Figure 1: The host–guest system and the encapsulation strategy. | Nature Communications

Figure 1: The host–guest system and the encapsulation strategy.

From: Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions

Figure 1

(a) The DegP protein guest in its monomeric form is constituted by three domains: a protease (red), a PDZ1 (green) and a PDZ2 (blue) domain. The 6-, 12- and 24-mer DegP states have different symmetries and sizes (PDB codes are, respectively: 1KY9, 3OTP and 3CS0). (b) The DNA origami host is internally decorated with protruding DNA strands (orange helices) for further hybridization to complementary DNA–peptide conjugates (grey helices). (c) The host is made of six planar faces connected into a hexagonal prism with an edge and outer radius of 23 nm and a free inner room of ca. 10 nm in radius. (d) The host has two different lengths 49 and 56 nm, associated, respectively, to four short and two long opposite edges. (e) Schematic representation of the design strategy used to link adjacent faces at a fixed 120° angle, using out-of-plane crossovers. (f) Molecular dynamics simulations illustrate the binding of three DNA-DPMFKLV ligands to the PDZ1 domains of DegP24 (top view). The side view of a small region of the complex is shown in the panel. (g) Detailed view of the binding of the DNA-DPMFKLV ligand to the PDZ1 domain in the interior cavity of DegP24 (last frame of the MD simulations).

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