Citrullination in proteins of the polycomb repressor complex 1

Area of Science:

• Biochemistry
• Molecular Biology
• Epigenetics

Background:

• Polycomb repressive complexes regulate gene expression via chromatin modification.
• Ring finger protein 1 (RING1) and RING1A and YY1 binding protein (RYBP) are key components of these complexes.
• Peptidyl arginine iminohydrolases (PADIs) are enzymes that modify arginine residues.

Purpose of the Study:

• To investigate the in vitro and in silico binding of PADI4 to specific peptides from RING1B and RYBP.
• To determine the effect of arginine citrullination on the binding affinity between PADI4 and these peptides.

Main Methods:

• Far-UV circular dichroism (CD) and Nuclear Magnetic Resonance (NMR) spectroscopy to assess peptide structure.
• Fluorescence spectroscopy, biolayer interferometry (BLI), and isothermal titration calorimetry (ITC) to measure binding affinities.
• Molecular docking simulations to analyze peptide-enzyme interactions.

Main Results:

• Isolated peptides from RING1B and RYBP, in both wild-type and citrullinated forms, were found to be monomeric and disordered.
• PADI4 exhibited low micromolar binding affinities (Kd ~10-20 μM) for these peptides.
• Binding affinity was reduced for the citrullinated peptide variants compared to their wild-type counterparts.
• Molecular docking confirmed that both peptide forms target PADI4's active site.

Conclusions:

• The study demonstrates that PADI4 can bind to isolated peptides of RING1B and RYBP.
• Arginine citrullination by PADI4 decreases the binding affinity of these peptides to the enzyme.
• These findings provide insights into the molecular mechanisms of PADI4-mediated regulation of Polycomb complex components.