Exploring DIX-DIX Homo- and Hetero-Oligomers in Wnt Signaling with AlphaFold2

Cells. 2024 Oct 3;13(19):1646. doi: 10.3390/cells13191646.

Abstract

Wnt signaling is involved in embryo development and cancer. The binding between the DIX domains of Axin1/2, Dishevelled1/2/3, and Coiled-coil-DIX1 is essential for Wnt/β-catenin signaling. Structural and biological studies have revealed that DIX domains are polymerized through head-to-tail interface interactions, which are indispensable for activating β-catenin Wnt signaling. Although different isoforms of Dvl and Axin proteins display both redundant and specific functions in Wnt signaling, the specificity of DIX-mediated interactions remains unclear due to technical challenges. Using AlphaFold2(AF2), we predict the structures of 6 homodimers and 22 heterodimers of DIX domains without templates and compare them with the reported X-ray complex structures. PRODIGY is used to calculate the binding affinities of these DIX complexes. Our results show that the Axin2 DIX homodimer has a stronger binding affinity than the Axin1 DIX homodimer. Among Dishevelled (Dvl) proteins, the binding affinity of the Dvl1 DIX homodimer is stronger than that of Dvl2 and Dvl3. The Coiled-coil-DIX1(Ccd1) DIX homodimer shows weaker binding than the Axin1 DIX homodimer. Generally, heterodimer interactions tend to be stronger than those of homodimers. Our findings provide insights into the mechanism of the Wnt signaling pathway and highlight the potential of AF2 and PRODIGY for studying protein-protein interactions in signaling pathways.

Keywords: AlphaFold2; DIX; PRODIGY; Wnt signaling; binding affinity.

MeSH terms

  • Amino Acid Sequence
  • Axin Protein* / metabolism
  • Dishevelled Proteins* / metabolism
  • Humans
  • Models, Molecular
  • Protein Binding*
  • Protein Domains
  • Protein Multimerization*
  • Wnt Signaling Pathway*

Substances

  • Axin Protein
  • Dishevelled Proteins

Grants and funding

This work was supported by a National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (RS-2023-00278134). HJS Fan would like to acknowledge the partial financial support from the Science Foundation of Sichuan University of Science & Engineering (2020RC06) and the Natural Science Foundation of Sichuan Province (SYZ202133 and 2022JDGD0041).