molecules toward one-dimensional low-resolution data. Biophys J 94(5):1589–1599. PubMedPubMedCentralGoogle Scholar
  45. Grant TD, Luft JR, Wolfley JR, Tsuruta H, Martel A, Montelione GT, Snell EH (2011) Small angle x-ray scattering as a complementary tool for high-throughput structural studies. Biopolymers 95(8):517–530. PubMedPubMedCentralGoogle Scholar
  46. Grishaev A, Wu J, Trewhella J, Bax A (2005) Refinement of multidomain protein structures by combination of solution small-angle x-ray scattering and NMR data. J Am Chem Soc 127(47):16621–16628. PubMedGoogle Scholar
  47. Grøftehauge MK, Hajizadeh NR, Swann MJ, Pohl E (2015) Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI). Acta Crystallogr D 71(1):36–44. PubMedGoogle Scholar
  48. von Gundlach AR, Garamus VM, Gorniak T, Davies HA, Reischl M, Mikut R, Hilpert K, Rosenhahn A (2016) Small angle x-ray scattering as a high-throughput method to classify antimicrobial modes of action. Biochim Biophys Acta, Biomembr 1858(5):918–925. Google Scholar
  49. Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, Muto Y, Yokoyama S (1999) Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398(6728):579–585. PubMedGoogle Scholar
  50. Harner MJ, Frank AO, Fesik SW (2013) Fragment-based drug discovery using NMR spectroscopy. J Biomol NMR 56(2):65–75. PubMedPubMedCentralGoogle Scholar
  51. Hassell AM, An G, Bledsoe RK, Bynum JM, Carter HL, Deng SJJ, Gampe RT, Grisard TE, Madauss KP, Nolte RT, Rocque WJ, Wang L, Weaver KL, Williams SP, Wisely GB, Xu R, Shewchuk LM (2007) Crystallization of protein ligand complexes. Acta Crystallogr D Biol Crystallogr 63 (1):72–79. PubMedGoogle Scholar
  52. Heller WT (2010) Small-angle neutron scattering and contrast variation: A powerful combination for studying biological structures. Acta Crystallogr D 66(11):1213–1217. PubMedGoogle Scholar
  53. Hennig J, Sattler M (2014) The dynamic duo: Combining NMR and small angle scattering in structural biology. Prot Sci 23(6):669–682. Google Scholar
  54. Hennig J, Wang I, Sonntag M, Gabel F, Sattler M (2013) Combining NMR and small angle x-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex. J Biomol NMR 56(1):17–30. PubMedGoogle Scholar
  55. Hennig J, Militti C, Popowicz GM, Wang I, Sonntag M, Geerlof A, Gabel F, Gebauer F, Sattler M (2014) Structural basis for the assembly of the Sxl-Unr translation regulatory complex. Nature 515 (7526):287–290. PubMedGoogle Scholar
  56. Henriques J, Arleth L, Lindorff-Larsen K, Skepö M (2018) On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations. J Mol Biol. PubMedGoogle Scholar
  57. Herranz-Trillo F, Groenning M, van Maarschalkerweerd A, Tauler R, Vestergaard B, Bernadó P (2017) Structural analysis of multi-component amyloid systems by chemometric SAXS data decomposition. Structure 25 (1):5–15. PubMedGoogle Scholar
  58. Huang R, Bonnichon A, Claridge TDW, Leung IKH (2017) Protein-ligand binding affinity determination by the waterLOGSY method: An optimised approach considering ligand rebinding. Sci Rep 7:43727. PubMedPubMedCentralGoogle Scholar
  59. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL II, Tsutakawa SE, Jenney FE Jr, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MWW, Tainer JA (2009) Robust, high-throughput solution structural analyses by small angle x-ray scattering (SAXS). Nat Methods 6(8):606–612. PubMedPubMedCentralGoogle Scholar
  60. Hura GL, Budworth H, Dyer KN, Rambo RP, Hammel M, McMurray CT, Tainer JA (2013) Comprehensive objective maps of macromolecular conformations by quantitative SAXS analysis. Nat Methods 10 (6):453–454. PubMedPubMedCentralGoogle Scholar
  61. Jacrot B (1976) The study of biological structures by neutron scattering from solution. Rep Prog Phys 39 (10):911. Google Scholar
  62. Jahnke W (2002) Spin labels as a tool to identify and characterize protein ligand interactions by NMR spectroscopy. ChemBioChem 3(2-3):167–173.<lt;167::AID-CBIC167>3.0.CO;2-S PubMedGoogle Scholar
  63. Jamros MA, Oliveira LC, Whitford PC, Onuchic JN, Adams JA, Blumenthal DK, Jennings PA (2010) Proteins at work: a combined small angle x-ray scattering and theoretical determination of the multiple structures involved on the protein kinase functional landscape. J Biol Chem 285(46):36121–36128. PubMedPubMedCentralGoogle Scholar
  64. Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J (2015) PyDockSAXS: protein protein complex structure by SAXS and computational docking. Nucl Acids Res 43(W1):W356–W361. PubMedGoogle Scholar
  65. Kantrowitz ER (2012) Allostery and cooperativity in Escherichia coli aspartate transcarbamoylase. Arch Biochem Biophys 519(2):81–90. PubMedGoogle Scholar
  66. Karaca E, Bonvin AMJJ (2013) On the usefulness of ion-mobility mass spectrometry and SAXS data in scoring docking decoys. Acta Crystallogr D 69(5):683–694. PubMedGoogle Scholar
  67. Kikhney AG, Svergun DI (2015) A practical guide to small angle x-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 589(19, Part A):2570–2577. PubMedGoogle Scholar
  68. Kim HS, Gabel F (2015) Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints. Acta Crystallogr D 71(1):57–66. PubMedGoogle Scholar
  69. Kimanius D, Pettersson I, Schluckebier G, Lindahl E, Andersson M (2015) SAXS-guided metadynamics. J Chem Theory Comput 11(7):3491–3498. PubMedGoogle Scholar
  70. Kirby NM, Mudie ST, Hawley AM, Cookson DJ, Mertens HDT, Cowieson N, Samardzic-Boban V (2013) A low-background-intensity focusing small-angle x-ray scattering undulator beamline. J Appl Crystallogr 46(6):1670–1680. Google Scholar
  71. Knight CJ, Hub JS (2015) WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics. Nucl Acids Res 43(W1):W225–W230. PubMedGoogle Scholar
  72. Koutsioubas A, Berthaud A, Mangenot S, Pérez J (2013) Ab initio and all-atom modeling of detergent organization around aquaporin-0 based on SAXS data. J Phys Chem B 117(43):13588–13594. PubMedGoogle Scholar
  73. Lafleur JP, Snakenborg D, Nielsen SS, Møller M, Toft KN, Menzel A, Jacobsen JK, Vestergaard B, Arleth L, Kutter JP (2011) Automated microfluidic sample-preparation platform for high-throughput structural investigation of proteins by small-angle x-ray scattering. J Appl Crystallogr 44 (5):1090–1099. Google Scholar
  74. Lapinaite A, Simon B, Skjaerven L, Rakwalska-Bange M, Gabel F, Carlomagno T (2013) The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature 502(7472):519–523. PubMedGoogle Scholar
  75. Lee CY, Chang CL, Wang YN, Fu LM (2011) Microfluidic mixing: a review. Int J Mol Sci 12 (5):3263–3287. PubMedPubMedCentralGoogle Scholar
  76. Lee JH, Okuno Y, Cavagnero S (2014) Sensitivity enhancement in solution NMR: Emerging ideas and new frontiers. J Magn Reson 241:18–31. PubMedPubMedCentralGoogle Scholar
  77. Li N, Li X, Wang Y, Liu G, Zhou P, Wu H, Hong C, Bian F, Zhang R (2016) The new NCPSS BL19u2 beamline at the SSRF for small-angle x-ray scattering from biological macromolecules in solution. J Appl Crystallogr 49(5):1428–1432. PubMedPubMedCentralGoogle Scholar
  78. Lipfert J, Columbus L, Chu VB, Lesley SA, Doniach S (2007) Size and shape of detergent micelles determined by small-angle x-ray scattering. J Phys Chem B 111(43):12427–12438. PubMedGoogle Scholar
  79. Liu Z, Gong Z, Dong X, Tang C (2016) Transient protein protein interactions visualized by solution NMR. Biochim Biophys Acta Proteins Proteomics 1864(1):115–122. Google Scholar
  80. Lopez CG, Watanabe T, Martel A, Porcar L, Cabral J a T (2015) Microfluidic-SANS: flow processing of complex fluids. Sci Rep 5:7727. PubMedPubMedCentralGoogle Scholar
  81. Madl T, Gabel F, Sattler M (2011) NMR and small-angle scattering-based structural analysis of protein complexes in solution. J Struct Biol 173(3):472–482. PubMedGoogle Scholar
  82. Makowski L, Gore D, Mandava S, Minh D, Park S, Rodi DJ, Fischetti RF (2011) X-ray solution scattering studies of the structural diversity intrinsic to protein ensembles. Biopolymers 95(8):531–542. PubMedPubMedCentralGoogle Scholar
  83. Mangel WF, Lin BH, Ramakrishnan V (1990) Characterization of an extremely large, ligand-induced conformational change in plasminogen. Science 248(4951):69–73. PubMedGoogle Scholar
  84. Martel A, Liu P, Weiss TM, Niebuhr M, Tsuruta H (2012) An integrated high-throughput data acquisition system for biological solution x-ray scattering studies. J Synchrotron Radiat 19(3):431–434. PubMedPubMedCentralGoogle Scholar
  85. Mayer M, Meyer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 38(12):1784–1788.<lt;1784::AID-ANIE1784>3.0.CO;2-Q Google Scholar
  86. Maynard JA, Lindquist NC, Sutherland JN, Lesuffleur A, Warrington AE, Rodriguez M, Oh SH (2009) Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteins. Biotechnol J 4(11):1542–1558. PubMedPubMedCentralGoogle Scholar
  87. Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L (2013) Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model. Biopolymers 99(12):1032–1045. PubMedGoogle Scholar
  88. Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis M, Pragani R, Boxer M, Earl LA, Milne JL, Subramaniam S (2016) Breaking cryo-EM resolution barriers to facilitate drug discovery. Cell 165(7):1698–1707. PubMedPubMedCentralGoogle Scholar
  89. Meyer B, Peters T (2003) NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors. Angew Chem Int Ed 42(8):864–890. Google Scholar
  90. Møller M, Nielsen SS, Ramachandran S, Li Y, Tria G, Streicher W, Petoukhov MV, Cerione RA, Gillilan RE, Vestergaard B (2013) Small angle x-ray scattering studies of mitochondrial glutaminase c reveal extended flexible regions, and link oligomeric state with enzyme activity. PLOS ONE 8(9):e74783. PubMedPubMedCentralGoogle Scholar
  91. Murray CW, Carr MG, Callaghan O, Chessari G, Congreve M, Cowan S, Coyle JE, Downham R, Figueroa E, Frederickson M, Graham B, McMenamin R, O’Brien MA, Patel S, Phillips TR, Williams G, Woodhead AJ, Woolford AJA (2010) Fragment-based drug discovery applied to hsp90. Discovery of two lead series with high ligand efficiency. J Med Chem 53(16):5942–5955. PubMedGoogle Scholar
  92. Navratilova I, Hopkins AL (2010) Fragment screening by surface plasmon resonance. ACS Med Chem Lett 1(1):44–48. PubMedPubMedCentralGoogle Scholar
  93. Neutze R, Moffat K (2012) Time-resolved structural studies at synchrotrons and x-ray free electron lasers: Opportunities and challenges. Curr Opin Struct Biol 22(5):651–659. PubMedPubMedCentralGoogle Scholar
  94. Olah GA, Trakhanov S, Trewhella J, Quiocho FA (1993) Leucine/isoleucine/valine-binding protein contracts upon binding of ligand. J Biol Chem 268(22):16241–16247PubMedGoogle Scholar
  95. Oliver RC, Lipfert J, Fox DA, Lo RH, Doniach S, Columbus L (2013) Dependence of micelle size and shape on detergent alkyl chain length and head group. PLoS ONE 8(5):e62488. PubMedPubMedCentralGoogle Scholar
  96. Patching SG (2014) Surface plasmon resonance spectroscopy for characterisation of membrane protein ligand interactions and its potential for drug discovery. Biochim Biophys Acta Biomembr 1838(1, Part A):43–55. Google Scholar
  97. Patel D, Bauman JD, Arnold E (2014) Advantages of crystallographic fragment screening: Functional and mechanistic insights from a powerful platform for efficient drug discovery. Prog Biophys Mol Biol 116(2):92–100. PubMedPubMedCentralGoogle Scholar
  98. Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL (2007) Drugs for bad bugs: Confronting the challenges of antibacterial discovery. Nat Rev Drug Discovery 6(1):29–40. PubMedGoogle Scholar
  99. Petoukhov MV, Svergun DI (2005) Global rigid body modeling of macromolecular complexes against small-angle scattering data. Biophys J 89(2):1237–1250. PubMedPubMedCentralGoogle Scholar
  100. Pham N, Radajewski D, Round A, Brennich M, Pernot P, Biscans B, Bonneté F, Teychené S (2017) Coupling high throughput microfluidics and small-angle x-ray scattering to study protein crystallization from solution. Anal Chem 89(4):2282–2287. PubMedGoogle Scholar
  101. Piliarik M, Vaisocherová H, Homola J (2005) A new surface plasmon resonance sensor for high-throughput screening applications. Biosens Bioelectron 20(10):2104–2110. PubMedGoogle Scholar
  102. Prati F, De Simone A, Armirotti A, Summa M, Pizzirani D, Scarpelli R, Bertozzi SM, Perez DI, Andrisano V, Perez-Castillo A, Monti B, Massenzio F, Polito L, Racchi M, Sabatino P, Bottegoni G, Martinez A, Cavalli A, Bolognesi ML (2015) 3,4-Dihydro-1,3,5-triazin-2(1H)-ones as the first dual BACE-1/GSK-3β fragment hits against Alzheimer’s disease. ACS Chem Neurosci 6(10):1665–1682. PubMedGoogle Scholar
  103. Puthenveetil R, Nguyen K, Vinogradova O (2017) Nanodiscs and solution NMR: Preparation, application and challenges. Nanotechnol Rev 6(1):111–126. PubMedGoogle Scholar
  104. 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. PubMedGoogle Scholar
  105. Rambo RP, Tainer JA (2011) Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the porod-Debye law. Biopolymers 95(8):559–571. PubMedPubMedCentralGoogle Scholar
  106. Rambo RP, Tainer JA (2013) Super-resolution in solution x-ray scattering and its applications to structural systems biology. Ann Rev Biophys 42(1):415–441. Google Scholar
  107. Ranganathan A, Heine P, Rudling A, Plückthun A, Kummer L, Carlsson J (2017) Ligand discovery for a peptide-binding GPCR by structure-based screening of fragment- and lead-like chemical libraries. ACS Chem Biol 12(3):735–745. PubMedGoogle Scholar
  108. Receveur-Bréchot V, Durand D (2012) How random are intrinsically disordered proteins? A small angle scattering perspective. Curr Protein Pept Sci 13(1):55–75. PubMedPubMedCentralGoogle Scholar
  109. Renaud JP, Cw Chung, Danielson UH, Egner U, Hennig M, Hubbard RE, Nar H (2016) Biophysics in drug discovery: Impact, challenges and opportunities. Nat Rev Drug Discovery 15(10):679–698. PubMedGoogle Scholar
  110. Renaud JP, Chari A, Ciferri C, Liu Wt, Rémigy HW, Stark H, Wiesmann C (2018) Cryo-EM in drug discovery: Achievements, limitations and prospects. Nat Rev Drug Discovery. PubMedGoogle Scholar
  111. Ritchie TK, Grinkova YV, Bayburt TH, Denisov IG, Zolnerciks JK, Atkins WM, Sligar SG (2009) Chapter eleven - reconstitution of membrane proteins in phospholipid bilayer Nanodiscs. In: Düzgünes N (ed) Methods in enzymology, liposomes, Part F, vol 464, Academic Press, pp 211–231. Google Scholar
  112. Rodriguez-Ruiź I, Radajewski D, Charton S, Phamvan N, Brennich M, Pernot P, Bonneté F, Teychené S, Rodriguez-Ruiź I, Radajewski D, Charton S, Phamvan N, Brennich M, Pernot P, Bonneté F, Teychené S (2017) Innovative high-throughput SAXS methodologies based on photonic lab-on-a-chip sensors: Application to macromolecular studies. Sensors 17(6):1266. Google Scholar
  113. Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG (2015) A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins 83(2):309–317. PubMedGoogle Scholar
  114. Round A, Felisaz F, Fodinger L, Gobbo A, Huet J, Villard C, Blanchet CE, Pernot P, McSweeney S, Roessle M, Svergun DI, Cipriani F (2015) BioSAXS sample changer: A robotic sample changer for rapid and reliable high-throughput X-ray solution scattering experiments. Acta Crystallogr D 71(1):67–75. PubMedGoogle Scholar
  115. RóŻycki B, Kim YC, Hummer G (2011) SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure 19(1):109–116. PubMedPubMedCentralGoogle Scholar
  116. Salamon Z, Macleod HA, Tollin G (1997a) Surface plasmon resonance spectroscopy as a tool for investigating the biochemical and biophysical properties of membrane protein systems. I: Theoretical principles. Biochim Biophys Acta Biomembr 1331(2):117–129. Google Scholar
  117. Salamon Z, Macleod HA, Tollin G (1997b) Surface plasmon resonance spectroscopy as a tool for investigating the biochemical and biophysical properties of membrane protein systems. II: Applications to biological systems. Biochim Biophys Acta Biomembr 1331(2):131–152. Google Scholar
  118. Sánchez-Pedregal VM, Reese M, Meiler J, Blommers MJJ, Griesinger C, Carlomagno T (2005) The INPHARMA method: Protein-mediated interligand NOEs for pharmacophore mapping. Angew Chem Int Ed 44(27):4172–4175. Google Scholar
  119. Schiebel J, Radeva N, Krimmer SG, Wang X, Stieler M, Ehrmann FR, Fu K, Metz A, Huschmann FU, Weiss MS, Mueller U, Heine A, Klebe G (2016) Six biophysical screening methods miss a large proportion of crystallographically discovered fragment hits: A case study. ACS Chem Biol 11(6):1693–1701. PubMedGoogle Scholar
  120. Schindler CEM, de Vries SJ, Sasse A, Zacharias M (2016) SAXS data alone can generate high-quality models of protein-protein complexes. Structure 24 (8):1387–1397. PubMedGoogle Scholar
  121. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A (2016) FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucl Acids Res 44(W1):W424–W429. PubMedGoogle Scholar
  122. Schwemmer F, E Blanchet C, Spilotros A, Kosse D, Zehnle S, T Mertens HD, A Graewert M, Rössle M, Paust N, I Svergun D, von Stetten F, Zengerle R, Mark D (2016) LabDisk for SAXS: A centrifugal microfluidic sample preparation platform for small-angle X-ray scattering. Lab Chip 16(7):1161–1170. PubMedGoogle Scholar
  123. Sedlak SM, Bruetzel LK, Lipfert J (2017) Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements. J Appl Crystallogr 50(2):621–630. PubMedPubMedCentralGoogle Scholar
  124. Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Discovering high-Affinity ligands for proteins: SAR by NMR. Science 274(5292):1531–1534. PubMedGoogle Scholar
  125. Skar-Gislinge N, Kynde SaR, Denisov IG, Ye X, Lenov I, Sligar SG, Arleth L (2015) Small-angle scattering determination of the shape and localization of human cytochrome p450 embedded in a phospholipid nanodisc environment. Acta Crystallogr D Biol Crystallogr 71(12):2412–2421. PubMedPubMedCentralGoogle Scholar
  126. Skjærven L, Codutti L, Angelini A, Grimaldi M, Latek D, Monecke P, Dreyer MK, Carlomagno T (2013) Accounting for conformational variability in protein–ligand docking with NMR-guided rescoring. J Am Chem Soc 135(15):5819–5827. PubMedGoogle Scholar
  127. Skou S, Gillilan RE, Ando N (2014) Synchrotron-based small-angle X-ray scattering of proteins in solution. Nat Protocols 9(7):1727–1739. PubMedGoogle Scholar
  128. Sonntag M, Jagtap PKA, Simon B, Appavou MS, Geerlof A, Stehle R, Gabel F, Hennig J, Sattler M (2017) Segmental, domain-Selective perdeuteration and small-Angle neutron scattering for structural analysis of multi-Domain proteins. Angew Chem Int Ed 56(32):9322–9325. Google Scholar
  129. Svergun DI, Koch MHJ, Pedersen JS, Serdyuk IN (1994) Structural model of the 50 S subunit of escherichia coli ribosomes from solution scattering: II. Neutron scattering study. J Mol Biol 240(1):78–86. PubMedGoogle Scholar
  130. Svergun DI, Koch MHJ, Timmins PA, May RP (2013) Small angle X-Ray and neutron scattering from solutions of biological macromolecules. Oxford University Press.
  131. Tian X, Langkilde AE, Thorolfsson M, Rasmussen HB, Vestergaard B (2014) Small-angle X-ray scattering screening complements conventional biophysical analysis: Comparative structural and biophysical analysis of monoclonal antibodies IgG1, IgG2, and IgG4. J Pharmaceut Sci 103(6):1701–1710. Google Scholar
  132. Tompa P (2012) Intrinsically disordered proteins: A 10-year recap. Trends Biochem Sci 37(12):509–516. PubMedGoogle Scholar
  133. Trewhella J (2016) Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol 40:1–7. PubMedGoogle Scholar
  134. Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE (2017) 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: An update. Acta Crystallogr D 73(9):710–728. Google Scholar
  135. Tsao DHH, Sutherland AG, Jennings LD, Li Y, Rush TS, Alvarez JC, Ding W, Dushin EG, Dushin RG, Haney SA, Kenny CH, Karl Malakian A, Nilakantan R, Mosyak L (2006) Discovery of novel inhibitors of the zipa/FtsZ complex by NMR fragment screening coupled with structure-based design. Bioorg Med Chem 14(23):7953–7961. PubMedGoogle Scholar
  136. Tuukkanen AT, Svergun DI (2014) Weak protein ligand interactions studied by small-angle X-ray scattering. FEBS J 281(8):1974–1987. PubMedGoogle Scholar
  137. Valentini E, Kikhney AG, Previtali G, Jeffries CM, Svergun DI (2015) SASBDB, a repository for biological small-angle scattering data. Nucl Acids Res 43(D1):D357–D363. PubMedGoogle Scholar
  138. Vanwetswinkel S, Heetebrij RJ, van Duynhoven J, Hollander JG, Filippov DV, Hajduk PJ, Siegal G (2005) TINS, Target Immobilized NMR Screening: An Efficient, and Sensitive Method for Ligand Discovery. Chem Biol 12(2):207–216. Google Scholar
  139. Vestergaard B, Sayers Z (2014) Investigating increasingly complex macromolecular systems with small-angle X-ray scattering. IUCrJ 1(6):523–529. PubMedPubMedCentralGoogle Scholar
  140. Wagstaff JL, Taylor SL, Howard MJ (2013) Recent developments and applications of saturation transfer difference nuclear magnetic resonance (STD NMR) spectroscopy. Mol BioSyst 9(4):571–577. PubMedGoogle Scholar
  141. Watkin SAJ, Ryan TM, Miller AG, M Nock V, Pearce FG, Dobson RCJ (2017) Microfluidics for Small-Angle X-ray Scattering. X-ray Scattering. Google Scholar
  142. Wilcox KC, Marunde MR, Das A, Velasco PT, Kuhns BD, Marty MT, Jiang H, Luan CH, Sligar SG, Klein WL (2015) Nanoscale synaptic membrane mimetic allows unbiased high throughput screen that targets binding sites for Alzheimer’s-Associated Aβ Oligomers. PLoS ONE 10(4):e0125263. PubMedPubMedCentralGoogle Scholar
  143. Williamson MP (2013) Using chemical shift perturbation to characterise ligand binding. Prog Nucl Magn Reson Spectrosc 73:1–16. PubMedGoogle Scholar
  144. Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis IC, Vajda S, Kozakov D (2015) Accounting for observed small angle X-ray scattering profile in the protein protein docking server cluspro. J Comput Chem 36(20):1568–1572. PubMedPubMedCentralGoogle Scholar
  145. Yang S, Blachowicz L, Makowski L, Roux B (2010) Multidomain Assembled States of hck tyrosine kinase in solution. Proc Natl Acad Sci USA 107(36):15757–15762. PubMedGoogle Scholar
  146. You JB, Kang K, Tran TT, Park H, Hwang WR, Kim JM, Im SG (2015) PDMS-based turbulent microfluidic mixer. Lab Chip 15(7):1727–1735. PubMedGoogle Scholar
  147. Zeng Y, Hu R, Wang L, Gu D, He J, Wu SY, Ho HP, Li X, Qu J, Gao BZ, Shao Y (2017) Recent advances in surface plasmon resonance imaging: Detection speed, sensitivity, and portability. Nanophotonics 6(5):1017–1030. Google Scholar
  148. Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Almo SC, Minor W (2015) X-ray crystallography over the past decade for novel drug discovery where are we heading next? Expert Opin Drug Discovery 10(9):975–989. Google Scholar
  149. Zheng W, Tekpinar M (2011) Accurate flexible fitting of high-Resolution protein structures to small-Angle x-Ray Scattering Data Using a coarse-Grained model with Implicit Hydration Shell. Biophys J 101(12):2981–2991. PubMedPubMedCentralGoogle Scholar

Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Structural and Computational Biology UnitEuropean Molecular Biology Laboratory HeidelbergHeidelbergGermany

Personalised recommendations