Letter | Published:

Proteins evolve on the edge of supramolecular self-assembly

Nature volume 548, pages 244247 (10 August 2017) | Download Citation

Abstract

The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life1,2,3,4,5,6. Symmetric complexes possess unique geometric and functional properties, but their internal symmetry can pose a risk. In sickle-cell disease, the symmetry of haemoglobin exacerbates the effect of a mutation, triggering assembly into harmful fibrils7. Here we examine the universality of this mechanism and its relation to protein structure geometry. We introduced point mutations solely designed to increase surface hydrophobicity among 12 distinct symmetric complexes from Escherichia coli. Notably, all responded by forming supramolecular assemblies in vitro, as well as in vivo upon heterologous expression in Saccharomyces cerevisiae. Remarkably, in four cases, micrometre-long fibrils formed in vivo in response to a single point mutation. Biophysical measurements and electron microscopy revealed that mutants self-assembled in their folded states and so were not amyloid-like. Structural examination of 73 mutants identified supramolecular assembly hot spots predictable by geometry. A subsequent structural analysis of 7,471 symmetric complexes showed that geometric hot spots were buffered chemically by hydrophilic residues, suggesting a mechanism preventing mis-assembly of these regions. Thus, point mutations can frequently trigger folded proteins to self-assemble into higher-order structures. This potential is counterbalanced by negative selection and can be exploited to design nanomaterials in living cells.

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Acknowledgements

We thank S. Wolf and E. Shimoni for help with electron microscopy experiments, and J. Georgeson for setting up the microscope time-lapse. We thank members of the laboratory, D. Fass and A. Horovitz for discussions throughout the realization of this work, H. Weissman for discussions about electron microscopy, and D. Fass for invaluable feedback on the manuscript. This work was supported by the Israel Science Foundation and the I-CORE Program of the Planning and Budgeting Committee (grants 1775/12 and 2179/14), by the Marie Curie Career Integration Grants Program (number 711715), by the Human Frontier Science Program Career Development Award (number CDA00077/2015), and by a research grant from A.-M. Boucher. H.G.S. received support from the Koshland Foundation and a McDonald-Leapman Grant. Electron microscopy studies were supported by the Irving and Cherna Moskowitz Center for Nano and Bio-Nano Imaging. E.D.L. is incumbent of the Recanati Career Development Chair of Cancer Research.

Author information

Author notes

    • Charly Empereur-Mot

    Present address: Conservatoire National des Arts et Métiers, 75003 Paris, France.

Affiliations

  1. Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel

    • Hector Garcia-Seisdedos
    • , Charly Empereur-Mot
    •  & Emmanuel D. Levy
  2. Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel

    • Nadav Elad

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Contributions

H.G.S. and E.D.L. designed the experiments. C.E.M. and E.D.L. designed the computational analyses of protein structure. H.G.S. performed all experiments with guidance from N.E. for electron microscopy techniques. N.E. and H.G.S. performed the single-particle reconstruction. C.E.M. performed the bioinformatics analyses. H.G.S. and E.D.L. analysed the experimental data. C.E.M. and E.D.L. analysed the computational results. E.D.L. and H.G.S. wrote the manuscript with help from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Emmanuel D. Levy.

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    Supplementary Information

    This file contains Supplementary Tables 1 to 4 and Supplementary Text 1. Supplementary Dataset 1 of all homo-oligomeric protein structures with pre-computed nDp measure (>800MB) is available at http://www.weizmann.ac.il/Structural_Biology/faculty_pages/ELevy/downloads/supMat_dPlan.html

CSV files

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    Supplementary Table 5

    Tabulated information about structural properties of mutated residues

  2. 2.

    Supplementary Table 6

    Tabulated dataset of protein structures and computed descriptors used to generate Fig. 4 and Extended Fig. 7

Videos

  1. 1.

    Cells divide while expressing the fiber-forming mutant of E. coli dipeptidase (1POK E239Y)

    Cells divide while expressing the fiber-forming mutant of E. coli dipeptidase. Budding yeasts grow as they express the fiber-forming mutant of E. coli dipeptidase (1pok E239Y) fused to a yellow fluorescent protein. Images were taken every 230 seconds for 10.5 hours. We overlaid the brightfield channel showing the cells (grey) onto the fluorescent channel showing the fibers (green).

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https://doi.org/10.1038/nature23320

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