A cyclic peptide toolkit reveals mechanistic principles of peptidylarginine deiminase IV regulation

  • Nat Commun. 2024 Nov 11;15(1):9746. doi: 10.1038/s41467-024-53554-1.
M Teresa Bertran  #  1 ,  Robert Walmsley  #  2 ,  Thomas Cummings  2  3 ,  Iker Valle Aramburu  4 ,  Donald J Benton  5 ,  Rocio Mora Molina  2 ,  Jayalini Assalaarachchi  2 ,  Maria Chasampalioti  2 ,  Tessa Swanton  4 ,  Dhira Joshi  6 ,  Stefania Federico  6 ,  Hanneke Okkenhaug  7 ,  Lu Yu  8 ,  David Oxley  8 ,  Simon Walker  7 ,  Venizelos Papayannopoulos  4 ,  Hiroaki Suga  9 ,  Maria A Christophorou  10  11 ,  Louise J Walport  12  13  14
Affiliations
  • 1. Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
  • 2. Epigenetics, The Babraham Institute, Cambridge, CB22 3AT, UK.
  • 3. MRC Human Genetics Unit, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
  • 4. Antimicrobial Defense Laboratory, The Francis Crick Institute, London, NW1 1AT, UK.
  • 5. Structural Biology, The Francis Crick Institute, London, NW1 1AT, UK.
  • 6. Chemical Biology, The Francis Crick Institute, London, NW1 1AT, UK.
  • 7. Imaging, The Babraham Institute, Cambridge, CB22 3AT, UK.
  • 8. Proteomics, The Babraham Institute, Cambridge, CB22 3AT, UK.
  • 9. The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
  • 10. Epigenetics, The Babraham Institute, Cambridge, CB22 3AT, UK. [email protected].
  • 11. MRC Human Genetics Unit, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK. [email protected].
  • 12. Protein-Protein Interaction Laboratory, The Francis Crick Institute, London, NW1 1AT, UK. [email protected].
  • 13. The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. [email protected].
  • 14. Imperial College London, Department of Chemistry, London, W12 0BZ, UK. [email protected].
  • # Contributed equally.
PMID: 39528459 DOI: 10.1038/s41467-024-53554-1
Abstract

Peptidylarginine deiminase IV (PADI4, PAD4) deregulation promotes the development of autoimmunity, Cancer, atherosclerosis and age-related tissue fibrosis. PADI4 additionally mediates immune responses and cellular reprogramming, although the full extent of its physiological roles is unexplored. Despite detailed molecular knowledge of PADI4 activation in vitro, we lack understanding of its regulation within cells, largely due to a lack of appropriate systems and tools. Here, we develop and apply a set of potent and selective PADI4 modulators. Using the mRNA-display-based RaPID system, we screen >1012 cyclic peptides for high-affinity, conformation-selective Binders. We report PADI4_3, a cell-active inhibitor specific for the active conformation of PADI4; PADI4_7, an inert binder, which we functionalise for the isolation and study of cellular PADI4; and PADI4_11, a cell-active PADI4 activator. Structural studies with PADI4_11 reveal an allosteric binding mode that may reflect the mechanism that promotes cellular PADI4 activation. This work contributes to our understanding of PADI4 regulation and provides a toolkit for the study and modulation of PADI4 across (patho)physiological contexts.

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