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Modulating co-translational protein folding by rational design and ribosome engineering

Author

Listed:
  • Minkoo Ahn

    (University College London)

  • Tomasz Włodarski

    (University College London)

  • Alkistis Mitropoulou

    (University College London)

  • Sammy H. S. Chan

    (University College London)

  • Haneesh Sidhu

    (University College London)

  • Elena Plessa

    (University College London)

  • Thomas A. Becker

    (Ludwig-Maximilians-Universität München)

  • Nediljko Budisa

    (Institute of Chemistry, Technische Universität Berlin
    University of Manitoba)

  • Christopher A. Waudby

    (University College London)

  • Roland Beckmann

    (Ludwig-Maximilians-Universität München)

  • Anaïs M. E. Cassaignau

    (University College London)

  • Lisa D. Cabrita

    (University College London)

  • John Christodoulou

    (University College London
    University of London)

Abstract

Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing 19F/15N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome.

Suggested Citation

  • Minkoo Ahn & Tomasz Włodarski & Alkistis Mitropoulou & Sammy H. S. Chan & Haneesh Sidhu & Elena Plessa & Thomas A. Becker & Nediljko Budisa & Christopher A. Waudby & Roland Beckmann & Anaïs M. E. Cass, 2022. "Modulating co-translational protein folding by rational design and ribosome engineering," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-31906-z
    DOI: 10.1038/s41467-022-31906-z
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    References listed on IDEAS

    as
    1. Christopher M. Dobson, 2003. "Protein folding and misfolding," Nature, Nature, vol. 426(6968), pages 884-890, December.
    2. William J. Netzer & F. Ulrich Hartl, 1997. "Recombination of protein domains facilitated by co-translational folding in eukaryotes," Nature, Nature, vol. 388(6640), pages 343-349, July.
    3. Cédric Orelle & Erik D. Carlson & Teresa Szal & Tanja Florin & Michael C. Jewett & Alexander S. Mankin, 2015. "Protein synthesis by ribosomes with tethered subunits," Nature, Nature, vol. 524(7563), pages 119-124, August.
    4. Elena Plessa & Lien P. Chu & Sammy H. S. Chan & Oliver L. Thomas & Anaïs M. E. Cassaignau & Christopher A. Waudby & John Christodoulou & Lisa D. Cabrita, 2021. "Nascent chains can form co-translational folding intermediates that promote post-translational folding outcomes in a disease-causing protein," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
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    Cited by:

    1. Julian O. Streit & Sammy H. S. Chan & Saifu Daya & John Christodoulou, 2025. "Rational design of 19F NMR labelling sites to probe protein structure and interactions," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    2. Felix Gersteuer & Martino Morici & Sara Gabrielli & Keigo Fujiwara & Haaris A. Safdari & Helge Paternoga & Lars V. Bock & Shinobu Chiba & Daniel N. Wilson, 2024. "The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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