Article | Published:

Accurate design of co-assembling multi-component protein nanomaterials

Nature volume 510, pages 103108 (05 June 2014) | Download Citation

Abstract

The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Data deposits

The crystal structures and structure factors for the designed materials have been deposited in the RCSB Protein Data Bank (http://www.rcsb.org/) under the accession codes 4NWN (T32-28), 4NWO (T33-15), 4NWP (T33-21, R32 crystal form), 4NWQ (T33-21, F4132 crystal form) and 4NWR (T33-28).

References

  1. 1.

    Rationally engineering natural protein assemblies in nanobiotechnology. Curr. Opin. Biotechnol. 22, 485–491 (2011)

  2. 2.

    & Viruses: making friends with old foes. Science 312, 873–875 (2006)

  3. 3.

    , & Principles for designing ordered protein assemblies. Trends Cell Biol. 22, 653–661 (2012)

  4. 4.

    & Practical approaches to designing novel protein assemblies. Curr. Opin. Struct. Biol. 23, 632–638 (2013)

  5. 5.

    Constructing arrays of proteins. Curr. Opin. Chem. Biol. 17, 946–951 (2013)

  6. 6.

    , & Metal-directed protein self-assembly. Acc. Chem. Res. 43, 661–672 (2010)

  7. 7.

    et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171–1174 (2012)

  8. 8.

    et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nature Chem. 4, 375–382 (2012)

  9. 9.

    et al. Computational design of a protein crystal. Proc. Natl Acad. Sci. USA 109, 7304–7309 (2012)

  10. 10.

    , , , & Computational design of a symmetric homodimer using beta-strand assembly. Proc. Natl Acad. Sci. USA 108, 20562–20567 (2011)

  11. 11.

    , , & Generation of protein lattices by fusing proteins with matching rotational symmetry. Nature Nanotechnol. 6, 558–562 (2011)

  12. 12.

    , & Structure of a 16-nm cage designed by using protein oligomers. Science 336, 1129 (2012)

  13. 13.

    et al. Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J. Am. Chem. Soc. 134, 375–385 (2012)

  14. 14.

    et al. Self-assembling cages from coiled-coil peptide modules. Science 340, 595–599 (2013)

  15. 15.

    et al. Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design. J. Am. Chem. Soc. 134, 15457–15467 (2012)

  16. 16.

    et al. Computational design of virus-like protein assemblies on carbon nanotube surfaces. Science 332, 1071–1076 (2011)

  17. 17.

    Nanomaterials based on DNA. Annu. Rev. Biochem. 79, 65–87 (2010)

  18. 18.

    Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006)

  19. 19.

    , , & Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012)

  20. 20.

    et al. DNA gridiron nanostructures based on four-arm junctions. Science 339, 1412–1415 (2013)

  21. 21.

    , & Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl Acad. Sci. USA 98, 2217–2221 (2001)

  22. 22.

    et al. Nanoscale elongating control of the self-assembled protein filament with the cysteine-introduced building blocks. Protein Sci. 18, 960–969 (2009)

  23. 23.

    & Structural symmetry and protein function. Annu. Rev. Biophys. Biomol. Struct. 29, 105–153 (2000)

  24. 24.

    , & Protein-protein interaction and quaternary structure. Q. Rev. Biophys. 41, 133–180 (2008)

  25. 25.

    , & A de novo designed protein protein interface. Protein Sci. 16, 2770–2774 (2007)

  26. 26.

    et al. Computational design of a PAK1 binding protein. J. Mol. Biol. 400, 257–270 (2010)

  27. 27.

    et al. A de novo protein binding pair by computational design and directed evolution. Mol. Cell 42, 250–260 (2011)

  28. 28.

    et al. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332, 816–821 (2011)

  29. 29.

    & Emerging themes in the computational design of novel enzymes and protein-protein interfaces. FEBS Lett. 587, 1147–1154 (2013)

  30. 30.

    & Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97, 10383–10388 (2000)

  31. 31.

    et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487, 545–574 (2011)

  32. 32.

    , , , & Modeling symmetric macromolecular structures in Rosetta3. PLoS ONE 6, e20450 (2011)

  33. 33.

    & Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946–950 (1993)

  34. 34.

    & Directed evolution of biocatalysts. Curr. Opin. Chem. Biol. 3, 54–59 (1999)

  35. 35.

    , & Protein design by directed evolution. Annu. Rev. Biophys. 37, 153–173 (2008)

  36. 36.

    , & Efficient in vitro encapsulation of protein cargo by an engineered protein container. J. Am. Chem. Soc. 134, 909–911 (2012)

  37. 37.

    , & Directed evolution of a protein container. Science 331, 589–592 (2011)

  38. 38.

    & Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65, 922–929 (2006)

Download references

Acknowledgements

We thank D. Shi and B. Nannenga (JFRC) for help with electron microscopy, F. DiMaio and R. Moretti for assistance with software development, P. Greisen for scripts used to compare side-chain conformations, J. Gallaher for technical assistance, M. Collazo for help with preliminary crystallization screening, D. Cascio and M. Sawaya for help with crystallographic experiments, and M. Capel, J. Schuermann and I. Kourinov at NE-CAT beamline 24-ID-C for help with data collection. This work was supported by the Howard Hughes Medical Institute (T.G. and D.B.) and the JFRC visitor program (S.G.), the National Science Foundation under CHE-1332907 (D.B. and T.O.Y.), grants from the International AIDS Vaccine Initiative, DTRA (N00024-10-D-6318/0024), AFOSR (FA950-12-10112) and DOE (DE-SC0005155) to D.B., an NIH Biotechnology Training Program award to D.E.M. (T32GM067555) and an NSF graduate research fellowship to J.B.B. (DGE-0718124). T.O.Y. and D.E.M. also acknowledge support from the BER programme of the DOE Office of Science. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding bodies.

Author information

Author notes

    • Neil P. King
    • , Jacob B. Bale
    •  & William Sheffler

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA

    • Neil P. King
    • , Jacob B. Bale
    • , William Sheffler
    • , Shane Gonen
    •  & David Baker
  2. Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA

    • Neil P. King
    •  & David Baker
  3. Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, Washington 98195, USA

    • Jacob B. Bale
  4. UCLA Department of Chemistry and Biochemistry, Los Angeles, California 90095, USA

    • Dan E. McNamara
    •  & Todd O. Yeates
  5. Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, USA

    • Shane Gonen
    •  & Tamir Gonen
  6. UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, California 90095, USA

    • Todd O. Yeates
  7. UCLA Molecular Biology Institute, Los Angeles, California 90095, USA

    • Todd O. Yeates
  8. Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA

    • David Baker

Authors

  1. Search for Neil P. King in:

  2. Search for Jacob B. Bale in:

  3. Search for William Sheffler in:

  4. Search for Dan E. McNamara in:

  5. Search for Shane Gonen in:

  6. Search for Tamir Gonen in:

  7. Search for Todd O. Yeates in:

  8. Search for David Baker in:

Contributions

N.P.K., J.B.B., W.S. and D.B. designed the research. N.P.K., J.B.B. and W.S. wrote program code and performed the docking and design calculations. N.P.K. and J.B.B. biophysically characterized the designed materials and prepared samples for structural analysis. S.G. characterized the designed materials by electron microscopy; S.G. and T.G. analysed electron microscopy data. D.E.M. crystallized the designed protein materials; D.E.M. and T.O.Y. analysed crystallographic data. N.P.K., J.B.B. and D.B. analysed data and wrote the manuscript. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Baker.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Methods, Supplementary Tables 1-7 and Supplementary References.

Zip files

  1. 1.

    Design Models

    Zipped folder containing design models.

  2. 2.

    Docking

    Zipped folder containing example files for docking protocol.

  3. 3.

    Design

    Zipped folder containing example files for design protocol.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nature13404

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.