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

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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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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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.

Corresponding author

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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