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

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

doi:10.1371/journal.pcbi.1002319

Abstract

Coregulator proteins (CoRegs) are part of multi-protein complexes that transiently assemble with transcription factors and chromatin modifiers to regulate gene expression. In this study we analyzed data from 3,290 immuno-precipitations (IP) followed by mass spectrometry (MS) applied to human cell lines aimed at identifying CoRegs complexes. Using the semi-quantitative spectral counts, we scored binary protein-protein and domain-domain associations with several equations. Unlike previous applications, our methods scored prey-prey protein-protein interactions regardless of the baits used. We also predicted domain-domain interactions underlying predicted protein-protein interactions. The quality of predicted protein-protein and domain-domain interactions was evaluated using known binary interactions from the literature, whereas one protein-protein interaction, between STRN and CTTNBP2NL, was validated experimentally; and one domain-domain interaction, between the HEAT domain of PPP2R1A and the Pkinase domain of STK25, was validated using molecular docking simulations. The scoring schemes presented here recovered known, and predicted many new, complexes, protein-protein, and domain-domain interactions. The networks that resulted from the predictions are provided as a web-based interactive application at http://maayanlab.net/HT-IP-MS-2-PPI-DDI/.

Highlights

Coregulator proteins (CoRegs) are members of multi-protein complexes transiently assembled for regulation of gene expression [1]
CoRegs complexes exist in many combinations that are determined by posttranslational modifications (PTMs) and presence of accessory proteins [6,7]
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

Summary

Introduction

CoRegs are members of multi-protein complexes transiently assembled for regulation of gene expression [1]. Of these complexes is affected by ligands that bind to nuclear receptors (NRs), such as steroids, retinoids, and glucocorticoids [2,3,4,5]. CoRegs complexes exist in many combinations that are determined by posttranslational modifications (PTMs) and presence of accessory proteins [6,7]. Many CoRegs complexes are considered master regulators of cell differentiation during embryonic and post-developmental stages [10,11], and evidence suggests that malfunction of these proteins can lead to the pathogenesis of endocrine-related cancers [3,12] and diabetes [13]. It is believed that development of better chemical modulators of CoRegs will lead to a ‘new generation’ of drugs with higher efficacy and selectivity [14,15]

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Conclusion