Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform

  • Benjamin Webb
  • Keren Lasker
  • Javier Velázquez-Muriel
  • Dina Schneidman-Duhovny
  • Riccardo Pellarin
  • Massimiliano Bonomi
  • Charles Greenberg
  • Barak Raveh
  • Elina Tjioe
  • Daniel Russel
  • Andrej Sali
Part of the Methods in Molecular Biology book series (MIMB, volume 1091)

Abstract

To understand the workings of the living cell, we need to characterize protein assemblies that constitute the cell (for example, the ribosome, 26S proteasome, and the nuclear pore complex). A reliable high-resolution structural characterization of these assemblies is frequently beyond the reach of current experimental methods, such as X-ray crystallography, NMR spectroscopy, electron microscopy, footprinting, chemical cross-linking, FRET spectroscopy, small angle X-ray scattering, and proteomics. However, the information garnered from different methods can be combined and used to build models of the assembly structures that are consistent with all of the available datasets, and therefore more accurate, precise, and complete. Here, we describe a protocol for this integration, whereby the information is converted to a set of spatial restraints and a variety of optimization procedures can be used to generate models that satisfy the restraints as well as possible. These generated models can then potentially inform about the precision and accuracy of structure determination, the accuracy of the input datasets, and further data generation. We also demonstrate the Integrative Modeling Platform (IMP) software, which provides the necessary computational framework to implement this protocol, and several applications for specific use cases.

Key words

Integrative modeling Protein structure modeling Proteomics of macromolecular assemblies X-ray crystallography Electron microscopy SAXS 

Notes

Acknowledgments

We are grateful to all members of our research group, especially to Frank Alber, Friedrich Förster, and Bret Peterson who contributed to early versions of IMP, and Marc Marti-Renom, Davide Baù, Benjamin Schwarz, and Yannick Spill who currently contribute to IMP. We also acknowledge support from National Institutes of Health (R01 GM54762, U54 RR022220, PN2 EY016525, and R01 GM083960) as well as computing hardware support from Ron Conway, Mike Homer, Hewlett-Packard, NetApp, IBM, and Intel.

References

  1. 1.
    Schmeing TM, Ramakrishnan V (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461:1234–1242CrossRefPubMedGoogle Scholar
  2. 2.
    Sali A, Glaeser R, Earnest T et al (2003) From words to literature in structural proteomics. Nature 422:216–225CrossRefPubMedGoogle Scholar
  3. 3.
    Mitra K, Frank J (2006) Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu Rev Biophys Biomol Struct 35:299–317CrossRefPubMedGoogle Scholar
  4. 4.
    Robinson C, Sali A, Baumeister W (2007) The molecular sociology of the cell. Nature 450:973–982CrossRefPubMedGoogle Scholar
  5. 5.
    Blundell T, Johnson L (1976) Protein crystallography. Academic, New YorkGoogle Scholar
  6. 6.
    Stahlberg H, Walz T (2008) Molecular electron microscopy: state of the art and current challenges. ACS Chem Biol 3:268–281CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Chiu W, Baker ML, Jiang W et al (2005) Electron cryomicroscopy of biological machines at subnanometer resolution. Structure 13:363–372CrossRefPubMedGoogle Scholar
  8. 8.
    Lucic V, Leis A, Baumeister W (2008) Cryo-electron tomography of cells: connecting structure and function. Histochem Cell Biol 130:185–196CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Parrish JR, Gulyas KD, Finley RL Jr (2006) Yeast two-hybrid contributions to interactome mapping. Curr Opin Biotechnol 17:387–393CrossRefPubMedGoogle Scholar
  10. 10.
    Gingras AC, Gstaiger M, Raught B et al (2007) Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8:645–654CrossRefPubMedGoogle Scholar
  11. 11.
    Russel D, Lasker K, Webb B et al (2012) Putting the pieces together: integrative structure determination of macromolecular assemblies. PLoS Biol 10:e1001244CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    Alber F, Kim M, Sali A (2005) Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13:435–445Google Scholar
  13. 13.
    Alber F, Dokudovskaya S, Veenhoff L et al (2007) Determining the architectures of macromolecular assemblies. Nature 450:683–694CrossRefPubMedGoogle Scholar
  14. 14.
    Alber F, Dokudovskaya S, Veenhoff L et al (2007) The molecular architecture of the nuclear pore complex. Nature 450:695–701CrossRefPubMedGoogle Scholar
  15. 15.
    Lasker K, Phillips JL, Russel D et al (2010) Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics 9:1689–1702CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Russel D, Lasker K, Phillips J et al (2009) The structural dynamics of macromolecular processes. Curr Opin Cell Biol 21:97–108CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Alber F, Forster F, Korkin D et al (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem 77:443–477CrossRefPubMedGoogle Scholar
  18. 18.
    Alber F, Chait BT, Rout MP et al (2008) Integrative structure determination of protein assemblies by satisfaction of spatial restraints. In: Panchenko A, Przytycka T (eds) Protein–protein interactions and networks: identification, characterization and prediction. Springer, London, UK, pp 99–114CrossRefGoogle Scholar
  19. 19.
    Bonvin AM, Boelens R, Kaptein R (2005) NMR analysis of protein interactions. Curr Opin Chem Biol 9:501–508CrossRefPubMedGoogle Scholar
  20. 20.
    Fiaux J, Bertelsen EB, Horwich AL et al (2002) NMR analysis of a 900K GroEL GroES complex. Nature 418:207–211CrossRefPubMedGoogle Scholar
  21. 21.
    Neudecker P, Lundstrom P, Kay LE (2009) Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding. Biophys J 96:2045–2054CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Takamoto K, Chance MR (2006) Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes. Annu Rev Biophys Biomol Struct 35:251–276CrossRefPubMedGoogle Scholar
  23. 23.
    Guan JQ, Chance MR (2005) Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci 30:583–592CrossRefPubMedGoogle Scholar
  24. 24.
    Taverner T, Hernandez H, Sharon M et al (2008) Subunit architecture of intact protein complexes from mass spectrometry and homology modeling. Acc Chem Res 41:617–627CrossRefPubMedGoogle Scholar
  25. 25.
    Chen ZA, Jawhari A, Fischer L et al (2010) Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J 29:717–726CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Sinz A (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions. Mass Spectrom Rev 25:663–682CrossRefPubMedGoogle Scholar
  27. 27.
    Trester-Zedlitz M, Kamada K, Burley SK et al (2003) A modular cross-linking approach for exploring protein interactions. J Am Chem Soc 125:2416–2425CrossRefPubMedGoogle Scholar
  28. 28.
    Joo C, Balci H, Ishitsuka Y et al (2008) Advances in single-molecule fluorescence methods for molecular biology. Annu Rev Biochem 77:51–76CrossRefPubMedGoogle Scholar
  29. 29.
    Mertens HD, Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering. J Struct Biol 172:128–141CrossRefPubMedGoogle Scholar
  30. 30.
    Hura GL, Menon AL, Hammel M et al (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS). Nat Methods 6:606–612CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Schneidman-Duhovny D, Kim SJ, Sali A (2012) Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12:17CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Berggard T, Linse S, James P (2007) Methods for the detection and analysis of protein–protein interactions. Proteomics 7:2833–2842CrossRefPubMedGoogle Scholar
  33. 33.
    Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815CrossRefPubMedGoogle Scholar
  34. 34.
    Sali A, Blundell T (1994) Comparative protein modeling by statisfaction of spatial restraints. In: Bohr H, Brunak S (eds) Protein structure by distance analysis. Symposium on distance based approaches to protein structure determination. CTR Biol Sequence Anal. Tech Univ Denmark, Lyngby, Denmark, pp 64–86Google Scholar
  35. 35.
    Vajda S, Kozakov D (2009) Convergence and combination of methods in protein–protein docking. Curr Opin Struct Biol 19:164–170CrossRefPubMedPubMedCentralGoogle Scholar
  36. 36.
    Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15:2507–2524CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Melo F, Sanchez R, Sali A (2002) Statistical potentials for fold assessment. Protein Sci 11:430–448CrossRefPubMedPubMedCentralGoogle Scholar
  38. 38.
    Brooks BR, Brooks CL 3rd, Mackerell AD Jr et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Case DA, Cheatham TE 3rd, Darden T et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668–1688CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Christen M, Hunenberger PH, Bakowies D et al (2005) The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem 26:1719–1751CrossRefPubMedGoogle Scholar
  41. 41.
    Forster F, Lasker K, Beck F et al (2009) An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun 388:228–233CrossRefPubMedPubMedCentralGoogle Scholar
  42. 42.
    Nickell S, Beck F, Scheres SHW et al (2009) Insights into the molecular architecture of the 26S proteasome. Proc Natl Acad Sci USA 29:11943–11947CrossRefGoogle Scholar
  43. 43.
    Lasker K, Forster F, Bohn S et al (2012) Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109: 1380–1387CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Lasker K, Sali A, Wolfson HJ (2010) Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins 78:3205–3211CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Lasker K, Topf M, Sali A et al (2009) Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. J Mol Biol 388:180–194CrossRefPubMedPubMedCentralGoogle Scholar
  46. 46.
    Webb B, Lasker K, Schneidman-Duhovny D et al (2011) Modeling of proteins and their assemblies with the integrative modeling platform. Methods Mol Biol 781:377–397CrossRefPubMedGoogle Scholar
  47. 47.
    Lensink MF, Wodak SJ (2010) Docking and scoring protein interactions: CAPRI 2009. Proteins 78:3073–3084CrossRefPubMedGoogle Scholar
  48. 48.
    Ritchie DW (2008) Recent progress and future directions in protein–protein docking. Curr Protein Pept Sci 9:1–15CrossRefPubMedGoogle Scholar
  49. 49.
    Schneidman-Duhovny D, Rossi A, Avila-Sakar A et al (2012) A method for integrative structure determination of protein–protein complexes. Bioinformatics 28:3282–3289CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Reese ML, Dotsch V (2003) Fast mapping of protein–protein interfaces by NMR spectroscopy. J Am Chem Soc 125:14250–14251CrossRefPubMedGoogle Scholar
  51. 51.
    Rappsilber J (2011) The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J Struct Biol 173:530–540CrossRefPubMedPubMedCentralGoogle Scholar
  52. 52.
    Berman HM, Battistuz T, Bhat TN et al (2002) The Protein Data Bank. Acta Crystallogr D 58:899–907Google Scholar
  53. 53.
    Lawson CL, Baker ML, Best C et al (2011) EMDataBank.org: unified data resource for CryoEM. Nucleic Acids Res 39:D456–D464Google Scholar
  54. 54.
    Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefPubMedGoogle Scholar
  55. 55.
    Velazquez-Muriel JA, Lasker K, Russel D et al (2012) Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci USA 109:18821–18826CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Ritchie DW, Venkatraman V (2010) Ultra-fast FFT protein docking on graphics processors. Bioinformatics 26:2398–2405CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Benjamin Webb
    • 1
  • Keren Lasker
    • 2
  • Javier Velázquez-Muriel
    • 2
  • Dina Schneidman-Duhovny
    • 2
  • Riccardo Pellarin
    • 2
  • Massimiliano Bonomi
    • 3
  • Charles Greenberg
    • 2
  • Barak Raveh
    • 2
  • Elina Tjioe
    • 2
  • Daniel Russel
    • 2
  • Andrej Sali
    • 2
  1. 1.Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quanstitative Biosciences (QB3)University of California San FranciscoSan FranciscoUSA
  2. 2.Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3)University of California San FranciscoSan FranciscoUSA
  3. 3.Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3)University of California San FranciscoSan FranciscoUSA

Personalised recommendations