Abstract
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Here, we demonstrate how the tailored encapsulation of proteins in DNA-based voxels can be combined with programmable assembly that directs these voxels into biologically functional protein arrays with prescribed and ordered two-dimensional (2D) and three-dimensional (3D) organizations. We apply the presented concept to ferritin, an iron storage protein, and its iron-free analog, apoferritin, in order to form single-layers, double-layers, as well as several types of 3D protein lattices. Our study demonstrates that internal voxel design and inter-voxel encoding can be effectively employed to create protein lattices with designed organization, as confirmed by in situ X-ray scattering and cryo-electron microscopy 3D imaging. The assembled protein arrays maintain structural stability and biological activity in environments relevant for protein functionality. The framework design of the arrays then allows small molecules to access the ferritins and their iron cores and convert them into apoferritin arrays through the release of iron ions. The presented study introduces a platform approach for creating bio-active protein-containing ordered nanomaterials with desired 2D and 3D organizations.
Highlights
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems
We demonstrate that the structural stability of ferritin and its biological activity to release iron ions are maintained within the assembled arrays
Ferritin showed a smaller amplitude and period of oscitations than apoferritin (Fig. 2c and Supplementary Fig. 3), and these observations were in good agreement with our scattering models, accounting for the core-shell protein structure
Summary
Versatile methods to organize proteins in space are required to enable complex biomaterials, engineered biomolecular scaffolds, cell-free biology, and hybrid nanoscale systems. Establishing approaches for creating protein-based well-ordered structures has been a long-standing focus of structural biology for revealing their atomic structures[5] Such protein crystals can teach us about the bio-machinery through detailed structural information, crystallization methods are not compatible with creating biologically active protein organizations, nor exploring their function in operando. Several challenges have to be solved in order to establish a broadly applicable strategy for creating bio-active protein arrays, regardless of their shape and surface groups, while maintaining an environment and molecular transport for their operation. They include: (i) “transparency” for molecular transport, (ii) a structural designability; and (iii) a broad protein integration suitability. These problems, as we show below, can be tackled by DNA-based approaches by trading a complex interprotein interaction for Watson–Crick base-pairing, which can be controlled on multiple length scales
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