Skip to main content
SpringerLink
Log in

Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform

  • Protocol
  • First Online:
Book cover Network Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 781))

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 computational models of the assembly structures that are consistent with all of the available datasets. 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 much 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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Schmeing TM, and Ramakrishnan V (2009) What recent ribosome structures have revealed about the mechanism of translation, Nature 461, 1234–1242.

    Article  PubMed  CAS  Google Scholar 

  2. Sali A, Glaeser R, Earnest T, and Baumeister W (2003) From words to literature in structural proteomics, Nature 422, 216–225.

    Article  PubMed  CAS  Google Scholar 

  3. Mitra K, and Frank J (2006) Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps, Annu Rev Biophys Biomol Struct 35, 299–317.

    Article  PubMed  CAS  Google Scholar 

  4. Robinson C, Sali A, and Baumeister W (2007) The molecular sociology of the cell, Nature 450, 973–982.

    Article  PubMed  CAS  Google Scholar 

  5. Blundell T, and Johnson L (1976) Protein Crystallography, Academic Press, New York.

    Google Scholar 

  6. Stahlberg H, and Walz T (2008) Molecular electron microscopy: state of the art and current challenges, ACS Chem Biol 3, 268–281.

    Article  PubMed  CAS  Google Scholar 

  7. Chiu W, Baker ML, Jiang W, Dougherty M, and Schmid MF (2005) Electron cryomicroscopy of biological machines at subnanometer resolution, Structure 13, 363–372.

    Article  PubMed  CAS  Google Scholar 

  8. Lucic V, Leis A, and Baumeister W (2008) Cryo-electron tomography of cells: connecting structure and function, Histochem Cell Biol 130, 185–196.

    Article  PubMed  CAS  Google Scholar 

  9. Parrish JR, Gulyas KD, and Finley RL Jr. (2006) Yeast two-hybrid contributions to interactome mapping, Curr Opin Biotechnol 17, 387–393.

    Article  PubMed  CAS  Google Scholar 

  10. Gingras AC, Gstaiger M, Raught B, and Aebersold R (2007) Analysis of protein complexes using mass spectrometry, Nat Rev Mol Cell Biol 8, 645–654.

    Article  PubMed  CAS  Google Scholar 

  11. Alber F, Kim M, and Sali A (2005) Structural characterization of assemblies from overall shape and subcomplex compositions, Structure 13, 435–445.

    Article  PubMed  CAS  Google Scholar 

  12. Alber F, Dokudovskaya S, Veenhoff L, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait B, Rout M, and Sali A (2007) Determining the architectures of macromolecular assemblies, Nature 450, 683–694.

    Article  PubMed  CAS  Google Scholar 

  13. Alber F, Dokudovskaya S, Veenhoff L, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait B, Sali A, and Rout M (2007) The molecular architecture of the nuclear pore complex, Nature 450, 695–701.

    Article  PubMed  CAS  Google Scholar 

  14. Lasker K, Phillips JL, Russel D, Velazquez-Muriel J, Schneidman-Duhovny D, Webb B, Schlessinger A, and Sali A (2010) Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data, Mol Cell Proteomics 9, 1689–1702.

    Article  PubMed  CAS  Google Scholar 

  15. Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velazquez-Muriel J, and Sali A (2009) The structural dynamics of macromolecular processes, Curr Opin Cell Biol 21, 97–108.

    Article  PubMed  CAS  Google Scholar 

  16. Alber F, Forster F, Korkin D, Topf M, and Sali A (2008) Integrating diverse data for structure determination of macromolecular assemblies, Annu Rev Biochem 77, 443–477.

    Article  PubMed  CAS  Google Scholar 

  17. Alber F, Chait BT, Rout MP, and Sali A (2008) Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints, In Protein-protein interactions and networks: identification, characterization and prediction. (Panchenko, A., and Przytycka, T., Eds.), pp 99–114, Springer-Verlag, London, UK.

    Google Scholar 

  18. Bonvin AM, Boelens R, and Kaptein R (2005) NMR analysis of protein interactions, Curr Opin Chem Biol 9, 501–508.

    Article  PubMed  CAS  Google Scholar 

  19. Fiaux J, Bertelsen EB, Horwich AL, and Wuthrich K (2002) NMR analysis of a 900K GroEL GroES complex, Nature 418, 207–211.

    Article  PubMed  CAS  Google Scholar 

  20. Neudecker P, Lundstrom P, and Kay LE (2009) Relaxation dispersion NMR spectroscopy as a tool for detailed studies of protein folding, Biophys J 96, 2045–2054.

    Article  PubMed  CAS  Google Scholar 

  21. Takamoto K, and Chance MR (2006) Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes, Annu Rev Biophys Biomol Struct 35, 251–276.

    Article  PubMed  CAS  Google Scholar 

  22. Guan JQ, and Chance MR (2005) Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry, Trends Biochem Sci 30, 583–592.

    Article  PubMed  CAS  Google Scholar 

  23. Taverner T, Hernandez H, Sharon M, Ruotolo BT, Matak-Vinkovic D, Devos D, Russell RB, and Robinson CV (2008) Subunit architecture of intact protein complexes from mass spectrometry and homology modeling, Acc Chem Res 41, 617–627.

    Article  PubMed  CAS  Google Scholar 

  24. Chen ZA, Jawhari A, Fischer L, Buchen C, Tahir S, Kamenski T, Rasmussen M, Lariviere L, Bukowski-Wills JC, Nilges M, Cramer P, and Rappsilber J (2010) Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry, EMBO J 29, 717–726.

    Article  PubMed  CAS  Google Scholar 

  25. Sinz A (2006) Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions, Mass Spectrom Rev 25, 663–682.

    Article  PubMed  CAS  Google Scholar 

  26. Trester-Zedlitz M, Kamada K, Burley SK, Fenyo D, Chait BT, and Muir TW (2003) A modular cross-linking approach for exploring protein interactions, J Am Chem Soc 125, 2416–2425.

    Article  PubMed  CAS  Google Scholar 

  27. Joo C, Balci H, Ishitsuka Y, Buranachai C, and Ha T (2008) Advances in single-molecule fluorescence methods for molecular biology, Annu Rev Biochem 77, 51–76.

    Article  PubMed  CAS  Google Scholar 

  28. Mertens HD, and Svergun DI (2010) Structural characterization of proteins and complexes using small-angle X-ray solution scattering, J Struct Biol 172, 128–141.

    Article  PubMed  CAS  Google Scholar 

  29. Hura GL, Menon AL, Hammel M, Rambo RP, Poole FL 2nd, Tsutakawa SE, Jenney FE Jr, Classen S, Frankel KA, Hopkins RC, Yang SJ, Scott JW, Dillard BD, Adams MW, and Tainer JA (2009) Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS), Nat Methods 6, 606–612.

    Article  PubMed  CAS  Google Scholar 

  30. Berggard T, Linse S, and James P (2007) Methods for the detection and analysis of protein-protein interactions, Proteomics 7, 2833–2842.

    Article  PubMed  Google Scholar 

  31. Sali A, and Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints, J Mol Biol 234, 779–815.

    Article  PubMed  CAS  Google Scholar 

  32. Sali A, and Blundell TL (1994) Comparative protein modeling by statisfaction of spatial restraints, In Protein Structure by Distance Analysis (Bohr, H., and Brunak, S., Eds.), pp 64–86, TECH UNIV DENMARK, CTR BIOL SEQUENCE ANAL, LYNGBY, DENMARK.

    Google Scholar 

  33. Vajda S, and Kozakov D (2009) Convergence and combination of methods in protein-protein docking, Curr Opin Struct Biol 19, 164–170.

    Article  PubMed  CAS  Google Scholar 

  34. Shen MY, and Sali A (2006) Statistical potential for assessment and prediction of protein structures, Protein Sci 15, 2507–2524.

    Article  PubMed  CAS  Google Scholar 

  35. Melo F, Sanchez R, and Sali A (2002) Statistical potentials for fold assessment, Protein Sci 11, 430–448.

    Article  PubMed  CAS  Google Scholar 

  36. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, and Karplus M (2009) CHARMM: the biomolecular simulation program, J Comput Chem 30, 1545–1614.

    Article  PubMed  CAS  Google Scholar 

  37. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, and Woods RJ (2005) The Amber biomolecular simulation programs, J Comput Chem 26, 1668–1688.

    Article  PubMed  CAS  Google Scholar 

  38. Christen M, Hunenberger PH, Bakowies D, Baron R, Burgi R, Geerke DP, Heinz TN, Kastenholz MA, Krautler V, Oostenbrink C, Peter C, Trzesniak D, and van Gunsteren WF (2005) The GROMOS software for biomolecular simulation: GROMOS05, J Comput Chem 26, 1719–1751.

    Article  PubMed  CAS  Google Scholar 

  39. Forster F, Lasker K, Beck F, Nickell S, Sali A, and Baumeister W (2009) An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome, Biochem Biophys Res Commun 388, 228–233.

    Article  PubMed  Google Scholar 

  40. Nickell S, Beck F, Scheres SHW, Korinek A, Forster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko J, Carazo J, Mann M, and Baumeister W (2009) Insights into the Molecular Architecture of the 26S Proteasome, Proc Natl Acad Sci USA 29, 11943–11947.

    Article  Google Scholar 

  41. Lasker K, Sali A, and Wolfson HJ (2010) Determining macromolecular assembly structures by molecular docking and fitting into an electron density map, Proteins: Struct Funct Bioinform 78, 3205–3211.

    Article  CAS  Google Scholar 

  42. Lasker K, Topf M, Sali A, and Wolfson H (2009) Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly, J Mol Biol 388, 180–194.

    Article  PubMed  CAS  Google Scholar 

  43. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, and Ferrin TE (2004) UCSF Chimera--a visualization system for exploratory research and analysis, J Comput Chem 25, 1605–1612.

    Article  PubMed  CAS  Google Scholar 

  44. Kampmann M, and Blobel G (2009) Three-dimensional structure and flexibility of a membrane-coating module of the nuclear pore complex, Nat Struct Mol Biol 16, 782–788.

    Article  PubMed  CAS  Google Scholar 

  45. Sampathkumar P, Gheyi T, Miller SA, Bain K, Dickey M, Bonanno J, Kim S, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson D, Emtage JS, Wasserman S, Rout MP, Sali A, Sauder JM, and Burley SK (2011) Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the Nuclear Pore Complex, Proteins: Struct Funct Bioinform 79, 1672–1677.

    Article  CAS  Google Scholar 

  46. Putnam CD, Hammel M, Hura GL, and 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, 191–285.

    Article  PubMed  CAS  Google Scholar 

  47. Petoukhov MV, and Svergun DI (2007) Analysis of X-ray and neutron scattering from biomacromolecular solutions, Curr Opin Struct Biol 17, 562–571.

    Article  PubMed  CAS  Google Scholar 

  48. Schneidman-Duhovny D, Hammel A, and Sali A. (2010) FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles, Nucleic Acids Res 38, W540–4.

    Article  PubMed  CAS  Google Scholar 

  49. Forster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, and Sali A (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies, J Mol Biol 382, 1089–1106.

    Article  PubMed  CAS  Google Scholar 

  50. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, and Zardecki C (2002) The Protein Data Bank, Acta Crystallogr D Biol Crystallogr 58, 899–907.

    Article  PubMed  Google Scholar 

  51. Robinson RC, Turbedsky K, Kaiser DA, Marchand JB, Higgs HN, Choe S, and Pollard TD (2001) Crystal structure of Arp2/3 complex, Science 294, 1679–1684.

    Article  PubMed  CAS  Google Scholar 

  52. DeLano WL (2002) The PyMOL molecular graphics system, Version 1.2r3pre, Schrödinger, LLC.

    Google Scholar 

  53. Galassi M, Davies J, Theiler J, Gough B, Jungman G, Booth M, and Rossi F (2002) GNU Scientific Library.

    Google Scholar 

  54. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, and Sali A (2008) Protein structure fitting and refinement guided by cryo-EM density, Structure 16, 295–307.

    Article  PubMed  CAS  Google Scholar 

Download references

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. 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.

Author information

Authors and Affiliations

  1. Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA

    Benjamin Webb, Keren Lasker, Dina Schneidman-Duhovny, Elina Tjioe, Jeremy Phillips, Seung Joong Kim, Javier Velázquez-Muriel, Daniel Russel & Andrej Sali

  2. Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA

    Benjamin Webb, Keren Lasker, Dina Schneidman-Duhovny, Elina Tjioe, Jeremy Phillips, Seung Joong Kim, Javier Velázquez-Muriel, Daniel Russel & Andrej Sali

Authors
  1. Benjamin Webb
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Keren Lasker
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dina Schneidman-Duhovny
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Elina Tjioe
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jeremy Phillips
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Seung Joong Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Javier Velázquez-Muriel
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Daniel Russel
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Andrej Sali
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Benjamin Webb .

Editor information

Editors and Affiliations

  1. Conway Institute, Sch. Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, 4, Ireland

    Gerard Cagney

  2. Donnelly Ctr Cell. & Biomolecular Res., Banting & Best Dept. Medical Research, University of Toronto, College St. 160, Toronto, M5S 3E1, Ontario, Canada

    Andrew Emili

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Webb, B. et al. (2011). Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform. In: Cagney, G., Emili, A. (eds) Network Biology. Methods in Molecular Biology, vol 781. Humana Press. https://doi.org/10.1007/978-1-61779-276-2_19

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-276-2_19

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-275-5

  • Online ISBN: 978-1-61779-276-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation