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Rescue of conformational dynamics in enzyme catalysis by directed evolution

Author

Listed:
  • Renee Otten

    (Brandeis University)

  • Lin Liu

    (University of California, San Francisco)

  • Lillian R. Kenner

    (University of California, San Francisco)

  • Michael W. Clarkson

    (Brandeis University
    The University of Arizona)

  • David Mavor

    (University of California, San Francisco)

  • Dan S. Tawfik

    (Weizmann Institute of Science)

  • Dorothee Kern

    (Brandeis University)

  • James S. Fraser

    (University of California, San Francisco)

Abstract

Rational design and directed evolution have proved to be successful approaches to increase catalytic efficiencies of both natural and artificial enzymes. Protein dynamics is recognized as important, but due to the inherent flexibility of biological macromolecules it is often difficult to distinguish which conformational changes are directly related to function. Here, we use directed evolution on an impaired mutant of the proline isomerase CypA and identify two second-shell mutations that partially restore its catalytic activity. We show both kinetically, using NMR spectroscopy, and structurally, by room-temperature X-ray crystallography, how local perturbations propagate through a large allosteric network to facilitate conformational dynamics. The increased catalysis selected for in the evolutionary screen is correlated with an accelerated interconversion between the two catalytically essential conformational sub-states, which are both captured in the high-resolution X-ray ensembles. Our data provide a glimpse of an evolutionary trajectory and show how subtle changes can fine-tune enzyme function.

Suggested Citation

  • Renee Otten & Lin Liu & Lillian R. Kenner & Michael W. Clarkson & David Mavor & Dan S. Tawfik & Dorothee Kern & James S. Fraser, 2018. "Rescue of conformational dynamics in enzyme catalysis by directed evolution," Nature Communications, Nature, vol. 9(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03562-9
    DOI: 10.1038/s41467-018-03562-9
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    Cited by:

    1. Iktae Kim & Alyssa Dubrow & Bryan Zuniga & Baoyu Zhao & Noah Sherer & Abhishek Bastiray & Pingwei Li & Jae-Hyun Cho, 2022. "Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Yasmine S. Zubi & Kosuke Seki & Ying Li & Andrew C. Hunt & Bingqing Liu & Benoît Roux & Michael C. Jewett & Jared C. Lewis, 2022. "Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Christos S. Karamitros & Kyle Murray & Yoichi Kumada & Kenneth A. Johnson & Sheena D’Arcy & George Georgiou, 2024. "Mechanistic conformational and substrate selectivity profiles emerging in the evolution of enzymes via parallel trajectories," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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