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Computational design of self-assembling cyclic protein homo-oligomers

Nature Chemistry volume 9, pages 353–360 (2017)Cite this article

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Abstract

Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein–protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were characterized experimentally, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (four homodimers, six homotrimers, six homotetramers and one homopentamer) had solution small-angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each is very close to their corresponding computational model.

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Figure 1: Computational design protocol.
Figure 2: Assessment of the solution conformation of selected cyclic oligomers.
Figure 3: Comparison between the experimentally determined crystal structures and corresponding design models.
Figure 4: Robustness of designs to subunit extension by repeat addition.

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Acknowledgements

This work was supported by the Howard Hughes Medical Institute (HHMI), Air Force Office for Scientific Research (AFOSR FA950-12-10112), the National Science Foundation (NSF MCB-1445201 and CHE-1332907), the Bill and Melinda Gates Foundation (OPP1120319) and the Defense Threat Reduction Agency (HDTRA1-11-C-0026 AM06). We thank R. Koga and L. Carter for assistance with SEC–MALS. We thank M. Collazo and M. Sawaya supported by Department of Energy (DOE Grant DE-FC02-02ER63421. We thank M. Capel, K. Rajashankar, N. Sukumar, J. Schuermann, I. Kourinov and F. Murphy at Northeastern Collaborative Access Team supported by grants from the National Center for Research Resources (5P41RR015301-10) and the National Institute of General Medical Sciences (NIGMS P41GM103403-10) from the National Institutes of Health (NIH). Use of the APS is supported by the DOE under Contract DE-AC02-06CH11357. X-ray crystallography and SAXS data were collected at the Advanced Light Source (ALS, Lawrence Berkeley National Laboratory, Berkeley, California Department of Energy, contract no. DE-AC02-05CH11231); SAXS data were collected through the SIBYLS mail-in SAXS program under the aforementioned contract no. and is funded by DOE BER IDAT, NIH MINOS (RO1GM105404) and the ALS, and we thank K. Burnett and G. Hura. The Berkeley Center for Structural Biology is supported in part by the NIH, NIGMS and the HHMI. The ALS is supported by the Director, Office of Science, Office of Basic Energy Sciences of the US DOE under contract no. DE-AC02-05CH11231.

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Author notes

  1. Dan E. McNamara

    Present address: Present address: Departments of Structural Biology and of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA,

  2. Jorge A. Fallas, George Ueda and William Sheffler: These authors contributed equally to this work

Authors and Affiliations

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

    Jorge A. Fallas, George Ueda, William Sheffler, Fabio Parmeggiani, T. J. Brunette & David Baker

  2. Institute for Protein Design, University of Washington, Seattle, 98195, Washington, USA

    Jorge A. Fallas, George Ueda, William Sheffler, Vanessa Nguyen, Fabio Parmeggiani, T. J. Brunette & David Baker

  3. Department of Chemistry and Biochemistry, University of California Los Angles, Los Angeles, 90095, California, USA

    Dan E. McNamara, Duilio Cascio & Todd R. Yeates

  4. Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, 94720, California, USA

    Banumathi Sankaran, Jose Henrique Pereira & Peter Zwart

  5. Joint BioEnergy Institute, Emeryville, 94608, California, USA

    Jose Henrique Pereira

  6. Howard Hughes Medical Institute, University of Washington, Seattle, 98195, Washington, USA

    David Baker

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Contributions

J.A.F., G.U., W.S. and D.B. designed the research. W.S. developed the RPX method and wrote the program code. J.A.F., G.U. and V.N. carried out design calculations, and purified and biophysically characterized the designed proteins. F.P. and T.J.B. designed and characterized the monomeric repeat proteins used as scaffolds. D.E.M., D.C., T.R.Y., J.H.P., G.U. and J.A.F crystallized the designed proteins. D.E.M, D.C., B.S. and P.Z. collected and analysed crystallographic data. J.A.F., D.E.M., D.C., B.S. and P.Z. solved the structures. All the authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to David Baker.

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Supplementary information

Supplementary information

Supplementary information (PDF 6942 kb)

Symmetry Definition File

symmetry name C2 (TXT 0 kb)

Supplementary information

symmetry name C3 (TXT 0 kb)

Symmetry Definition File

symmetry name C4 (TXT 0 kb)

Symmetry Definition File

symmetry name C5 (TXT 0 kb)

Symmetry Definition File

symmetry name C6 (TXT 0 kb)

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Fallas, J., Ueda, G., Sheffler, W. et al. Computational design of self-assembling cyclic protein homo-oligomers. Nature Chem 9, 353–360 (2017). https://doi.org/10.1038/nchem.2673

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