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

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

“…The measured K d for the RYBP/ARM-PKP1 complex (~10 µM) is comparable to that observed for ARM-PKP1 in complexes with other proteins, including NUPR1 (~10 µM) [53], or well-folded proteins such as the SAM of p73 (~5 µM) [52] and PADI4 (1.4 µM) [54]. On the other hand, the value of K d is also similar to that measured in the interaction between RYBP and PADI4 (~10 µM) [33]. The strengths of the interactions with the different molecular partners of any of these two proteins were similar in all cases, indicating that despite a moderately favorable binding, the affinity might be enough to drive (or at least contribute to impact) a proper regulation in several pathways where ARM-PKP1 or RYBP intervene, determining a high specificity.…”

“…We have recently shown that PADI4 binds to ARM-PKP1 [54] and RYBP [33]. Furthermore, both proteins are implicated in the progression of several cancer types [18,38,46,73,74], and they can act as oncogenes or tumor suppressors.…”

“…Furthermore, it interacts with the sterile alpha motif (SAM) of p73 [52] and with NUPR1, an IDP intervening in the development of pancreatic cancer [53]. Since PKP1 and RYBP (i) are involved in the development of several types of cancers, (ii) can both be oncogenes and tumor suppressors, and (iii) mutually interact with the citrullinating enzyme PADI4 [33,54], we hypothesized that RYBP could also be capable of binding to ARM-PKP1. In this study, we provided evidence for the binding between ARM-PKP1 and RYBP by using in cellulo, in vitro, and in silico techniques.…”

“…It is considered that PLA resolves the binding of endogenous proteins as it can detect whether the two proteins are separated by less than 40 nm of distance [67]. This technology has been broadly used to visualize the intracellular binding of proteins in a precise manner by several groups including ours, and it is broadly accepted in the field [33,53,[68][69][70][71]. Proteins that interact directly will appear as red fluorescent spots, corresponding to the PLA signals.…”

“…The rest of the structure of the RYBP model is unfolded, including a polypeptide region rich in Lys and Arg residues and a C-terminal region with a high percentage of Ser and Thr residues. Like other IDPs, the RYBP model does lack a unique stable tertiary conformation, resulting in a high structural flexibility and paving the way to interact with several macromolecules [29][30][31][32] as described above, including also citrullinating enzymes [33].…”