A Practical Guide to iSPOT Modeling: An Integrative Structural Biology Platform

  • An Hsieh
  • Lanyuan Lu
  • Mark R. Chance
  • Sichun Yang
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1009)

Abstract

Integrative structure modeling is an emerging method for structural determination of protein-protein complexes that are challenging for conventional structural techniques. Here, we provide a practical protocol for implementing our integrated iSPOT platform by integrating three different biophysical techniques: small-angle X-ray scattering (SAXS), hydroxyl radical footprinting, and computational docking simulations. Specifically, individual techniques are described from experimental and/or computational perspectives, and complementary structural information from these different techniques are integrated for accurate characterization of the structures of large protein-protein complexes.

Keywords

iSPOT Integrative structural biology SAXS Hydroxyl radical footprinting Computational docking simulation Structural mass spectrometry Protein-protein interaction 

Notes

Acknowledgements

This work was supported by the NIH (R01GM114056 and P30EB009998), the DoD (W81XWH-11-1033), and by the Ministry of Education of Singapore (2014-T2-1-065). Beamtime access was supported via the BioCAT at the Advanced Photo Source and the LiX beamline at the NSLS-II by the DoE (DE-AC02-06CH11357 and KP1605010) and by the NIH (9P41GM103622 and P41GM111244). Additional support was provided by the Ohio Supercomputer Center and the Clinical and Translational Science Collaborative of Cleveland (4UL1TR000439). The content is solely the responsibility of the authors and does not necessarily reflect the official views of the National Institute of General Medical Sciences or the National Institutes of Health.

References

  1. Bernado P, Blackledge M (2010) Structural biology: proteins in dynamic equilibrium. Nature 468:1046–1048CrossRefPubMedGoogle Scholar
  2. Blanchet CE, Svergun DI (2013) Small-angle X-ray scattering on biological macromolecules and nanocomposites in solution. Annu Rev Phys Chem 64:37–54CrossRefPubMedGoogle Scholar
  3. Chen R, Li L, Weng Z (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52:80–87CrossRefPubMedGoogle Scholar
  4. Comeau SR, Gatchell DW, Vajda S, Camacho CJ (2004) ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32:W96–W99CrossRefPubMedPubMedCentralGoogle Scholar
  5. Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737CrossRefPubMedGoogle Scholar
  6. Gabb HA, Jackson RM, Sternberg MJE (1997) Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272:106–120CrossRefPubMedGoogle Scholar
  7. Huang W, Ravikumar KM, Yang S (2014) A newfound cancer-activating mutation reshapes the energy landscape of estrogen-binding domain. J Chem Theory Comput 10:2897–2900CrossRefPubMedGoogle Scholar
  8. Huang W, Ravikumar KM, Chance MR, Yang S (2015) Quantitative mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry: a protection factor analysis. Biophys J 108:1–9CrossRefGoogle Scholar
  9. Huang W, Ravikumar KM, Parisien M, Yang S (2016) Theoretical modeling of multiprotein complexes by iSPOT: integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking. J Struct Biol 196:340CrossRefPubMedPubMedCentralGoogle Scholar
  10. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ, Critical Assessment of, P.I (2003) CAPRI: a critical assessment of predicted interactions. Proteins 52:2–9CrossRefPubMedGoogle Scholar
  11. Jeffries CM, Graewert MA, Blanchet CE, Langley DB, Whitten AE, Svergun DI (2016) Preparing monodisperse macromolecular samples for successful biological small-angle X-ray and neutron-scattering experiments. Nat Protoc 11:2122–2153CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kaur P, Kiselar J, Yang S, Chance MR (2015) Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry. Mol Cell Proteomics (in press)Google Scholar
  13. Kikhney AG, Svergun DI (2015) A practical guide to small angle X-ray scattering (SAXS) of flexible and intrinsically disordered proteins. FEBS Lett 589:2570–2577CrossRefPubMedGoogle Scholar
  14. Pierce BG, Wiehe K, Hwang H, Kim BH, Vreven T, Weng Z (2014) ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 30:1771–1773CrossRefPubMedPubMedCentralGoogle Scholar
  15. 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 40:191–285CrossRefPubMedGoogle Scholar
  16. Ravikumar KM, Huang W, Yang S (2012) Coarse-grained simulations of protein-protein association: an energy landscape perspective. Biophys J 103:837–845CrossRefPubMedPubMedCentralGoogle Scholar
  17. Ravikumar KM, Huang W, Yang S (2013) Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. J Chem Phys 138:024112CrossRefPubMedGoogle Scholar
  18. Skou S, Gillilan RE, Ando N (2014) Synchrotron-based small-angle X-ray scattering of proteins in solution. Nat Protoc 9:1727–1739CrossRefPubMedPubMedCentralGoogle Scholar
  19. 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
  20. Tong D, Yang S, Lu L (2016) Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures. J Appl Crystallogr 49:1148–1161CrossRefPubMedPubMedCentralGoogle Scholar
  21. Tovchigrechko A, Vakser IA (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34:W310–W314CrossRefPubMedPubMedCentralGoogle Scholar
  22. Xu G, Chance MR (2007) Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem Rev 107:3514–3543CrossRefPubMedGoogle Scholar
  23. Yang S (2014) Methods for SAXS-based structure determination of biomolecular complexes. Adv Mater 26:7902–7910CrossRefPubMedPubMedCentralGoogle Scholar
  24. Yang S, Park S, Makowski L, Roux B (2009) A rapid coarse residue-based computational method for x-ray solution scattering characterization of protein folds and multiple conformational states of large protein complexes. Biophys J 96:4449–4463CrossRefPubMedPubMedCentralGoogle Scholar
  25. Yang S, Blachowicz L, Makowski L, Roux B (2010a) Multidomain assembled states of Hck tyrosine kinase in solution. Proc Natl Acad Sci U S A 107:15757–15762CrossRefPubMedPubMedCentralGoogle Scholar
  26. Yang S, Parisien M, Major F, Roux B (2010b) RNA structure determination using SAXS data. J Phys Chem B 114:10039–10048CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • An Hsieh
    • 1
  • Lanyuan Lu
    • 2
  • Mark R. Chance
    • 1
  • Sichun Yang
    • 1
  1. 1.Center for Proteomics and Bioinformatics and Department of NutritionCase Western Reserve UniversityClevelandUSA
  2. 2.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore

Personalised recommendations