Poster Presentation The 43rd Lorne Conference on Protein Structure and Function 2018

Deciphering the combinatorial complexity of Wnt-Frizzled interactions (#155)

Mark Agostino 1 , Sebastian O-G Pohl 1 , Arun Dharmarajan 1
  1. Curtin University, Perth, WA, Australia

Wnt signalling pathways are of great interest in embryonic development and as targets for cancer treatment. The first step of all Wnt pathways involves Wnt protein binding to the extracellular cysteine-rich domain (CRD) of a Frizzled (Fzd) receptor. There are 19 Wnts and 10 Fzds known in humans, hampering systematic experimental investigation. Additionally, Wnt proteins are lipidated, which directly facilitates their binding to Fzd. These issues have delayed a comprehensive understanding of Wnt signaling pathways using either experimental or computational approaches, and hence, have limited opportunities for rational drug design targeting these pathways.

In this study, we have developed a computational method for predicting Wnt-Fzd binding affinities. Homology models of the entire set of human and mouse Wnt-Fzd interactions were built based on the crystal structure of a representative Wnt-Fzd interaction. A model for predicting Wnt-Fzd binding affinities was developed and validated using affinities determined by biolayer interferometry for a small set of mouse interactions; the derived model is capable of considering both protein-protein and lipid-protein contributions to the binding affinity, and is estimated to predict accurate binding affinities for 75-80% of complexes, with an error range similar to experiment. The model was used to predict the binding affinities of all mouse and human Wnt-Fzd CRD interactions, revealing trends in the binding promiscuity of specific Wnts and Fzds. We have also applied the model to investigate Wnt interactions with the five secreted Frizzled-related proteins (sFRPs); these endogenous Wnt signalling antagonists feature a Frizzled-type CRD that most likely interacts directly with Wnt to prevent its interaction with Frizzled.

The comprehensive predictions made here provide the basis for laboratory-based studies of previously unexplored Wnt-Fzd and Wnt-sFRP interactions, which may reveal further Wnt signalling pathways. Furthermore, the generated model may be valuable for the discovery of Wnt signaling antagonists as potential cancer treatments.

  1. Agostino M, Pohl SO-G, Dharmarajan A. (2017) Structure-based prediction of Wnt binding affinities for Frizzled-type cysteine-rich domains. J Biol Chem, v292, p11218-11229.