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Reshaping of the conformational search of a protein by the chaperone trigger factor

Nature volume 500, pages 98–101 (2013)Cite this article

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Abstract

Protein folding is often described as a search process, in which polypeptides explore different conformations to find their native structure. Molecular chaperones are known to improve folding yields by suppressing aggregation between polypeptides before this conformational search starts1,2, as well as by rescuing misfolds after it ends1,3. Although chaperones have long been speculated to also affect the conformational search itself—by reshaping the underlying folding landscape along the folding trajectory4,5—direct experimental evidence has been scarce so far. In Escherichia coli, the general chaperone trigger factor6,7,8 (TF) could play such a role. TF has been shown to interact with nascent chains at the ribosome9,10, with polypeptides released from the ribosome into the cytosol11, and with fully folded proteins before their assembly into larger complexes12. To investigate the effect of TF from E. coli on the conformational search of polypeptides to their native state, we investigated individual maltose binding protein (MBP) molecules using optical tweezers. Here we show that TF binds folded structures smaller than one domain, which are then stable for seconds and ultimately convert to the native state. Moreover, TF stimulates native folding in constructs of repeated MBP domains. The results indicate that TF promotes correct folding by protecting partially folded states from distant interactions that produce stable misfolded states. As TF interacts with most newly synthesized proteins in E. coli, we expect these findings to be of general importance in understanding protein folding pathways.

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Figure 1: TF promotes partial protein folds.
Figure 2: TF stabilizes partial folds and mediates folding transitions.
Figure 3: TF binds partially folded states, not the native state.
Figure 4: TF suppresses misfolding between domains.

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References

  1. Hartl, F. U., Bracher, A. & Hayer-Hartl, M. Molecular chaperones in protein folding and proteostasis. Nature 475, 324–332 (2011)

    Article  CAS  Google Scholar 

  2. Kramer, G., Boehringer, D., Ban, N. & Bukau, B. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nature Struct. Mol. Biol. 16, 589–597 (2009)

    Article  CAS  Google Scholar 

  3. Sharma, S. K., De los Rios, P., Christen, P., Lustig, A. & Goloubinoff, P. The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase. Nature Chem. Biol. 6, 914–920 (2010)

    Article  CAS  Google Scholar 

  4. Dobson, C. M. Protein folding and misfolding. Nature 426, 884–890 (2003)

    Article  CAS  ADS  Google Scholar 

  5. Bartlett, A. I. & Radford, S. E. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nature Struct. Mol. Biol. 16, 582–588 (2009)

    Article  CAS  Google Scholar 

  6. Hoffmann, A., Bukau, B. & Kramer, G. Structure and function of the molecular chaperone Trigger Factor. Biochim. Biophys. Acta 1803, 650–661 (2010)

    Article  CAS  Google Scholar 

  7. Wegrzyn, R. D. & Deuerling, E. Molecular guardians for newborn proteins: ribosome-associated chaperones and their role in protein folding. Cell. Mol. Life Sci. 62, 2727–2738 (2005)

    Article  CAS  Google Scholar 

  8. Merz, F. et al. Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J. 27, 1622–1632 (2008)

    Article  CAS  Google Scholar 

  9. Ferbitz, L. et al. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature 431, 590–596 (2004)

    Article  CAS  ADS  Google Scholar 

  10. Kramer, G. et al. L23 protein functions as a chaperone docking site on the ribosome. Nature 419, 171–174 (2002)

    Article  CAS  ADS  Google Scholar 

  11. Agashe, V. R. et al. Function of trigger factor and DnaK in multidomain protein folding: increase in yield at the expense of folding speed. Cell 117, 199–209 (2004)

    Article  CAS  Google Scholar 

  12. Martinez-Hackert, E. & Hendrickson, W. A. Promiscuous substrate recognition in folding and assembly activities of the trigger factor chaperone. Cell 138, 923–934 (2009)

    Article  CAS  Google Scholar 

  13. Borgia, A., Williams, P. M. & Clarke, J. Single-molecule studies of protein folding. Annu. Rev. Biochem. 77, 101–125 (2008)

    Article  CAS  Google Scholar 

  14. Fisher, T. E., Marszalek, P. E. & Fernandez, J. M. Stretching single molecules into novel conformations using the atomic force microscope. Nature Struct. Biol. 7, 719–724 (2000)

    Article  CAS  Google Scholar 

  15. Cecconi, C., Shank, E. A., Bustamante, C. & Marqusee, S. Direct observation of the three-state folding of a single protein molecule. Science 309, 2057–2060 (2005)

    Article  CAS  ADS  Google Scholar 

  16. Fernandez, J. M. & Li, H. Force-clamp spectroscopy monitors the folding trajectory of a single protein. Science 303, 1674–1678 (2004)

    Article  CAS  ADS  Google Scholar 

  17. Jakobi, A. J., Mashaghi, A., Tans, S. J. & Huizinga, E. G. Calcium modulates force sensing by the von Willebrand factor A2 domain. Nature Commun. 2, 385 (2011)

    Article  ADS  Google Scholar 

  18. Junker, J. P., Ziegler, F. & Rief, M. Ligand-dependent equilibrium fluctuations of single calmodulin molecules. Science 323, 633–637 (2009)

    Article  CAS  ADS  Google Scholar 

  19. Cao, Y., Balamurali, M. M., Sharma, D. & Li, H. A functional single-molecule binding assay via force spectroscopy. Proc. Natl Acad. Sci. USA 104, 15677–15681 (2007)

    Article  CAS  ADS  Google Scholar 

  20. Bechtluft, P. et al. Direct observation of chaperone-induced changes in a protein folding pathway. Science 318, 1458–1461 (2007)

    Article  CAS  ADS  Google Scholar 

  21. Bertz, M. & Rief, M. Mechanical unfoldons as building blocks of maltose-binding protein. J. Mol. Biol. 378, 447–458 (2008)

    Article  CAS  Google Scholar 

  22. Maier, R., Scholz, C. & Schmid, F. X. Dynamic association of trigger factor with protein substrates. J. Mol. Biol. 314, 1181–1190 (2001)

    Article  CAS  Google Scholar 

  23. Kaiser, C. M. et al. Real-time observation of trigger factor function on translating ribosomes. Nature 444, 455–460 (2006)

    Article  CAS  ADS  Google Scholar 

  24. Lakshmipathy, S. K., Gupta, R., Pinkert, S., Etchells, S. A. & Hartl, F. U. Versatility of trigger factor interactions with ribosome-nascent chain complexes. J. Biol. Chem. 285, 27911–27923 (2010)

    Article  CAS  Google Scholar 

  25. Park, S., Klein, T. E. & Pande, V. S. Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations. Biophys. J. 93, 4108–4115 (2007)

    Article  CAS  ADS  Google Scholar 

  26. Hoffmann, A. et al. Concerted action of the ribosome and the associated chaperone trigger factor confines nascent polypeptide folding. Mol. Cell 48, 63–74 (2012)

    Article  CAS  Google Scholar 

  27. Han, J. H., Batey, S., Nickson, A. A., Teichmann, S. A. & Clarke, J. The folding and evolution of multidomain proteins. Nature Rev. Mol. Cell Biol. 8, 319–330 (2007)

    Article  CAS  Google Scholar 

  28. Jaenicke, R. Stability and folding of domain proteins. Prog. Biophys. Mol. Biol. 71, 155–241 (1999)

    Article  CAS  Google Scholar 

  29. Marko, J. F. & Siggia, E. D. Stretching DNA. Macromolecules 28, 8759–8770 (1995)

    Article  CAS  ADS  Google Scholar 

  30. Thomas, P. D. & Dill, K. A. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl Acad. Sci. USA 93, 11628–11633 (1996)

    Article  CAS  ADS  Google Scholar 

Download references

Acknowledgements

Work in the laboratory of S.J.T. is part of the research programme of the Stichting voor Fundamenteel Onderzoek der Materie (FOM), which is financially supported by the Nederlandse Organisatie voor Wetenschappelijke Onderzoek (NWO). Work in the laboratory of B.B. and G.K. is supported by grants from the Deutsche Forschungsgemeinschaft (SFB 638, FOR967). We are grateful to M. Meyer for his support in performing and analysing FTIR experiments. We thank T. Shimizu, L. Guilbride, M. Dogterom and members of the Tans group for critical reading of the manuscript.

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Authors and Affiliations

  1. FOM institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands,

    Alireza Mashaghi, Philipp Bechtluft & Sander J. Tans

  2. Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, Heidelberg 69120, Germany,

    Günter Kramer, Beate Zachmann-Brand & Bernd Bukau

  3. Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and the Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9749 AG Groningen, The Netherlands,

    Arnold J. M. Driessen

Authors
  1. Alireza Mashaghi
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  2. Günter Kramer
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  7. Sander J. Tans
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Contributions

S.J.T. and A.M. conceived and designed the research; P.B., A.J.M.D. and B.Z.-B. designed and purified the MBP protein constructs; A.M. and P.B. performed the optical tweezers experiments; G.K. and B.Z.-B. purified the TF and MBP truncates and performed the bulk refolding experiments; A.M. and S.J.T. analysed the data; and A.M., G.K., B.B. and S.J.T. wrote the paper.

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Correspondence to Sander J. Tans.

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The authors declare no competing financial interests.

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Mashaghi, A., Kramer, G., Bechtluft, P. et al. Reshaping of the conformational search of a protein by the chaperone trigger factor. Nature 500, 98–101 (2013). https://doi.org/10.1038/nature12293

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