Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may compete for binding to a common SLiM and vice versa. To investigate the effects of competition on RTK signaling, we used a rule-based modeling approach to develop and analyze models for ligand-induced recruitment of SH2/PTB domain-containing proteins to autophosphorylation sites in the insulin-like growth factor 1 (IGF1) receptor (IGF1R). Models were parameterized using published datasets reporting protein copy numbers and site-specific binding affinities. Simulations were facilitated by a novel application of model restructuration, to reduce redundancy in rule-derived equations. We compare predictions obtained via numerical simulation of the model to those obtained through simple prediction methods, such as through an analytical approximation, or ranking by copy number and/or KD value, and find that the simple methods are unable to recapitulate the predictions of numerical simulations. We created 45 cell line-specific models that demonstrate how early events in IGF1R signaling depend on the protein abundance profile of a cell. Simulations, facilitated by model restructuration, identified pairs of IGF1R binding partners that are recruited in anti-correlated and correlated fashions, despite no inclusion of cooperativity in our models. This work shows that the outcome of competition depends on the physicochemical parameters that characterize pairwise interactions, as well as network properties, including network connectivity and the relative abundances of competitors.Author summary: Cells rely on networks of interacting biomolecules to sense and respond to environmental perturbations and signals. However, it is unclear how information is processed to generate appropriate and specific responses to signals, especially given that these networks tend to share many components. For example, receptors that detect distinct ligands and regulate distinct cellular activities commonly interact with overlapping sets of downstream signaling proteins. Here, to investigate the downstream signaling of a well-studied receptor tyrosine kinase (RTK), the insulin-like growth factor 1 (IGF1) receptor (IGF1R), we formulated and analyzed 45 cell line-specific mathematical models, which account for recruitment of 18 different binding partners to six sites of receptor autophosphorylation in IGF1R. The models were parameterized using available protein copy number and site-specific affinity measurements, and restructured to allow for network generation. We find that recruitment is influenced by the protein abundance profile of a cell, with different patterns of recruitment in different cell lines. Furthermore, in a given cell line, we find that pairs of IGF1R binding partners may be recruited in a correlated or anti-correlated fashion. We demonstrate that the simulations of the model have greater predictive power than protein copy number and/or binding affinity data, and that even a simple analytical model cannot reproduce the predicted recruitment ranking obtained via simulations. These findings represent testable predictions and indicate that the outputs of IGF1R signaling depend on cell line-specific properties in addition to the properties that are intrinsic to the biomolecules involved.