A mechanism of ferritin crystallization revealed by cryo-STEM tomography

Abstract

Protein crystallization is important in structural biology, disease research and pharmaceuticals. It has recently been recognized that nonclassical crystallization—involving initial formation of an amorphous precursor phase—occurs often in protein, organic and inorganic crystallization processes1,2,3,4,5. A two-step nucleation theory has thus been proposed, in which initial low-density, solvated amorphous aggregates subsequently densify, leading to nucleation4,6,7. This view differs from classical nucleation theory, which implies that crystalline nuclei forming in solution have the same density and structure as does the final crystalline state1. A protein crystallization mechanism involving this classical pathway has recently been observed directly8. However, a molecular mechanism of nonclassical protein crystallization9,10,11,12,13,14,15 has not been established9,11,14. To determine the nature of the amorphous precursors and whether crystallization takes place within them (and if so, how order develops at the molecular level), three-dimensional (3D) molecular-level imaging of a crystallization process is required. Here we report cryogenic scanning transmission microscopy tomography of ferritin aggregates at various stages of crystallization, followed by 3D reconstruction using simultaneous iterative reconstruction techniques to provide a 3D picture of crystallization with molecular resolution. As crystalline order gradually increased in the studied aggregates, they exhibited an increase in both order and density from their surface towards their interior. We observed no highly ordered small structures typical of a classical nucleation process, and occasionally we observed several ordered domains emerging within one amorphous aggregate, a phenomenon not predicted by either classical or two-step nucleation theories. Our molecular-level analysis hints at desolvation as the driver of the continuous order-evolution mechanism, a view that goes beyond current nucleation models, yet is consistent with a broad spectrum of protein crystallization mechanisms.

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Fig. 1: Cryo-TEM image of a ferritin solution.
Fig. 2: Methodological approach for the 3D characterization of ferritin crystallization.
Fig. 3: Site-specific distance order parameters and nearest-neighbour coordination for ferritin aggregates.
Fig. 4: Steinhardt bond-orientation order parameters.

Data availability

The data that supports the findings of this study are available from the corresponding authors upon request.

Code availability

The program code for the database implemented orientation order parameter analysis performed in this manuscript is available from https://github.com/LotharHouben/diOpa.

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Acknowledgements

This work was supported by the Helen and Martin Kimmel Center for Molecular Design. We thank S. Albeck, M. Peretz and J. Jacobovitch for assistance with GPC experiments, I. Biran for help acquiring cryo-STEM tomograms, and B. Palmer and R. Diskin for discussions. The electron microscopy studies were partially supported by the Irving and Cherna Moskowitz Center for Nano and BioNano Imaging (Weizmann Institute of Science). S.G.W. acknowledges support for cryo-STEM tomography studies from the Israel Science Foundation (grant number 1285/14).

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Contributions

B.R., L.H. and H.W. conceived the project. H.W. performed the crystallization experiments and the 2D cryo-TEM imaging; S.G.W., H.W. and L.H. performed the cryo-STEM tomography imaging; and L.H performed the cryo-STEM tomography data analysis. B.R. and L.H. wrote the manuscript. All authors contributed to the discussion and commented on the manuscript.

Corresponding authors

Correspondence to Lothar Houben or Boris Rybtchinski.

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The authors declare no competing interests.

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Peer review information Nature thanks Mike Sleutel, Peter Vekilov and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

41586_2020_2104_MOESM2_ESM.mp4

An animated representation of the procedure for the identification of ferritin coordinates from cryo-STEM data. The movie shows in sequence a tilt series of annular dark field images of a ferritin aggregate after image alignment, tomogram reconstruction slices in the viewing direction from the top of the cryo sample, the identification of peak signals associated with iron-rich cores of ferritin monomers in the two-dimensional reconstruction slices, and the remaining ferritin coordinates in the 3D tomogram volume after refinement that eliminates the peak overlap in the third dimension.

41586_2020_2104_MOESM3_ESM.mp4

An animated representation of a highly ordered ferritin aggregate in a cryo-STEM tilt series of bright-field images and the tomogram reconstruction slices in the viewing direction from the top. SI Video 2 exemplifies the accurate reproduction of the crystalline structure with monomer resolution.

Supplementary Information

Description, Supplementary Figures and references related to crystallization procedures, Cryo-(S)TEM experiments, and order analysis methods.

Video 1

An animated representation of the procedure for the identification of ferritin coordinates from cryo-STEM data. The movie shows in sequence a tilt series of annular dark field images of a ferritin aggregate after image alignment, tomogram reconstruction slices in the viewing direction from the top of the cryo sample, the identification of peak signals associated with iron-rich cores of ferritin monomers in the two-dimensional reconstruction slices, and the remaining ferritin coordinates in the 3D tomogram volume after refinement that eliminates the peak overlap in the third dimension.

Video 2

An animated representation of a highly ordered ferritin aggregate in a cryo-STEM tilt series of bright-field images and the tomogram reconstruction slices in the viewing direction from the top. SI Video 2 exemplifies the accurate reproduction of the crystalline structure with monomer resolution.

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Houben, L., Weissman, H., Wolf, S.G. et al. A mechanism of ferritin crystallization revealed by cryo-STEM tomography. Nature 579, 540–543 (2020). https://doi.org/10.1038/s41586-020-2104-4

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