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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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.
The authors declare no competing financial interests.
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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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