IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-29239-y.html
   My bibliography  Save this article

Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches

Author

Listed:
  • Yasmine S. Zubi

    (Indiana University, Bloomington)

  • Kosuke Seki

    (Northwestern University)

  • Ying Li

    (University of Chicago)

  • Andrew C. Hunt

    (Northwestern University)

  • Bingqing Liu

    (Indiana University, Bloomington)

  • Benoît Roux

    (University of Chicago)

  • Michael C. Jewett

    (Northwestern University)

  • Jared C. Lewis

    (Indiana University, Bloomington)

Abstract

Dynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.

Suggested Citation

  • 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.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29239-y
    DOI: 10.1038/s41467-022-29239-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-29239-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-022-29239-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Minwoo Yang & Woon Ju Song, 2019. "Diverse protein assembly driven by metal and chelating amino acids with selectivity and tunability," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    2. 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.
    3. Rey W. Martin & Benjamin J. Des Soye & Yong-Chan Kwon & Jennifer Kay & Roderick G. Davis & Paul M. Thomas & Natalia I. Majewska & Cindy X. Chen & Ryan D. Marcum & Mary Grace Weiss & Ashleigh E. Stodda, 2018. "Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids," Nature Communications, Nature, vol. 9(1), pages 1-9, December.
    4. Robert A. Langan & Scott E. Boyken & Andrew H. Ng & Jennifer A. Samson & Galen Dods & Alexandra M. Westbrook & Taylor H. Nguyen & Marc J. Lajoie & Zibo Chen & Stephanie Berger & Vikram Khipple Mulliga, 2019. "De novo design of bioactive protein switches," Nature, Nature, vol. 572(7768), pages 205-210, August.
    5. Alfredo Quijano-Rubio & Hsien-Wei Yeh & Jooyoung Park & Hansol Lee & Robert A. Langan & Scott E. Boyken & Marc J. Lajoie & Longxing Cao & Cameron M. Chow & Marcos C. Miranda & Jimin Wi & Hyo Jeong Hon, 2021. "De novo design of modular and tunable protein biosensors," Nature, Nature, vol. 591(7850), pages 482-487, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Xueyan Chen & Qianqian Ding & Chao Bi & Jian Ruan & Shikuan Yang, 2022. "Lossless enrichment of trace analytes in levitating droplets for multiphase and multiplex detection," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    2. Zhihong Xiao & Jinyin Zha & Xu Yang & Tingting Huang & Shuxin Huang & Qi Liu & Xiaozheng Wang & Jie Zhong & Jianting Zheng & Rubing Liang & Zixin Deng & Jian Zhang & Shuangjun Lin & Shaobo Dai, 2024. "A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Shodai Komatsu & Hirohisa Ohno & Hirohide Saito, 2023. "Target-dependent RNA polymerase as universal platform for gene expression control in response to intracellular molecules," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Akter, Shahriar & Dwivedi, Yogesh K. & Sajib, Shahriar & Biswas, Kumar & Bandara, Ruwan J. & Michael, Katina, 2022. "Algorithmic bias in machine learning-based marketing models," Journal of Business Research, Elsevier, vol. 144(C), pages 201-216.
    5. Huimeng Wang & Yi Fan & Yaqi Hou & Baiyi Chen & Jinmei Lei & Shijie Yu & Xinyu Chen & Xu Hou, 2022. "Host-guest liquid gating mechanism with specific recognition interface behavior for universal quantitative chemical detection," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    6. Migchelbrink, Koen & Raymaekers, Pieter, 2023. "Nudging people to pay their parking fines on time. Evidence from a cluster-randomized field experiment," Journal of Behavioral and Experimental Economics (formerly The Journal of Socio-Economics), Elsevier, vol. 105(C).
    7. William M. Dawson & Kathryn L. Shelley & Jordan M. Fletcher & D. Arne Scott & Lucia Lombardi & Guto G. Rhys & Tania J. LaGambina & Ulrike Obst & Antony J. Burton & Jessica A. Cross & George Davies & F, 2023. "Differential sensing with arrays of de novo designed peptide assemblies," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    8. Andrew C. Hunt & Bastian Vögeli & Ahmed O. Hassan & Laura Guerrero & Weston Kightlinger & Danielle J. Yoesep & Antje Krüger & Madison DeWinter & Michael S. Diamond & Ashty S. Karim & Michael C. Jewett, 2023. "A rapid cell-free expression and screening platform for antibody discovery," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    9. 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.
    10. Robert E. Jefferson & Aurélien Oggier & Andreas Füglistaler & Nicolas Camviel & Mahdi Hijazi & Ana Rico Villarreal & Caroline Arber & Patrick Barth, 2023. "Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    11. Joongoo Lee & Jaime N. Coronado & Namjin Cho & Jongdoo Lim & Brandon M. Hosford & Sangwon Seo & Do Soon Kim & Camila Kofman & Jeffrey S. Moore & Andrew D. Ellington & Eric V. Anslyn & Michael C. Jewet, 2022. "Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    12. Heonjoon Lee & Tian Xie & Byunghwa Kang & Xinjie Yu & Samuel W. Schaffter & Rebecca Schulman, 2024. "Plug-and-play protein biosensors using aptamer-regulated in vitro transcription," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    13. 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.
    14. 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.
    15. Zhijin Tian & Dandan Shao & Linlin Tang & Zhen Li & Qian Chen & Yongxiu Song & Tao Li & Friedrich C. Simmel & Jie Song, 2024. "Circular single-stranded DNA as a programmable vector for gene regulation in cell-free protein expression systems," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    16. Yuanli Gao & Lei Wang & Baojun Wang, 2023. "Customizing cellular signal processing by synthetic multi-level regulatory circuits," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    17. Zhong Guo & Rinky D. Parakra & Ying Xiong & Wayne A. Johnston & Patricia Walden & Selvakumar Edwardraja & Shayli Varasteh Moradi & Jacobus P. J. Ungerer & Hui-wang Ai & Jonathan J. Phillips & Kirill A, 2022. "Engineering and exploiting synthetic allostery of NanoLuc luciferase," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29239-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.