Modeling of RAS complexes supports roles in cancer for less studied partners

H Billur Engin,Dexter Pratt,Daniel Carlin,Hannah Carter

doi:10.1186/s13628-017-0037-6

H Billur Engin, Dexter Pratt + Show 2 more

Open Access

https://doi.org/10.1186/s13628-017-0037-6

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Abstract

BackgroundRAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, however it is not clear whether these proteins also interact with RAS via the switch regions.ResultsTo address this question we constructed a RAS isoform-specific protein-protein interaction network and predicted 3D complexes involving RAS isoforms and interaction partners to identify the most probable interaction interfaces. The resulting models correctly captured the binding interfaces for well-studied effectors, and additionally implicated residues in the allosteric and hyper-variable regions of RAS proteins as the predominant binding site for non-canonical effectors. Several partners binding to this new interface (SRC, LGALS1, RABGEF1, CALM and RARRES3) have been implicated as important regulators of oncogenic RAS signaling. We further used these models to investigate competitive binding and multi-protein complexes compatible with RAS surface occupancy and the putative effects of somatic mutations on RAS protein interactions.ConclusionsWe discuss our findings in the context of RAS localization to the plasma membrane versus within the cytoplasm and provide a list of RAS protein interactions with possible cancer-related consequences, which could help guide future therapeutic strategies to target RAS proteins.

Highlights

RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways
All RAS isoforms transition between active and inactive states, a process that is regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs)
We used the 20 models of RAS interactions to determine which amino acids on the surface of RAS participate in each interaction. This resulted in a map of interface residues on RAS proteins (Fig. 3) enabling us to analyze patterns of interface residue usage across interaction partners (Fig. 4). This map revealed two categories of RAS interaction partners: proteins that bind via the switch regions, and proteins that bind via the allosteric region and/or the HVR

Summary

Introduction

RAS protein interactions have predominantly been studied in the context of the RAF and PI3kinase oncogenic pathways. Structural modeling and X-ray crystallography have demonstrated that RAS isoforms bind to canonical downstream effector proteins in these pathways using the highly conserved switch I and II regions. Other non-canonical RAS protein interactions have been experimentally identified, it is not clear whether these proteins interact with RAS via the switch regions. Tumor exome sequencing studies have uncovered RAS mutations in over 30% of solid tumors, yet to date no therapy has been discovered to effectively treat RAS driven cancers. RAS proteins themselves provide an attractive therapeutic target but efforts aimed at drugging RAS directly far have failed [1]. More complete characterization of RAS signaling may provide badly needed insights to support renewed efforts aimed at developing RAS-targeted therapies [1, 2]. The first 87 residues are 100% homologous and most of the sequence differences occur in the short C-terminal hypervariable region

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