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Dynamic allostery can drive cold adaptation in enzymes

Author

Listed:
  • Harry G. Saavedra

    (Johns Hopkins University
    Johns Hopkins University)

  • James O. Wrabl

    (Johns Hopkins University
    Johns Hopkins University)

  • Jeremy A. Anderson

    (Johns Hopkins University
    Johns Hopkins University)

  • Jing Li

    (Johns Hopkins University
    Johns Hopkins University)

  • Vincent J. Hilser

    (Johns Hopkins University
    Johns Hopkins University)

Abstract

Adaptation of organisms to environmental niches is a hallmark of evolution. One prevalent example is that of thermal adaptation, in which two descendants evolve at different temperature extremes1,2. Underlying the physiological differences between such organisms are changes in enzymes that catalyse essential reactions 3 , with orthologues from each organism undergoing adaptive mutations that preserve similar catalytic rates at their respective physiological temperatures4,5. The sequence changes responsible for these adaptive differences, however, are often at surface-exposed sites distant from the substrate-binding site, leaving the active site of the enzyme structurally unperturbed6,7. How such changes are allosterically propagated to the active site, to modulate activity, is not known. Here we show that entropy-tuning changes can be engineered into distal sites of Escherichia coli adenylate kinase, allowing us to quantitatively assess the role of dynamics in determining affinity, turnover and the role in driving adaptation. The results not only reveal a dynamics-based allosteric tuning mechanism, but also uncover a spatial separation of the control of key enzymatic parameters. Fluctuations in one mobile domain (the LID) control substrate affinity, whereas dynamic attenuation in the other domain (the AMP-binding domain) affects rate-limiting conformational changes that govern enzyme turnover. Dynamics-based regulation may thus represent an elegant, widespread and previously unrealized evolutionary adaptation mechanism that fine-tunes biological function without altering the ground state structure. Furthermore, because rigid-body conformational changes in both domains were thought to be rate limiting for turnover8,9, these adaptation studies reveal a new model for understanding the relationship between dynamics and turnover in adenylate kinase.

Suggested Citation

  • Harry G. Saavedra & James O. Wrabl & Jeremy A. Anderson & Jing Li & Vincent J. Hilser, 2018. "Dynamic allostery can drive cold adaptation in enzymes," Nature, Nature, vol. 558(7709), pages 324-328, June.
  • Handle: RePEc:nat:nature:v:558:y:2018:i:7709:d:10.1038_s41586-018-0183-2
    DOI: 10.1038/s41586-018-0183-2
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    Cited by:

    1. Federica Maschietto & Uriel N. Morzan & Florentina Tofoleanu & Aria Gheeraert & Apala Chaudhuri & Gregory W. Kyro & Peter Nekrasov & Bernard Brooks & J. Patrick Loria & Ivan Rivalta & Victor S. Batist, 2023. "Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Nicholas J Ose & Brandon M Butler & Avishek Kumar & I Can Kazan & Maxwell Sanderford & Sudhir Kumar & S Banu Ozkan, 2022. "Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants," PLOS Computational Biology, Public Library of Science, vol. 18(4), pages 1-22, April.
    3. Jia Zheng & Ning Guo & Yuxiang Huang & Xiang Guo & Andreas Wagner, 2024. "High temperature delays and low temperature accelerates evolution of a new protein phenotype," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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