The SH2 Domain Interaction Landscape

Tinti, Michele; Kiemer, Lars; Costa, Stefano; Miller, Martin L.; Sacco, Francesca; Olsen, Jesper V.; Carducci, Martina; Paoluzi, Serena; Langone, Francesca; Workman, Christopher; Blom, Nikolaj; Machida, Kazuya; Thompson, Christopher; Schutkowski, Mike; Brunak, Søren; Mann, Matthias; Mayer, Bruce J.; Castagnoli, Luisa; Cesareni, Gianni

doi:10.1016/j.celrep.2013.03.001

Cited by 113 publications

(136 citation statements)

References 47 publications

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“…The Src Homology 2 (SH2) domain phosphotyrosine interactome is a system of prominent physiological importance that has been the subject of multiple preceding interaction mapping and platform development efforts (17,19,31,32,37,38). Tyrosine phosphorylation and its recognition by SH2 domains is a uniquely metazoan adaptation (39), prominently involved in the transduction of growth signals (1,2,40).…”

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confidence: 99%

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The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Engelmann

Kim

Wang

et al. 2014

Molecular & Cellular Proteomics

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Protein interaction domain (PID) linear peptide motif interactions direct diverse cellular processes in a specific and coordinated fashion. PID specificity, or the interaction selectivity derived from affinity preferences between possible PID-peptide pairs is the basis of this ability. Here, we develop an integrated experimental and computational cellulose peptide conjugate microarray (CPCMA) based approach for the high throughput analysis of PID specificity that provides unprecedented quantitative resolution and reproducibility. As a test system, we quantify the specificity preferences of four Src Homology 2 domains and 124 physiological phosphopeptides to produce a novel quantitative interactome. The quantitative data set covers a broad affinity range, is highly precise, and agrees well with orthogonal biophysical validation, in vivo interactions, and peptide library trained algorithm predictions. In contrast to preceding approaches, the CPCMAs proved capable of confidently assigning interactions into affinity categories, resolving the subtle affinity contributions of residue correlations, and yielded predictive peptide motif affinity matrices. Unique CPCMA enabled modes of systems level analysis reveal a physiological interactome with expected node degree value decreasing as a function of affinity, resulting in minimal high affinity binding overlap between domains; uncover that Src Homology 2 domains bind ligands with a similar average affinity yet strikingly different levels of promiscuity and binding dynamic range; and parse with unprecedented quantitative resolution contextual factors directing specificity. The CPCMA platform promises broad application within the fields of PID specificity, synthetic biology, specificity focused drug design, and network biology. Molecular & Cellular Proteomics 13: 10.1074/mcp.O114.038695, 3647-3662, 2014. Protein interaction domains (PIDs)1 often compete for the same linear motif binding sites across a range of affinities, resulting in many potential interactions that may enable the rapid assembly and disassembly of signaling proteins in response to external and internal cues (1, 2). PID-peptide interactions have small binding interfaces, resulting in moderate affinity interactions mediated primarily by a few amino acid "hot-spots" within motifs specific for a particular PID family (3-5). The power of individual residues to direct interactions, the absence of structural constraint for linear motifs, and the modularity of PIDs has enabled the rapid evolution of these networks resulting in many large multimember PID families in higher eukaryotes (6 -9). For these large families dedicated to the recognition of similar ligands, PID specificity-or the interaction selectivity derived from affinity preferences between possible PID-peptide pairs-underpins the effective conveyance of specific cell signals. High throughput interaction mapping efforts are used to decipher how this PID "specificity space" is populated, thereby providing insight into protein function and the principles ...

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confidence: 99%

“…Peptide arrays (16,17), degenerate libraries (18,19), and phage display (20) are the most frequently applied high throughput approaches for investigating PID specificity. Phage display and degenerate library approaches sample a large ligand space and can produce consensus selectivity motifs that represent the most preferred residues at every position panned.…”

mentioning

confidence: 99%

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Engelmann

Kim

Wang

et al. 2014

Molecular & Cellular Proteomics

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“…In the context of a neuronal network prediction framework these data provided a wealth of new potential conditional interactions [52]. Furthermore, remarkable interaction specificity was seen in SILAC based quantitative pull-downs that captured cellular binding partners with methylated histone-derived peptides [54,55].…”

Section: Conditional/ptma-dependent Protein Interactionsmentioning

confidence: 99%

“…Recently, Src homology 2 domains (SH2), known to bind phospho-tyrosine residues, were tested for interactions on peptide arrays containing phospho-peptides that resemble known in vivo phospho-sites [52,53].…”

Section: Conditional/ptma-dependent Protein Interactionsmentioning

confidence: 99%

Studying post-translational modifications with protein interaction networks

Woodsmith

Stelzl

2014

Current Opinion in Structural Biology

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At least 46 interactome studies, broad at proteome scale or biologically more focused, have together mapped about 75,000 human protein-protein interactions (PPIs). Many of the studies addressed local interactome data paucity analyzing specific homeostatic and regulatory systems, with recent focus demonstrating the involvement of post-translational protein modification (PTM) enzyme families in a wide range of cellular functions. These datasets provided insight into binding mechanisms, the dynamic modularity of complexes or delineated combinatorial enzymatic cascades. Furthermore, the combined study of PPI and PTM dynamics has begun to reveal conditional rewiring of molecular networks through PTMmediated recognition events. Taken together these studies highlight the utility of local and global interaction networks to functionally prioritize the many changing PTMs mapped in human cells.

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“…Parallel chemical synthesis approaches (e.g. SPOT arrays) allow testing of peptides including PTMs, but cannot provide quantitative information about affinities, require large amounts of purified protein, and lack in-line quality controls to ensure that the correct peptides were synthesized at each spot 15 .…”

Section: Introductionmentioning

confidence: 99%

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

Nguyen

Roy

Harink

et al. 2018

Preprint

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Weak, transient binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drive cellular signaling. Mapping the energy landscape of such interactions is essential for deciphering signaling networks and developing therapeutic inhibitors, but is complicated by technical challenges associated with quantitatively measuring weak interactions in high-throughput. Here, we synthesize peptide libraries on spectrally encoded beads with each peptide sequence uniquely linked to a spectral code (MRBLE-pep), allowing high-throughput quantification of protein-peptide binding via imaging. Using computational modeling and MRBLEpep assays, we map the affinity landscape for human calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, interacting with a known SLiM (PxIxIT). We find that PxIxIT recognition depends critically on flanking residues and is regulated by post-translational modifications. Using this information, we designed PxIxIT peptides with unprecedented affinity and therapeutic potential that strongly inhibit CN function in vivo.

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The SH2 Domain Interaction Landscape

Cited by 113 publications

References 47 publications

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

The Development and Application of a Quantitative Peptide Microarray Based Approach to Protein Interaction Domain Specificity Space

Studying post-translational modifications with protein interaction networks

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

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