Isolated auto-citrullinated regions of PADI4 associate to the intact protein without altering their disordered conformation

• Published in: Biophysical chemistry 2024-09, Vol.312, p.107288, Article 107288
• Main Authors: Neira, José L., Rizzuti, Bruno, Abian, Olga, Velazquez-Campoy, Adrian
• Format: Article
• Language: English
• Subjects: Citrullination; Disordered peptides; Fluorescence; Isothermal titration calorimetry; Kinetics; Molecular docking
• ISSN: 0301-4622; 1873-4200; 1873-4200
• DOI: 10.1016/j.bpc.2024.107288

PADI4 is one of the human isoforms of a group of enzymes intervening in the conversion of arginine to citrulline. It is involved in the development of several types of tumors, as well as other immunological illnesses, such as psoriasis, multiple sclerosis, or rheumatoid arthritis. PADI4 auto-citrullinates in several regions of its sequence, namely in correspondence of residues Arg205, Arg212, Arg218, and Arg383. We wanted to study whether the citrullinated moiety affects the conformation of nearby regions and its binding to intact PADI4. We designed two series of synthetic peptides comprising either the wild-type or the relative citrullinated versions of such regions – i.e., a first series of peptides comprising the first three arginines, and a second series comprising Arg383. We studied their conformational properties in isolation by using fluorescence, far-ultraviolet (UV) circular dichroism (CD), and 2D1H NMR. Furthermore, we characterized the binding of the wild-type and citrullinated peptides in the two series to the intact PADI4, by using isothermal titration calorimetry (ITC), fluorescence, and biolayer interferometry (BLI), as well as by molecular docking simulations. We observed that citrullination did not alter the local conformational propensities of the isolated peptides. Nevertheless, for all the peptides in the two series, citrullination slowed down the kinetic koff rates of the binding reaction to PADI4, probably due to differences in electrostatic effects compared to the presence of arginine. The affinities of PADI4 for unmodified peptides were slightly larger than those of the corresponding citrullinated ones in the two series, but they were all within the same range, indicating that there were no relevant variations in the thermodynamics of binding due to sequence effects. These results highlight details of the self-citrullination of PADI4 and, more generally, of possible auto-catalytic mechanisms taking place in vivo for other citrullinating enzymes or, alternatively, in proteins undergoing citrullination passively. [Display omitted] •Citrullinated regions of PADI4 have the same conformation as wild-type counterparts.•Citrullinated regions bind to PADI4 with different kinetic rates than wild-type.•Citrullinated and wild-type regions bind to PADI4 with nearly the same affinity.