Unveiling the Binding between the Armadillo-Repeat Domain of Plakophilin 1 and the Intrinsically Disordered Transcriptional Repressor RYBP.

Plakophilin 1 (PKP1), a member of the p120ctn subfamily of the armadillo (ARM)-repeat-containing proteins, is an important structural component of cell-cell adhesion scaffolds although it can also be ubiquitously found in the cytoplasm and the nucleus. RYBP (RING 1A and YY1 binding protein) is a multifunctional intrinsically disordered protein (IDP) best described as a transcriptional regulator. Both proteins are involved in the development and metastasis of several types of tumors. We studied the binding of the armadillo domain of PKP1 (ARM-PKP1) with RYBP by using in cellulo methods, namely immunofluorescence (IF) and proximity ligation assay (PLA), and in vitro biophysical techniques, namely fluorescence, far-ultraviolet (far-UV) circular dichroism (CD), and isothermal titration calorimetry (ITC). We also characterized the binding of the two proteins by using in silico experiments. Our results showed that there was binding in tumor and non-tumoral cell lines. Binding in vitro between the two proteins was also monitored and found to occur with a dissociation constant in the low micromolar range (~10 µM). Finally, in silico experiments provided additional information on the possible structure of the binding complex, especially on the binding ARM-PKP1 hot-spot. Our findings suggest that RYBP might be a rescuer of the high expression of PKP1 in tumors, where it could decrease the epithelial-mesenchymal transition in some cancer cells.

The intrinsically disordered, epigenetic factor RYBP binds to the citrullinating enzyme PADI4 in cancer cells.

RYBP (Ring1 and YY 1 binding protein) is a multifunctional, intrinsically disordered protein (IDP), best described as a transcriptional regulator. It exhibits a ubiquitin-binding functionality, binds to other transcription factors, and has a key role during embryonic development. RYBP, which folds upon binding to DNA, has a Zn-finger domain at its N-terminal region. By contrast, PADI4 is a well-folded protein and it is one the human isoforms of a family of enzymes implicated in the conversion of arginine to citrulline. As both proteins intervene in signaling pathways related to cancer development and are found in the same localizations within the cell, we hypothesized they may interact. We observed their association in the nucleus and cytosol in several cancer cell lines, by using immunofluorescence (IF) and proximity ligation assays (PLAs). Binding also occurred in vitro, as measured by isothermal titration calorimetry (ITC) and fluorescence, with a low micromolar affinity (~1 µM). AlphaFold2-multimer (AF2) results indicate that PADI4's catalytic domain interacts with the Arg53 of RYBP docking into its active site. As RYBP sensitizes cells to PARP (Poly (ADP-ribose) polymerase) inhibitors, we applied them in combination with an enzymatic inhibitor of PADI4 observing a change in cell proliferation, and the hampering of the interaction of both proteins. This study unveils for the first time the possible citrullination of an IDP, and suggests that this new interaction, whether it involves or not citrullination of RYBP, might have implications in cancer development and progression.

Novel bifunctional epoxy/thiol-reactive support to immobilize thiol containing proteins by the epoxy chemistry.

In this manuscript, we present a new bifunctional support containing epoxide and thiol-reactive groups for its use in protein immobilization. In a first step, the proteins are reversibly immobilized by reaction of its thiol groups with the thiol-reactive groups of the support under mild experimental conditions (pH 7.0, 24 degrees C). Then, the remaining epoxides of the support can form irreversible bonds with nucleophile surface groups of the already immobilized protein in a rapid way. The partial derivatization of EP-Sepabeads (a commercial matrix containing 120 micromol epoxy groups/g drained support) was optimized, using dithiotreitol (DTT) as thiolating agent. It was possible to achieve a partial thiolation of the support proportional to the concentration of DTT used (3, 8, and 15 micromol SH groups/g wet support). The remaining epoxide content after the thiolation treatment was high (e.g., nearly 70% for the highest thiolation degree). High immobilization yields were obtained for the three model enzymes selected (60% for Penicillin G acylase, 65% and 100% for K. lactis and E. coli beta-galactosidase, respectively). In all cases, no significant immobilization onto an unmodified epoxy support was found, thus demonstrating that the first step of attachment takes place through thiol-disulfide exchange reactions. In the case of the bifunctional support, progressive formation of enzyme-support attachments involving the epoxy groups was showed by the irreversible covalent attachment of the proteins on the support. The promotion of this multipoint covalent immobilization required long incubation periods at basic pH values.