Skip to main content
SpringerLink
Log in

Fabrication of Protein Macromolecular Frameworks (PMFs) and Their Application in Catalytic Materials

  • Protocol
  • First Online:
Protein Cages

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2671))

Abstract

The construction of three-dimensional (3D) array materials from nanoscale building blocks has drawn significant interest because of their potential to exhibit collective properties and functions arising from the interactions between individual building blocks. Protein cages such as virus-like particles (VLPs) have distinct advantages as building blocks for higher-order assemblies because they are extremely homogeneous in size and can be engineered with new functionalities by chemical and/or genetic modification. In this chapter, we describe a protocol for constructing a new class of protein-based superlattices, called protein macromolecular frameworks (PMFs). We also describe an exemplary method to evaluate the catalytic activity of enzyme-enclosed PMFs, which exhibit enhanced catalytic activity due to the preferential partitioning of charged substrates into the PMF.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Douglas T, Young M (2006) Viruses: making friends with old foes. Science 312:873–875

    Article  CAS  Google Scholar 

  2. Aumiller WM, Uchida M, Douglas T (2018) Protein cage assembly across multiple length scales. Chem Soc Rev 47:3433–3469

    Article  CAS  Google Scholar 

  3. Patterson DP, Prevelige PE, Douglas T (2012) Nanoreactors by programmed enzyme encapsulation inside the capsid of the bacteriophage P22. ACS Nano 6:5000–5009

    Article  CAS  Google Scholar 

  4. Jordan PC, Patterson DP, Saboda KN, Edwards EJ, Miettinen HM, Basu G, Thielges MC, Douglas T (2016) Self-assembling biomolecular catalysts for hydrogen production. Nat Chem 8:179–185

    Article  CAS  Google Scholar 

  5. Patterson DP, Schwarz B, Waters RS, Gedeon T, Douglas T (2014) Encapsulation of an enzyme cascade within the bacteriophage p22 virus-like particle. ACS Chem Biol 9:359–365

    Article  CAS  Google Scholar 

  6. Wang Y, Uchida M, Waghwani HK, Douglas T (2020) Synthetic virus-like particles for glutathione biosynthesis. ACS Synth Biol 9:3298–3310

    Article  CAS  Google Scholar 

  7. O’Neil A, Prevelige PE, Douglas T (2013) Stabilizing viral nano-reactors for nerve-agent degradation. Biomater Sci 1:881–886

    Article  Google Scholar 

  8. Selivanovitch E, Douglas T (2019) Virus capsid assembly across different length scales inspire the development of virus-based biomaterials. Curr Opin Virol 36:38–46

    Article  CAS  Google Scholar 

  9. Kostiainen MA, Kasyutich O, Cornelissen JJLM, Nolte RJM (2010) Self-assembly and optically triggered disassembly of hierarchical dendron-virus complexes. Nat Chem 2:394–399

    Article  CAS  Google Scholar 

  10. Kostiainen MA, Hiekkataipale P, Laiho A, Lemieux V, Seitsonen J, Ruokolainen J, Ceci P (2012) Electrostatic assembly of binary nanoparticle superlattices using protein cages. Nat Nanotechnol 8:52–56

    Article  Google Scholar 

  11. Liljeström V, Ora A, Hassinen J, Rekola HT, Nonappa HM, Hynninen V, Joensuu JJ, Ras RHA, Törmä P, Ikkala O, Kostiainen MA (2017) Cooperative colloidal self-assembly of metal- protein superlattice wires. Nat Commun 8:671

    Article  Google Scholar 

  12. Künzle M, Eckert T, Beck T (2016) Binary protein crystals for the assembly of inorganic nanoparticle superlattices. J Am Chem Soc 138:12731–12734

    Article  Google Scholar 

  13. Uchida M, McCoy K, Fukuto M, Yang L, Yoshimura H, Miettinen HM, Lafrance B, Patterson DP, Schwarz B, Karty JA, Prevelige PE Jr, Lee B, Douglas T (2018) Modular self-assembly of protein cage lattices for multistep catalysis. ACS Nano 12:942–953

    Article  CAS  Google Scholar 

  14. Chakraborti S, Korpi A, Kumar M, Stepien P, Kostiainen MA, Heddle JG (2019) Three-dimensional protein cage array capable of active enzyme capture and artificial chaperone activity. Nano Lett 19:3918–3924

    Article  CAS  Google Scholar 

  15. Ramberg KO, Engilberge S, Skorek T, Crowley PB (2021) Facile fabrication of protein-macrocycle frameworks. J Am Chem Soc 143:1896–1907

    Article  CAS  Google Scholar 

  16. Zheng B, Zhou K, Zhang T, Lv C, Zhao G (2019) Designed two- and three-dimensional protein nanocage networks driven by hydrophobic interactions contributed by amyloidogenic motifs. Nano Lett 19:4023–4028

    Article  CAS  Google Scholar 

  17. Strable E, Johnson JE, Finn MG (2004) Natural nanochemical building blocks: icosahedral virus particles organized by attached oligonucleotides. Nano Lett 4:1385–1389

    Article  CAS  Google Scholar 

  18. McMillan JR, Brodin JD, Millan JA, Lee B, Olvera de la Cruz M, Mirkin CA (2017) Modulating nanoparticle superlattice structure using proteins with tunable bond distributions. J Am Chem Soc 139:1754–1757

    Article  CAS  Google Scholar 

  19. Tian Y, Lhermitte JR, Bai L, Vo T, Xin HL, Li H, Li R, Fukuto M, Yager KG, Kahn JS, Xiong Y, Minevich B, Kumar SK, Gang O (2020) Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels. Nat Mater 19:789–796

    Article  CAS  Google Scholar 

  20. Bailey JB, Zhang L, Chiong JA, Ahn S, Tezcan FA (2017) Synthetic modularity of protein–metal–organic frameworks. J Am Chem Soc 139:8160–8166

    Article  CAS  Google Scholar 

  21. McCoy K, Uchida M, Lee B, Douglas T (2018) Templated assembly of a functional ordered protein macromolecular framework from p22 virus-like particles. ACS Nano 12:3541–3550

    Article  CAS  Google Scholar 

  22. Selivanovitch E, Uchida M, Lee B, Douglas T (2021) Substrate partitioning into protein macromolecular frameworks for enhanced catalytic turnover. ACS Nano 15(10):15687–15699

    Article  CAS  Google Scholar 

  23. Thuman-Commike PA, Greene B, Jakana J, Prasad BV, King J, Prevelige PE Jr, Chiu W (1996) Three-dimensional structure of scaffolding-containing phage p22 procapsids by electron cryo-microscopy. J Mol Biol 260:85–98

    Article  CAS  Google Scholar 

  24. Tuma R, Prevelige PE, Thomas GJ (1998) Mechanism of capsid maturation in a double-stranded DNA virus. Proc Natl Acad Sci U S A 95:9885–9890

    Article  CAS  Google Scholar 

  25. Teschke CM, McGough A, Thuman-Commike PA (2003) Penton release from P22 heat-expanded capsids suggests importance of stabilizing penton-hexon interactions during capsid maturation. Biophys J 84:2585–2592

    Article  CAS  Google Scholar 

  26. Kang S, Uchida M, O’Neil A, Li R, Prevelige PE, Douglas T (2010) Implementation of P22 viral capsids as nanoplatforms. Biomacromolecules 11:2804–2809

    Article  CAS  Google Scholar 

  27. Tang L, Gilcrease EB, Casjens SR, Johnson JE (2006) Highly discriminatory binding of capsid-cementing proteins in bacteriophage L. Structure 14:837–845

    Article  CAS  Google Scholar 

  28. Parent KN, Deedas CT, Egelman EH, Casjens SR, Baker TS, Teschke CM (2012) Stepwise molecular display utilizing icosahedral and helical complexes of phage coat and decoration proteins in the development of robust nanoscale display vehicles. Biomaterials 33:5628–5637

    Article  CAS  Google Scholar 

  29. Uchida M, Lafrance B, Broomell CC, Prevelige PE Jr, Douglas T (2015) Higher order assembly of Virus-like Particles (VLPs) mediated by multi-valent protein linkers. Small 11:1562–1570

    Article  CAS  Google Scholar 

  30. Yaghi OM, O’Keeffe M, Ockwig NW, Chae HK, Eddaoudi M, Kim J (2003) Reticular synthesis and the design of new materials. Nature 423:705–714

    Article  CAS  Google Scholar 

  31. McCoy K, Douglas T (2018) In vivo packaging of protein cargo inside of virus-like particle P22. Methods Mol Biol 1776:295–302

    Article  CAS  Google Scholar 

  32. Selivanovitch E, LaFrance B, Douglas T (2021) Molecular exclusion limits for diffusion across a porous capsid. Nat Commun 12:2903

    Article  CAS  Google Scholar 

  33. Selivanovitch E, Koliyatt R, Douglas T (2019) Chemically induced morphogenesis of P22 virus-like particles by the surfactant sodium dodecyl sulfate. Biomacromolecules 20:389–400

    Article  CAS  Google Scholar 

  34. Lucon J, Qazi S, Uchida M, Bedwell GJ, Lafrance B, Prevelige PE, Douglas T (2012) Use of the interior cavity of the P22 capsid for site-specific initiation of atom-transfer radical polymerization with high-density cargo loading. Nat Chem 4:781–788

    Article  CAS  Google Scholar 

  35. Sharma J, Douglas T (2020) Tuning the catalytic properties of P22 nanoreactors through compositional control. Nanoscale 12:336–346

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by a grant from the Human Frontier Science Program (HFSP) 4124801. M.U. was supported in part by the National Science Foundation grant CMMI-1922883. E.S. was partially supported by the Graduate Training Program in Quantitative and Chemical Biology under Award T32 GM109825 and Indiana University. T.D. was additionally supported by the National Science Foundation through grant 1720625.

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, California State University, Fresno, Fresno, CA, USA

    Masaki Uchida & Kimberly McCoy

  2. Department of Chemistry, Indiana University, Bloomington, IN, USA

    Ekaterina Selivanovitch & Trevor Douglas

Authors
  1. Masaki Uchida
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ekaterina Selivanovitch
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kimberly McCoy
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Trevor Douglas
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masaki Uchida .

Editor information

Editors and Affiliations

  1. Tokyo Institute Of Technology, Yokohama, Japan

    Takafumi Ueno

  2. Chemical & Biomedical Enginering, Nanyang Technological University, Singapore, Singapore

    Sierin Lim

  3. Nanyang Technological University, Singapore, Singapore

    Kelin Xia

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Uchida, M., Selivanovitch, E., McCoy, K., Douglas, T. (2023). Fabrication of Protein Macromolecular Frameworks (PMFs) and Their Application in Catalytic Materials. In: Ueno, T., Lim, S., Xia, K. (eds) Protein Cages. Methods in Molecular Biology, vol 2671. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3222-2_6

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3222-2_6

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3221-5

  • Online ISBN: 978-1-0716-3222-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation