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Structure of a designed protein cage that self-assembles into a highly porous cube

Nature Chemistry volume 6, pages 1065–1071 (2014)Cite this article

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Abstract

Natural proteins can be versatile building blocks for multimeric, self-assembling structures. Yet, creating protein-based assemblies with specific geometries and chemical properties remains challenging. Highly porous materials represent particularly interesting targets for designed assembly. Here, we utilize a strategy of fusing two natural protein oligomers using a continuous alpha-helical linker to design a novel protein that self assembles into a 750 kDa, 225 Å diameter, cube-shaped cage with large openings into a 130 Å diameter inner cavity. A crystal structure of the cage showed atomic-level agreement with the designed model, while electron microscopy, native mass spectrometry and small angle X-ray scattering revealed alternative assembly forms in solution. These studies show that accurate design of large porous assemblies with specific shapes is feasible, while further specificity improvements will probably require limiting flexibility to select against alternative forms. These results provide a foundation for the design of advanced materials with applications in bionanotechnology, nanomedicine and material sciences.

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Figure 1: Models of the engineered fusion protein and its assembled cage structure.
Figure 2: Crystal structure of the designed cubic cage ATC-HL3.
Figure 3: Native MS of the ATC-HL3 protein cage.
Figure 4: Negatively stained TEM of the ATC-HL3 cage.
Figure 5: SAXS profile of ATC-HL3.

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Acknowledgements

This work was supported by the National Science Foundation (grant CHE-1332907, T.O.Y.), the BER programme of the Department of Energy Office of Science, and the National Institutes of Health (NIH, grant R01GM067167, F.J.A.). The authors thank M. Sawaya, D. Cascio, D. McNamara and D. Leibly for X-ray data collection at the Advanced Photon Source (APS), the staff at APS beamline 24-ID-C and the National Resource for Automated Macromolecular Microscopy (NRAMM) for support. The authors thank D. Woolfson, N. King and members of the D. Baker laboratory for discussions and T. Goddard for advice on modelling in UCSF Chimera. SAXS data collection and analysis at BL12.3.1 at the Advanced Light Source (ALS) was supported by the Integrated Diffraction Analysis Technologies (IDAT) program (DOE/BER), by the Department of Energy (contract DE-AC02-05CH11231) and by NIH MINOS (R01GM105404).

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Authors and Affiliations

  1. UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 90095, California, USA

    Yen-Ting Lai & Todd O. Yeates

  2. Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, UK

    Eamonn Reading, Arthur Laganowsky & Carol V. Robinson

  3. Lawrence Berkeley National Laboratory, Berkeley, 94704, California, USA

    Greg L. Hura & John A. Tainer

  4. Department of Chemistry and Biochemistry, University of California, Santa Cruz, 95064, California, USA

    Greg L. Hura

  5. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, 92037, California, USA

    Kuang-Lei Tsai, Francisco J. Asturias & John A. Tainer

  6. The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, 92037, California, USA

    John A. Tainer

  7. Department of Chemistry and Biochemistry, University of California, Los Angeles, 90095-1569, California, USA

    Todd O. Yeates

  8. California Nanosystems Institute, University of California, Los Angeles, 90095, California, USA

    Todd O. Yeates

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Contributions

Y-T.L. and T.O.Y. conceived the project. Y-T.L., E.R., G.H., K-L.T., A.L., J.A.T. and T.O.Y. performed the experiments and analysed the data. Y-T.L. and T.O.Y. drafted the manuscript. All other authors contributed to the writing and editing of individual sections of the complete manuscript.

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Correspondence to Todd O. Yeates.

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Lai, YT., Reading, E., Hura, G. et al. Structure of a designed protein cage that self-assembles into a highly porous cube. Nature Chem 6, 1065–1071 (2014). https://doi.org/10.1038/nchem.2107

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