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Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids

Nature Chemistry volume 10, pages 405–412 (2018)Cite this article

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A Publisher Correction to this article was published on 31 May 2018

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Abstract

Translation, the mRNA-templated synthesis of peptides by the ribosome, can be manipulated to incorporate variants of the 20 cognate amino acids. Such approaches for expanding the range of chemical entities that can be produced by the ribosome may accelerate the discovery of molecules that can perform functions for which poorly folded, short peptidic sequences are ill suited. Here, we show that the ribosome tolerates some artificial helical aromatic oligomers, so-called foldamers. Using a flexible tRNA-acylation ribozyme—flexizyme—foldamers were attached to tRNA, and the resulting acylated tRNAs were delivered to the ribosome to initiate the synthesis of non-cyclic and cyclic foldamer–peptide hybrid molecules. Passing through the ribosome exit tunnel requires the foldamers to unfold. Yet foldamers encode sufficient folding information to influence the peptide structure once translation is completed. We also show that in cyclic hybrids, the foldamer portion can fold into a helix and force the peptide segment to adopt a constrained and stretched conformation.

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Fig. 1: Aromatic oligoamide foldamers and their initiation of in vitro translation.
Fig. 2: In vitro translation of oligomeric foldamer–peptide/protein hybrids.
Fig. 3: NMR studies of aromatic foldamer segments.
Fig. 4: Macrocyclization of foldamer–peptide hybrids.

Change history

  • 31 May 2018

    In the version of this Article originally published, in Fig.1f there was an erroneous ‘Gly–Gly’ label placed above the foldamer–peptide structure. Furthermore, in Fig. 2a, the expected target structures from substrates 9 and 10 were inadvertently swapped. These errors have been corrected in the online versions.

References

  1. Fischer, N. et al. Structure of the E. coli ribosome–EF–Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 520, 567–570 (2015).

    Article  CAS  PubMed  Google Scholar 

  2. Ernst, R. J. et al. Genetic code expansion in the mouse brain. Nat. Chem. Biol. 12, 776–778 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Maini, R. et al. Ribosome-mediated incorporation of dipeptides and dipeptide analogues into proteins in vitro. J. Am. Chem. Soc. 137, 11206–11209 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Murakami, H., Ohta, A., Ashigai, H. & Suga, H. A highly flexible tRNA acylation method for non-natural polypeptide synthesis. Nat. Methods 3, 357–359 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Hartman, M. C., Josephson, K., Lin, C. W. & Szostak, J. W. An expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. PLoS One 2, e972 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755 (2001).

    Article  CAS  Google Scholar 

  8. Rogers, J. M. & Suga, H. Discovering functional, non-proteinogenic amino acid containing, peptides using genetic code reprogramming. Org. Biomol. Chem. 13, 9353–9363 (2015).

    Article  CAS  PubMed  Google Scholar 

  9. Katoh, T., Tajima, K. & Suga, H. Consecutive elongation of d-amino acids in translation. Cell Chem. Biol. 24, 46–54 (2017).

    Article  CAS  PubMed  Google Scholar 

  10. Fujino, T., Goto, Y., Suga, H. & Murakami, H. Reevaluation of the d-amino acid compatibility with the elongation event in translation. J. Am. Chem. Soc. 135, 1830–1837 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Fujino, T., Goto, Y., Suga, H. & Murakami, H. Ribosomal synthesis of peptides with multiple β-amino acids. J. Am. Chem. Soc. 138, 1962–1969 (2016).

    Article  CAS  PubMed  Google Scholar 

  12. Goto, Y. et al. Reprogramming the translation initiation for the synthesis of physiologically stable cyclic peptides. ACS Chem. Biol. 3, 120–129 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Ohta, A., Murakami, H., Higashimura, E. & Suga, H. Synthesis of polyester by means of genetic code reprogramming. Chem. Biol. 14, 1315–1322 (2007).

    Article  CAS  PubMed  Google Scholar 

  14. Kawakami, T., Murakami, H. & Suga, H. Ribosomal synthesis of polypeptoids and peptoid–peptide hybrids. J. Am. Chem. Soc. 130, 16861–16863 (2008).

    Article  CAS  PubMed  Google Scholar 

  15. Goto, Y. & Suga, H. Translation initiation with initiator tRNA charged with exotic peptides. J. Am. Chem. Soc. 131, 5040–5041 (2009).

    Article  CAS  PubMed  Google Scholar 

  16. Torikai, K. & Suga, H. Ribosomal synthesis of an amphotericin-B inspired macrocycle. J. Am. Chem. Soc. 136, 17359–17361 (2014).

    Article  CAS  PubMed  Google Scholar 

  17. Passioura, T. & Suga, H. A RaPID way to discover nonstandard macrocyclic peptide modulators of drug targets. Chem. Commun. 53, 1931–1940 (2017).

    Article  CAS  Google Scholar 

  18. Terasaka, N., Hayashi, G., Katoh, T. & Suga, H. An orthogonal ribosome–tRNA pair via engineering of the peptidyl transferase center. Nat. Chem. Biol. 10, 555–557 (2014).

    Article  CAS  PubMed  Google Scholar 

  19. Jiang, H., Léger, J. M. & Huc, I. Aromatic δ-peptides. J. Am. Chem. Soc. 125, 3448–3449 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Boersma, M. D. et al. Evaluation of diverse α/β-backbone patterns for functional α-helix mimicry: analogues of the Bim BH3 domain. J. Am. Chem. Soc. 134, 315–323 (2012).

    Article  CAS  PubMed  Google Scholar 

  21. Fuller, A. A. et al. Evaluating β-turn mimics as β-sheet folding nucleators. Proc. Natl Acad. Sci. USA 106, 11067–11072 (2009).

    Article  PubMed  Google Scholar 

  22. Walensky, L. D. & Bird, G. H. Hydrocarbon-stapled peptides: principles, practice, and progress. J. Med. Chem. 57, 6275–6288 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Lao, B. B. et al. In vivo modulation of hypoxia-inducible signaling by topographical helix mimetics. Proc. Natl Acad. Sci. USA 111, 7531–7536 (2014).

    Article  CAS  PubMed  Google Scholar 

  24. Fremaux, J. et al. α-Peptide-oligourea chimeras: stabilization of short α-helices by non-peptide helical foldamers. Angew. Chem. Int. Ed. 54, 9816–9820 (2015).

    Article  CAS  Google Scholar 

  25. Cheng, P. N. & Nowick, J. S. Giant macrolactams based on β-sheet peptides. J. Org. Chem. 76, 3166–3173 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Goodman, C. M., Choi, S., Shandler, S. & DeGrado, W. F. Foldamers as versatile frameworks for the design and evolution of function. Nat. Chem. Biol. 3, 252–262 (2007).

    Article  CAS  PubMed  Google Scholar 

  27. Guichard, G. & Huc, I. Synthetic foldamers. Chem. Commun. 47, 5933–5941 (2011).

    Article  CAS  Google Scholar 

  28. Gillies, E. R., Deiss, F., Staedel, C., Schmitter, J. M. & Huc, I. Development and biological assessment of fully water-soluble helical aromatic amide foldamers. Angew. Chem. Int. Ed. 46, 4081–4084 (2007).

    Article  CAS  Google Scholar 

  29. Delaurière, L. et al. Deciphering aromatic oligoamide foldamer–DNA interactions. Angew. Chem. Int. Ed. 51, 473–477 (2012).

    Article  CAS  Google Scholar 

  30. Kudo, M., Maurizot, V., Kauffmann, B., Tanatani, A. & Huc, I. Folding of a linear array of α-amino acids within a helical aromatic oligoamide frame. J. Am. Chem. Soc. 135, 9628–9631 (2013).

    Article  CAS  PubMed  Google Scholar 

  31. Hu, X., Dawson, S. J., Nagaoka, Y., Tanatani, A. & Huc, I. Solid-phase synthesis of water-soluble helically folded hybrid α-amino acid/quinoline oligoamides. J. Org. Chem. 81, 1137–1150 (2016).

    Article  CAS  PubMed  Google Scholar 

  32. Saito, H., Kourouklis, D. & Suga, H. An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J. 20, 1797–1806 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Goto, Y., Ashigai, H., Sako, Y., Murakami, H. & Suga, H. Translation initiation by using various N-acylaminoacyl tRNAs. Nucleic Acids Symp. Ser. 50, 293–294 (2006).

  34. Goto, Y., Murakami, H. & Suga, H. Initiating translation with d-amino acids. RNA 14, 1390–1398 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Qi, T. et al. Solvent dependence of helix stability in aromatic oligoamide foldamers. Chem. Commun. 48, 6337–6339 (2012).

    Article  CAS  Google Scholar 

  36. Delsuc, N. et al. Kinetics of helix-handedness inversion: folding and unfolding in aromatic amide oligomers. ChemPhysChem 9, 1882–1890 (2008).

    Article  CAS  PubMed  Google Scholar 

  37. Voss, N. R., Gerstein, M., Steitz, T. A. & Moore, P. B. The geometry of the ribosomal polypeptide exit tunnel. J. Mol. Biol. 360, 893–906 (2006).

    Article  CAS  PubMed  Google Scholar 

  38. Sánchez-García, D. et al. Nanosized hybrid oligoamide foldamers: aromatic templates for the folding of multiple aliphatic units. J. Am. Chem. Soc. 131, 8642–8648 (2009).

    Article  CAS  PubMed  Google Scholar 

  39. Baptiste, B., Douat-Casassus, C., Laxmi-Reddy, K., Godde, F. & Huc, I. Solid phase synthesis of aromatic oligoamides: application to helical water-soluble foldamers. J. Org. Chem. 75, 7175–7185 (2010).

    Article  CAS  PubMed  Google Scholar 

  40. Cabrita, L. D. et al. A structural ensemble of a ribosome–nascent chain complex during cotranslational protein folding. Nat. Struct. Mol. Biol. 23, 278–285 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Nilsson, O. B. et al. Cotranslational protein folding inside the ribosome exit tunnel. Cell. Rep. 12, 1533–1540 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Dolain, C. et al. Solution structure of quinoline- and pyridine-derived oligoamide foldamers. Chemistry 11, 6135–6144 (2005).

    Article  CAS  PubMed  Google Scholar 

  43. Solà, J., Helliwell, M. & Clayden, J. N- versus C-terminal control over the screw-sense preference of the configurationally achiral, conformationally helical peptide motif Aib8GlyAib8. J. Am. Chem. Soc. 132, 4548–4549 (2010).

    Article  CAS  PubMed  Google Scholar 

  44. Kendhale, A. M. et al. Absolute control of helical handedness in quinoline oligoamides. J. Org. Chem. 76, 195–200 (2011).

    Article  CAS  PubMed  Google Scholar 

  45. Li, J. et al. An in-tether sulfoxide chiral center influences the biophysical properties of the N-capped peptides. Bioorg. Med. Chem. 25, 1756–1761 (2017).

    Article  CAS  PubMed  Google Scholar 

  46. Kodan, A. et al. Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog. Proc. Natl Acad. Sci. USA 111, 4049–4054 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Yu, H. et al. Macrocycle peptides delineate locked-open inhibition mechanism for microorganism phosphoglycerate mutases. Nat. Commun. 8, 14932 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Gillies, E. R., Dolain, C., Léger, J. M. & Huc, I. Amphipathic helices from aromatic amino acid oligomers. J. Org. Chem. 71, 7931–7939 (2006).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was mainly supported by a joint ANR-JST grant (ANR-14-JTIC-2014-003 and JST-SICORP, to H.S. and I.H.), and partly supported by the European Research Council under the European Union’s Seventh Framework Programme (ERC-2012-AdG-320892 to I.H.), a Japan Society for the Promotion of Science post-doctoral fellowship (P13766, to J.M.R.) and the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1A6A3A03006364, to S.K). This work benefited from the facilities and expertise of the Biophysical and Structural Chemistry platform at IECB, CNRS UMS3033, INSERM US001, Bordeaux University, France.

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Author notes

  1. Ivan Huc

    Present address: Department of Pharmacy, Ludwig-Maximilians-Universität, München, Germany

  2. These authors contributed equally: Joseph M. Rogers, Sunbum Kwon.

Authors and Affiliations

  1. Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Joseph M. Rogers & Hiroaki Suga

  2. CBMN Laboratory, Univ. Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, Pessac, France

    Sunbum Kwon, Simon J. Dawson, Pradeep K. Mandal & Ivan Huc

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Contributions

S.K. and J.M.R. contributed equally to this work. S.K. and S.J.D. synthesized new compounds. S.K. carried out solution conformational studies. J.M.R. performed in vitro aminoacylation and translation experiments. P.K.M. carried out crystallographic studies. All authors contributed to designing the research, to discussing the results and to writing the manuscript.

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Correspondence to Hiroaki Suga or Ivan Huc.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–35, Supplementary Methods and data

Supplementary Movie 1

Crystal structure of macrocyclic foldamer-peptide hybrid 17

Crystallographic data

Crystallographic data for compound 17, CCDC reference 1554263

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Rogers, J.M., Kwon, S., Dawson, S.J. et al. Ribosomal synthesis and folding of peptide-helical aromatic foldamer hybrids. Nature Chem 10, 405–412 (2018). https://doi.org/10.1038/s41557-018-0007-x

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