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Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices

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    Enzyme-Directed Functionalization of Designed, Two-Dimensional Protein Lattices
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    • Rohit H. Subramanian
      Rohit H. Subramanian
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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      Orcidhttp://orcid.org/0000-0001-8750-7055
    • Yuta Suzuki
      Yuta Suzuki
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      Hakubi Center for Advanced Research, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
      More by Yuta Suzuki
    • Lorillee Tallorin
      Lorillee Tallorin
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      More by Lorillee Tallorin
    • Swagat Sahu
      Swagat Sahu
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      More by Swagat Sahu
    • Matthew Thompson
      Matthew Thompson
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, Chemistry of Life Processes Institute, International Institute for Nanotechnology, and Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
      More by Matthew Thompson
    • Nathan C. Gianneschi
      Nathan C. Gianneschi
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      Departments of Chemistry, Materials Science & Engineering, and Biomedical Engineering, Chemistry of Life Processes Institute, International Institute for Nanotechnology, and Simpson Querrey Institute, Northwestern University, Evanston, Illinois 60208, United States
      More by Nathan C. Gianneschi
      Orcidhttp://orcid.org/0000-0001-9945-5475
    • Michael D. Burkart
      Michael D. Burkart
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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      Orcidhttp://orcid.org/0000-0002-4472-2254
    • F. Akif Tezcan*
      F. Akif Tezcan
      Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
      Materials Science and Engineering, University of California, San Diego, La Jolla, California 92093-0418, United States
      *Email: [email protected]
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      Orcidhttp://orcid.org/0000-0002-4733-6500
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    Biochemistry

    Cite this: Biochemistry 2021, 60, 13, 1050–1062
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    https://doi.org/10.1021/acs.biochem.0c00363
    Published July 24, 2020
    Copyright © 2020 American Chemical Society
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    Abstract

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    The design and construction of crystalline protein arrays to selectively assemble ordered nanoscale materials have potential applications in sensing, catalysis, and medicine. Whereas numerous designs have been implemented for the bottom-up construction of protein assemblies, the generation of artificial functional materials has been relatively unexplored. Enzyme-directed post-translational modifications are responsible for the functional diversity of the proteome and, thus, could be harnessed to selectively modify artificial protein assemblies. In this study, we describe the use of phosphopantetheinyl transferases (PPTases), a class of enzymes that covalently modify proteins using coenzyme A (CoA), to site-selectively tailor the surface of designed, two-dimensional (2D) protein crystals. We demonstrate that a short peptide (ybbR) or a molecular tag (CoA) can be covalently tethered to 2D arrays to enable enzymatic functionalization using Sfp PPTase. The site-specific modification of two different protein array platforms is facilitated by PPTases to afford both small molecule- and protein-functionalized surfaces with no loss of crystalline order. This work highlights the potential for chemoenzymatic modification of large protein surfaces toward the generation of sophisticated protein platforms reminiscent of the complex landscape of cell surfaces.

    Copyright © 2020 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.biochem.0c00363.

    • Scheme for enzymatic labeling of ybbR (Figure S1), characterization of the synthesized ybbR-N3 peptide (Figure S2), TEM characterization and quantification of modified RIDC3 crystals (Figure S3), identification of lysines on the RIDC3 crystal surface (Figure S4), MS/MS analysis of conjugation of ybbR onto RIDC3 arrays (Figure S5), TEM characterization of enzymatically labeled RIDC3-ybbR arrays (Figure S6), generation and characterization of GFP-CoA (Figure S7), UV–vis characterization of RIDC3-ybbR monomers (Figure S8), quantification of fluorescent labeling of RIDC3-ybbR crystals (Figure S9), quantification of enzymatically labeled RIDC3-CoA arrays (Figure S10), characterization of genetically modified ybbRRIDC3 (Figure S11), and characterization of genetically modified ybbRRhuA (Figure S12) (PDF)

    Accession Codes

    RhuA, P32169; RIDC3 (or parent cytochrome b562), P0ABE7.

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    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

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    This article is cited by 10 publications.

    1. Kosuke Kikuchi, Koki Date, Takafumi Ueno. Design of a Hierarchical Assembly at a Solid–Liquid Interface Using an Asymmetric Protein Needle. Langmuir 2023, 39 (6) , 2389-2397. https://doi.org/10.1021/acs.langmuir.2c03146
    2. Jie Zhu, Nicole Avakyan, Albert Kakkis, Alexander M. Hoffnagle, Kenneth Han, Yiying Li, Zhiyin Zhang, Tae Su Choi, Youjeong Na, Chung-Jui Yu, F. Akif Tezcan. Protein Assembly by Design. Chemical Reviews 2021, 121 (22) , 13701-13796. https://doi.org/10.1021/acs.chemrev.1c00308
    3. Victor R. Mann, Francesca Manea, Nicholas J. Borys, Caroline M. Ajo-Franklin, Bruce E. Cohen. Controlled and Stable Patterning of Diverse Inorganic Nanocrystals on Crystalline Two-Dimensional Protein Arrays. Biochemistry 2021, 60 (13) , 1063-1074. https://doi.org/10.1021/acs.biochem.1c00032
    4. Yijia Li, Ruizhen Tian, Yingping Zou, Tingting Wang, Junqiu Liu. Strategies and Applications for Supramolecular Protein Self‐Assembly. Chemistry – A European Journal 2024, 30 (66) https://doi.org/10.1002/chem.202402624
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    6. Thomas A. King, Laura Rodríguez Pérez, Sabine L. Flitsch. Application of Biocatalysis for Protein Bioconjugation. 2024, 389-437. https://doi.org/10.1016/B978-0-32-390644-9.00122-0
    7. Dharmendra Kumar, Nandan Sarkar, Kuldeep K. Roy, Dheeraj Bisht, Deepak Kumar, Bitasta Mandal, Mogana Rajagopal, Yadu Nandan Dey. The Potential of Mur Enzymes as Targets for Antimicrobial Drug Discovery. Current Drug Targets 2023, 24 (8) , 627-647. https://doi.org/10.2174/1389450124666230608150759
    8. Koji Oohora. Supramolecular assembling systems of hemoproteins using chemical modifications. Journal of Inclusion Phenomena and Macrocyclic Chemistry 2023, 103 (3-4) , 97-107. https://doi.org/10.1007/s10847-023-01181-6
    9. Fania Geiger, Tim Wendlandt, Tim Berking, Joachim P. Spatz, Christina Wege. Convenient site-selective protein coupling from bacterial raw lysates to coenzyme A-modified tobacco mosaic virus (TMV) by Bacillus subtilis Sfp phosphopantetheinyl transferase. Virology 2023, 578 , 61-70. https://doi.org/10.1016/j.virol.2022.11.013
    10. Yijia Li, Linlu Zhao, Hongwei Chen, Ruizhen Tian, Fei Li, Quan Luo, Jiayun Xu, Chunxi Hou, Junqiu Liu. Hierarchical protein self-assembly into dynamically controlled 2D nanoarrays via host–guest chemistry. Chemical Communications 2021, 57 (81) , 10620-10623. https://doi.org/10.1039/D1CC03654H
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    Biochemistry

    Cite this: Biochemistry 2021, 60, 13, 1050–1062
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.biochem.0c00363
    Published July 24, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

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