Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.

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Transcription factors (TFs) bind DNA in a sequence-specific manner and are generally cell type-specific factors and/or developmental master regulators. In contrast, general TFs (GTFs) are part of very large protein complexes and serve for RNA polymerases’ recruitment to promoter sequences, generally in a cell type-independent manner. Whereas, several TFs have been proven to serve as anchors for the 3D genome organization, the role of GTFs in genome architecture have not been carefully explored. Here, we used ChIP-seq and Hi-C data to depict the role of TFIIIC, one of the RNA polymerase III GTFs, in 3D genome organization. We find that TFIIIC genome occupancy mainly occurs at specific regions, which largely correspond to Alu elements; other characteristic classes of repetitive elements (REs) such as MIR, FLAM-C and ALR/alpha are also found depending on the cell’s developmental origin. The analysis also shows that TFIIIC-enriched regions are involved in cell type-specific DNA looping, which does not depend on colocalization with the master architectural protein CTCF. This work extends previous knowledge on the role of TFIIIC as a bona fide genome organizer whose action participates in cell type-dependent 3D genome looping via binding to REs.

We have studied the ground-state properties of boron-related dia-and paramagnetic point defects in B-doped silica. Hartree-Fock and density functional theory calculations have been performed to determine the structure, charge, and spin distribution of the boron oxygen hole center ͑BOHC͒. The currently accepted model of the BOHC is that of a hole localized on a nonbonding 2p orbital of an O atom in a bridge position between a B and a Si atom, wB-O " uSiw. Our calculations do not support this model and show that the structure is not stable and spontaneously evolves into a planar trigonal diamagnetic boron center, ϾBu, and a nonbridging oxygen, wSi-O " . The results of this study suggest that the BOHC consists of a three-coordinated B atom bound to a non bridging oxygen, ϾBuO " . The computed hyperfine coupling constants for this model are in quantitative agreement with those measured experimentally for B-doped silica. This assignment is consistent with recent magnetic resonance studies on borosilicates and alkali borate glasses.