Figure 1.
Outline of D-MIST Method for Predicting Protein Interactions by Learned Binding Profiles
Identification of domain-binding profiles begins by extracting the short sequence motifs from structural complexes that contain the domain of interest.
(A) In this example, RhoGAP-interacting motifs are extracted from two structural complexes (PDB ID 1AM4, 1TX4) where RhoGAP is bound to small G proteins.
(B) Protein interactions containing the RhoGAP domain were collected from four databases to form the learning set for the Gibbs sampling to generate the binding profiles (shown here as sequence logos [57]). The sampling step is biased towards motifs that are similar to those found in the structural dataset.
(C) The resulting PSSMs are used to predict interactions for proteins with RhoGAP domains, such as the human ARHGAP1. A subset of the predicted interactions is subsequently tested by two experimental methods.
Figure 2.
Predicted Interactions Verified by IP-MS
Immunoaffinity purification of bait proteins complexes followed by mass spectrometry identification of associated proteins confirmed 37 predicted interactions. Predictions between proteins that were both co-purified with the tagged bait protein (i.e., both proteins were prey) were not considered validated. Proteins are coloured according to their Gene Ontology biological process annotation.
Figure 3.
Predicted Interactions Confirmed by Experiments or by Previously Published Results in the Primary Literature
Interactions are coloured according to their verification source. Dashed red lines are predictions that were confirmed by IP-MS but not confirmed by IP-western; dashed green lines are predictions that failed experimental validation by IP-western.