Design of biologically active binary protein 2D materials

Ariel J. Ben-Sasson, Joseph L. Watson, William Sheffler, Matthew Camp Johnson, Alice Bittleston, Logeshwaran Somasundaram, Justin Decarreau, Fang Jiao, Jiajun Chen, Ioanna Mela, Andrew A. Drabek, Sanchez M. Jarrett, Stephen C. Blacklow, Clemens F. Kaminski, Greg L. Hura, James J. Yoreo, Justin M. Kollman, Hannele Ruohola-Baker, Emmanuel Derivery () and David Baker ()
Additional contact information
Ariel J. Ben-Sasson: University of Washington
Joseph L. Watson: MRC Laboratory of Molecular Biology
William Sheffler: University of Washington
Matthew Camp Johnson: University of Washington
Alice Bittleston: MRC Laboratory of Molecular Biology
Logeshwaran Somasundaram: University of Washington, School of Medicine
Justin Decarreau: University of Washington
Fang Jiao: Pacific Northwest National Laboratory
Jiajun Chen: University of Washington
Ioanna Mela: University of Cambridge
Andrew A. Drabek: Harvard Medical School
Sanchez M. Jarrett: Harvard Medical School
Stephen C. Blacklow: Harvard Medical School
Clemens F. Kaminski: University of Cambridge
Greg L. Hura: Lawrence Berkeley National Laboratory
James J. Yoreo: University of Washington
Justin M. Kollman: University of Washington
Hannele Ruohola-Baker: University of Washington
Emmanuel Derivery: MRC Laboratory of Molecular Biology
David Baker: University of Washington

Nature, 2021, vol. 589, issue 7842, 468-473

Abstract: Abstract Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3–5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9–12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.

Date: 2021
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DOI: 10.1038/s41586-020-03120-8

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