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The folding cooperativity of a protein is controlled by its chain topology

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  • Elizabeth A. Shank

    (University of California, Berkeley, California 94720, USA
    Jason L. Choy Laboratory of Single Molecule Biophysics, Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
    Present addresses: Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA (E.A.S.); Department of Physics, University of Modena and Reggio Emilia, Via Campi 213/A 4100 Modena, Italy (C.C.).)

  • Ciro Cecconi

    (University of California, Berkeley, California 94720, USA
    Jason L. Choy Laboratory of Single Molecule Biophysics, Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
    Present addresses: Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA (E.A.S.); Department of Physics, University of Modena and Reggio Emilia, Via Campi 213/A 4100 Modena, Italy (C.C.).)

  • Jesse W. Dill

    (Jason L. Choy Laboratory of Single Molecule Biophysics, Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
    Biophysics Graduate Group, University of California, Berkeley, California 94720, USA)

  • Susan Marqusee

    (University of California, Berkeley, California 94720, USA
    Jason L. Choy Laboratory of Single Molecule Biophysics, Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA)

  • Carlos Bustamante

    (University of California, Berkeley, California 94720, USA
    Jason L. Choy Laboratory of Single Molecule Biophysics, Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
    Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
    University of California, Berkeley, California 94720, USA)

Abstract

Into the fold: protein domains reshuffled Protein molecules often include domains that can be distinguished as relatively separate regions in their three-dimensional structure, but how such domains communicate during folding or enzymatic function is largely unclear. Shank et al. have now developed a new technology to study this using single-molecule optical tweezers acting via DNA 'handles' to pull on a protein from different directions while monitoring the energetics of unfolding and refolding events in regions away from those submitted to mechanical forces. Comparing topological variants of a protein — the two-domain protein T4 lysozyme that is a familiar model for folding studies — they then derive new rules of cooperation between sub-domains and suggest how evolution may select reshuffled gene topologies that bypass folding dead-ends.

Suggested Citation

  • Elizabeth A. Shank & Ciro Cecconi & Jesse W. Dill & Susan Marqusee & Carlos Bustamante, 2010. "The folding cooperativity of a protein is controlled by its chain topology," Nature, Nature, vol. 465(7298), pages 637-640, June.
    • Handle: RePEc:nat:nature:v:465:y:2010:i:7298:d:10.1038_nature09021
    DOI: 10.1038/nature09021
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    Cited by:

    1. Jaka Vodeb & Michele Diego & Yevhenii Vaskivskyi & Leonard Logaric & Yaroslav Gerasimenko & Viktor Kabanov & Benjamin Lipovsek & Marko Topic & Dragan Mihailovic, 2024. "Non-equilibrium quantum domain reconfiguration dynamics in a two-dimensional electronic crystal and a quantum annealer," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    2. Willow Coyote-Maestas & David Nedrud & Antonio Suma & Yungui He & Kenneth A. Matreyek & Douglas M. Fowler & Vincenzo Carnevale & Chad L. Myers & Daniel Schmidt, 2021. "Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling," Nature Communications, Nature, vol. 12(1), pages 1-16, December.
    3. Seth Lichter & Benjamin Rafferty & Zachary Flohr & Ashlie Martini, 2012. "Protein High-Force Pulling Simulations Yield Low-Force Results," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-10, April.
    4. Sahar Foroutannejad & Lydia L. Good & Changfan Lin & Zachariah I. Carter & Mahlet G. Tadesse & Aaron L. Lucius & Brian R. Crane & Rodrigo A. Maillard, 2023. "The cofactor-dependent folding mechanism of Drosophila cryptochrome revealed by single-molecule pulling experiments," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    5. Ganesh Agam & Anders Barth & Don C. Lamb, 2024. "Folding pathway of a discontinuous two-domain protein," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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