Skip to main content
See More

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Biocatalytic cascades driven by enzymes encapsulated in metal–organic framework nanoparticles

Nature Catalysis volume 1, pages 689–695 (2018)Cite this article

Subjects

Abstract

Biocatalytic transformations in cells, such as enzyme cascades, involve complex networks proceeding in spatially confined microenvironments. Here, inspired by nature, we demonstrate effective biocatalytic cascades by the encapsulation of two or three enzymes, or enzyme/cofactor components, in zeolitic imidazolate framework-8 metal–organic framework nanoparticles (ZIF8-NMOFs) that act as nanoreactors. The integration of the two-enzyme system (glucose oxidase and horseradish peroxidase) or three-enzyme system (β-galactosidase, glucose oxidase and horseradish peroxidase) in the NMOFs leads to 7.5-fold and 5.3-fold enhancements in the activity of the catalytic cascades, respectively, compared with the bulk mixture of the catalysts in solution. In addition, the encapsulation of alcohol dehydrogenase, NAD+–polymer and lactate dehydrogenase in the NMOFs yields a coupled biocatalytic cascade involving coupled NAD+-dependent enzymes, leading to the catalytic reduction of pyruvic acid to lactic acid by ethanol.

Access through your institution
Buy or subscribe

This is a preview of subscription content, access via your institution

Access options

Access through your institution

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Operation of the GOx/HRP two-enzyme cascade integrated in the ZIF-8 NMOFs.
Fig. 2: Activation of a three-enzyme biocatalytic cascade encapsulated in the ZIF-8 NMOFs.
Fig. 3: NAD+-mediated biocatalytic cascade of a cofactor-dependent enzyme in ZIF-8 NMOFs.
Fig. 4: NAD+-mediated two-enzyme biocatalytic cascade in ZIF-8 NMOF nanoreactors.

Similar content being viewed by others

References

  1. Good, M. C., Zalatan, J. G. & Lim, W. A. Scaffold proteins: hubs for controlling the flow of cellular information. Science 332, 680–686 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Cooper, G. M. The Cell: A Molecular Approach (Sinauer Associates, Sunderland, 2000).

  3. Barabási, A. L. & Oltvai, Z. N. Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004).

    Article  CAS  PubMed  Google Scholar 

  4. Yeger-Lotem, E. et al. Network motifs in integrated cellular networks of transcription–regulation and protein–protein interaction. Proc. Natl Acad. Sci. USA 101, 5934–5939 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Davidson, E. & Levin, M. Gene regulatory networks. Proc. Natl Acad. Sci. USA 102, 4935–4942 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Quin, M. B., Wallin, K. K., Zhang, G. & Schmidt-Dannert, C. Spatial organization of multi-enzyme biocatalytic cascades. Org. Biomol. Chem. 15, 4260–4271 (2017).

    Article  CAS  PubMed  Google Scholar 

  7. Rabe, K. S., Müller, J., Skoupi, M. & Niemeyer, C. M. Cascades in compartments: en route to machine-assisted biotechnology. Angew. Chem. Int. Ed. 56, 13574–13589 (2017).

    Article  CAS  Google Scholar 

  8. Gröger, H. & Hummel, W. Combining the ‘two worlds’ of chemocatalysis and biocatalysis towards multi-step one-pot processes in aqueous media. Curr. Opin. Chem. Biol. 19, 171–179 (2014).

    Article  CAS  PubMed  Google Scholar 

  9. Li, J. et al. Synthesis of many different types of organic small molecules using one automated process. Science 347, 1221–1226 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Agapakis, C. M., Boyle, P. M. & Silver, P. A. Natural strategies for the spatial optimization of metabolism in synthetic biology. Nat. Chem. Biol. 8, 527–535 (2012).

    Article  CAS  PubMed  Google Scholar 

  11. Both, P. et al. Whole-cell biocatalysts for stereoselective C–H amination reactions. Angew. Chem. Int. Ed. 55, 1511–1513 (2016).

    Article  CAS  Google Scholar 

  12. Bayer, E. A., Belaich, J. P., Shoham, Y. & Lamed, R. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu. Rev. Microbiol. 58, 521–554 (2004).

    Article  CAS  PubMed  Google Scholar 

  13. Laursen, T. et al. Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum. Science 354, 890–893 (2016).

    Article  CAS  PubMed  Google Scholar 

  14. Schoffelen, S. & van Hest, J. C. Chemical approaches for the construction of multi-enzyme reaction systems. Curr. Opin. Struct. Biol. 23, 613–621 (2013).

    Article  CAS  PubMed  Google Scholar 

  15. Vance, S. et al. Sticky swinging arm dynamics: studies of an acyl carrier protein domain from the mycolactone polyketide synthase. Biochem. J. 473, 1097–1110 (2016).

    Article  CAS  PubMed  Google Scholar 

  16. Delebecque, C. J., Lindner, A. B., Silver, P. A. & Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470–474 (2011).

    Article  CAS  PubMed  Google Scholar 

  17. Wilner, O. I. et al. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat. Nanotech. 4, 249–254 (2009).

    Article  CAS  Google Scholar 

  18. Wang, Z. G., Wilner, O. I. & Willner, I. Self-assembly of aptamer-circular DNA nanostructures for controlled biocatalysis. Nano Lett. 9, 4098–4102 (2009).

    Article  CAS  PubMed  Google Scholar 

  19. Fu, J., Liu, M., Liu, Y., Woodbury, N. W. & Yan, H. Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. J. Am. Chem. Soc. 134, 5516–5519 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Timm, C. & Niemeyer, C. M. Assembly and purification of enzyme-functionalized DNA origami structures. Angew. Chem. Int. Ed. 54, 6745–6750 (2015).

    Article  CAS  Google Scholar 

  21. Liu, M. et al. A DNA tweezer-actuated enzyme nanoreactor. Nat. Commun. 4, 2127 (2013).

    Article  CAS  PubMed  Google Scholar 

  22. Aleman-Garcia, M. A., Orbach, R. & Willner, I. Ion-responsive hemin-G-quadruplexes for switchable DNAzyme and enzyme functions. Chem. Eur. J. 20, 5619–5624 (2014).

    Article  CAS  PubMed  Google Scholar 

  23. Wang, Z. & Cohen, S. M. Postsynthetic modification of metal–organic frameworks. Chem. Soc. Rev. 38, 1315–1329 (2009).

    Article  CAS  PubMed  Google Scholar 

  24. Furukawa, H., Cordova, K. E., O’Keeffe, M. & Yaghi, O. M. The chemistry and applications of metal–organic frameworks. Science 341, 1230444 (2013).

    Article  CAS  PubMed  Google Scholar 

  25. Cui, Y. et al. Metal–organic frameworks as platforms for functional materials. Acc. Chem. Res. 49, 483–493 (2016).

    Article  CAS  PubMed  Google Scholar 

  26. Stavila, V. et al. MOF-based catalysts for selective hydrogenolysis of carbon–oxygen ether bonds. ACS Catal. 6, 55–59 (2015).

    Article  CAS  Google Scholar 

  27. Yoon, M., Srirambalaji, R. & Kim, K. Homochiral metal–organic frameworks for asymmetric heterogeneous catalysis. Chem. Rev. 112, 1196–1231 (2012).

    Article  CAS  PubMed  Google Scholar 

  28. Liu, J. et al. Applications of metal–organic frameworks in heterogeneous supramolecular catalysis. Chem. Soc. Rev. 43, 6011–6061 (2014).

    Article  CAS  PubMed  Google Scholar 

  29. Liu, D., Huxford, R. C. & Lin, W. Phosphorescent nanoscale coordination polymers as contrast agents for optical imaging. Angew. Chem. Int. Ed. 50, 3696–3700 (2011).

    Article  CAS  Google Scholar 

  30. Horcajada, P. et al. Metal–organic frameworks in biomedicine. Chem. Rev. 112, 1232–1268 (2012).

    Article  CAS  PubMed  Google Scholar 

  31. Chen, W. H. et al. ATP-responsive aptamer-based metal–organic framework nanoparticles (NMOFs) for the controlled release of loads and drugs. Adv. Funct. Mater. 27, 1702102 (2017).

    Article  CAS  Google Scholar 

  32. Chen, W. H. et al. Stimuli-responsive nucleic acid-functionalized metal–organic framework nanoparticles using pH- and metal-ion-dependent DNAzymes as locks. Chem. Sci. 8, 5769–5780 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Chen, W. H. et al. Stimuli-responsive nucleic acid-based polyacrylamide hydrogel-coated metal–organic framework nanoparticles for controlled drug release. Adv. Funct. Mater. 28, 1705137 (2018).

    Article  CAS  Google Scholar 

  34. Kreno, L. E. et al. Metal–organic framework materials as chemical sensors. Chem. Rev. 112, 1105–1125 (2012).

    Article  CAS  PubMed  Google Scholar 

  35. Wu, L. L. et al. A metal–organic framework/DNA hybrid system as a novel fluorescent biosensor for mercury(II) ion detection. Chem. Eur. J. 22, 477–480 (2016).

    Article  CAS  PubMed  Google Scholar 

  36. Della Rocca, J., Liu, D. & Lin, W. Nanoscale metal–organic frameworks for biomedical imaging and drug delivery. Acc. Chem. Res. 44, 957–968 (2011).

    Article  CAS  PubMed  Google Scholar 

  37. Taylor, K. M., Jin, A. & Lin, W. Surfactant-assisted synthesis of nanoscale gadolinium metal–organic frameworks for potential multimodal imaging. Angew. Chem. Int. Ed. 47, 7722–7725 (2008).

    Article  CAS  Google Scholar 

  38. Li, S. L. & Xu, Q. Metal–organic frameworks as platforms for clean energy. Energy Environ. Sci. 6, 1656–1683 (2013).

    Article  CAS  Google Scholar 

  39. Hurd, J. A. et al. Anhydrous proton conduction at 150 °C in a crystalline metal–organic framework. Nat. Chem. 1, 705–710 (2009).

    Article  CAS  PubMed  Google Scholar 

  40. Lian, X. et al. Enzyme-MOF (metal–organic framework) composites. Chem. Soc. Rev. 46, 3386–3401 (2017).

    Article  CAS  PubMed  Google Scholar 

  41. Lian, X., Chen, Y. P., Liu, T. F. & Zhou, H. C. Coupling two enzymes into a tandem nanoreactor utilizing a hierarchically structured MOF. Chem. Sci. 7, 6969–6973 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Ge, J., Lei, J. & Zare, R. N. Protein–inorganic hybrid nanoflowers. Nat. Nanotechnol. 7, 428–432 (2012).

    Article  CAS  PubMed  Google Scholar 

  43. Doonan, C., Riccò, R., Liang, K., Bradshaw, D. & Falcaro, P. Metal–organic frameworks at the biointerface: synthetic strategies and applications. Acc. Chem. Res. 50, 1423–1432 (2017).

    Article  CAS  PubMed  Google Scholar 

  44. Zhuang, J., Young, A. P. & Tsung, C. K. Integration of biomolecules with metal–organic frameworks. Small 13, 1700880 (2017).

    Article  CAS  Google Scholar 

  45. Wu, X., Ge, J., Yang, C., Hou, M. & Liu, Z. Facile synthesis of multiple enzyme-containing metal–organic frameworks in a biomolecule-friendly environment. Chem. Commun. 51, 13408–13411 (2015).

    Article  CAS  Google Scholar 

  46. Wang, Q., Zhang, X., Huang, L., Zhang, Z. & Dong, S. GOx@ZIF-8(NiPd) nanoflower: an artificial enzyme system for tandem catalysis. Angew. Chem. Int. Ed. 56, 16082–16085 (2017).

    Article  CAS  Google Scholar 

  47. Liang, K. et al. Biomimetic mineralization of metal–organic frameworks as protective coatings for biomacromolecules. Nat. Commun. 6, 7240 (2015).

    Article  CAS  PubMed  Google Scholar 

  48. Karagiaridi, O. et al. Opening ZIF-8: a catalytically active zeolitic imidazolate framework of sodalite topology with unsubstituted linkers. J. Am. Chem. Soc. 134, 18790–18796 (2012).

    Article  CAS  PubMed  Google Scholar 

  49. Takahashi, H. et al. Immobilized enzymes in ordered mesoporous silica materials and improvement of their stability and catalytic activity in an organic solvent. Microporous Mesoporous Mater. 44, 755–762 (2001).

    Article  Google Scholar 

  50. Lei, C., Shin, Y., Liu, J. & Ackerman, E. J. Entrapping enzyme in a functionalized nanoporous support. J. Am. Chem. Soc. 124, 11242–11243 (2002).

    Article  CAS  PubMed  Google Scholar 

  51. Kula, M. R. & Wandrey, C. Continuous enzymatic transformation in an enzyme-membrane reactor with simultaneous NADH regeneration. Methods Enzymol. 136, 9–21 (1987).

    Article  CAS  PubMed  Google Scholar 

  52. Wandrey, C., Liese, A. & Kihumbu, D. Industrial biocatalysis: past, present, and future. Org. Process Res. Dev. 4, 286–290 (2000).

    Article  CAS  Google Scholar 

  53. Wichmann, R., Wandrey, C., Bückmann, A. F. & Kula, M. R. Continuous enzymatic transformation in an enzyme membrane reactor with simultaneous NAD(H) regeneration. Biotechnol. Bioeng. 67, 791–804 (2000).

    Article  CAS  PubMed  Google Scholar 

  54. Li, P. et al. Encapsulation of a nerve agent detoxifying enzyme by a mesoporous zirconium metal–organic framework engenders thermal and long-term stability. J. Am. Chem. Soc. 138, 8052–8055 (2016).

    Article  CAS  PubMed  Google Scholar 

  55. Li, P. et al. Nanosizing a metal–organic framework enzyme carrier for accelerating nerve agent hydrolysis. ACS Nano 10, 9174–9182 (2016).

    Article  CAS  PubMed  Google Scholar 

  56. Lyu, F., Zhang, Y., Zare, R. N., Ge, J. & Liu, Z. One-pot synthesis of protein-embedded metal–organic frameworks with enhanced biological activities. Nano Lett. 14, 5761–5765 (2014).

    Article  CAS  PubMed  Google Scholar 

  57. Liang, K. et al. Metal–organic framework coatings as cytoprotective exoskeletons for living cells. Adv. Mater. 28, 7910–7914 (2016).

    Article  CAS  PubMed  Google Scholar 

  58. Liang, K. et al. An enzyme-coated metal–organic framework shell for synthetically adaptive cell survival. Angew. Chem. Int. Ed. 129, 8630–8635 (2017).

    Article  Google Scholar 

Download references

Acknowledgements

This research was supported by the Israel Science Foundation. We thank M. Spira and S.-Y. Sung for assisting with the confocal microscopy experiments.

Author information

Author notes

  1. These authors contributed equally: Wei-Hai Chen, Margarita Vázquez-González.

Authors and Affiliations

  1. Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel

    Wei-Hai Chen, Margarita Vázquez-González, Amani Zoabi, Raed Abu-Reziq & Itamar Willner

Authors
  1. Wei-Hai Chen
    View author publications

    Search author on:PubMed Google Scholar

  2. Margarita Vázquez-González
    View author publications

    Search author on:PubMed Google Scholar

  3. Amani Zoabi
    View author publications

    Search author on:PubMed Google Scholar

  4. Raed Abu-Reziq
    View author publications

    Search author on:PubMed Google Scholar

  5. Itamar Willner
    View author publications

    Search author on:PubMed Google Scholar

Contributions

W.-H.C. and M.V.-G. performed the experiments, analysed the results and participated in writing the paper. I.W. supervised the project. A.Z. and R.A.-R. helped to perform some of the analytic experiments related to this study.

Corresponding author

Correspondence to Itamar Willner.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Methods, Supplementary Discussion, Supplementary Figures 1–13, Supplementary Table 1, Supplementary References

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, WH., Vázquez-González, M., Zoabi, A. et al. Biocatalytic cascades driven by enzymes encapsulated in metal–organic framework nanoparticles. Nat Catal 1, 689–695 (2018). https://doi.org/10.1038/s41929-018-0117-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41929-018-0117-2

This article is cited by

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research