Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes

Amin R. Mazloom, Ruth Dannenfelser, Neil R. Clark, Arsen V. Grigoryan, Kathryn M. Linder, Timothy Cardozo, Julia C. Bond, Aislyn D. W. Boran, Ravi Iyengar, Anna Malovannaya, Rainer B. Lanz, Avi Ma'ayan

Abstract: Author Summary In response to various extracellular stimuli, protein complexes are transiently assembled within the nucleus of cells to regulate gene transcription in a context dependent manner. Here we analyzed data from 3,290 proteomics experiments that used as bait different member proteins from regulatory complexes with different antibodies. Such proteomics experiments attempt to characterize complex membership for other proteins that associate with bait proteins. However, the experiments are noisy and aggregation of the data from many pull-down experiments is computationally challenging. To this end we developed and evaluated several equations that score pair-wise interactions based on co-occurrence in different but related pull-down experiments. We compared and evaluated the scoring methods and combined them to recover known, and discover new, complexes and protein-protein interactions. We also applied the same equations to predict domain-domain interactions that might underlie the protein interactions and complex formation. As a proof of concept, we experimentally validated one predicted protein-protein interaction and one predicted domain-domain interaction using different methods. Such rich information about binary interactions between proteins and domains should advance our knowledge of transcriptional regulation by CoRegs in normal and diseased human cells.