A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome

Yao, Zhong; Darowski, Katelyn Dawn; St‐Denis, Nicole; Wong, Victoria; Offensperger, Fabian; Villedieu, Annabel; Amin, Shahreen; Malty, Ramy H.; Aoki, Hiroyuki; Guo, Hongbo; Xu, Yang; Iorio, Caterina; Kotlyar, Max; Emili, Andrew; Jurišica, Igor; Neel, Benjamin G.; Babu, Mohan; Gingras, Anne‐Claude; Štagljar, Igor

doi:10.1016/j.molcel.2016.12.004

Cited by 127 publications

(107 citation statements)

References 53 publications

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“…This approach is bolstered by the fact that surveys of protein-protein interactions have revealed many interactions that, when disrupted, are deleterious. [39][40][41][42][43][44] Moreover, protein interactions can reveal defects in protein folding and stability, which helps to explain why approximately one-third of disease-related variants in proteins with multiple interaction partners disrupt all of the interactions of that protein. 45 Variants of protein-coding genes can also result in pathogenicity by altering splicing.…”

Section: Annotating Every Possible Variant In Disease-related Functiomentioning

confidence: 99%

Variant Interpretation: Functional Assays to the Rescue

Starita

Ahituv

Dunham

et al. 2017

The American Journal of Human Genetics

316

294

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Classical genetic approaches for interpreting variants, such as case-control or co-segregation studies, require finding many individuals with each variant. Because the overwhelming majority of variants are present in only a few living humans, this strategy has clear limits. Fully realizing the clinical potential of genetics requires that we accurately infer pathogenicity even for rare or private variation. Many computational approaches to predicting variant effects have been developed, but they can identify only a small fraction of pathogenic variants with the high confidence that is required in the clinic. Experimentally measuring a variant's functional consequences can provide clearer guidance, but individual assays performed only after the discovery of the variant are both time and resource intensive. Here, we discuss how multiplex assays of variant effect (MAVEs) can be used to measure the functional consequences of all possible variants in disease-relevant loci for a variety of molecular and cellular phenotypes. The resulting large-scale functional data can be combined with machine learning and clinical knowledge for the development of ''lookup tables'' of accurate pathogenicity predictions. A coordinated effort to produce, analyze, and disseminate large-scale functional data generated by multiplex assays could be essential to addressing the variant-interpretation crisis.

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Section: Annotating Every Possible Variant In Disease-related Functiomentioning

confidence: 99%

Variant Interpretation: Functional Assays to the Rescue

Starita

Ahituv

Dunham

et al. 2017

The American Journal of Human Genetics

316

294

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“…The study of PTPs has long suffered from a paucity of tools for probing and measuring their intracellular activities 46 . In this study, we developed a photoswitchable variant of PTP1B and used it to exert spatiotemporal control over the phosphorylation state of a genetically encoded biosensor in living cells.…”

Section: Discussionmentioning

confidence: 99%

Minimally disruptive optical control of protein tyrosine phosphatase 1B

Hongdusit

Zwart²,

Sankaran³

et al. 2019

Preprint

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Protein tyrosine phosphatases regulate a myriad of essential subcellular signaling events, yet they remain difficult to study in their native biophysical context. Here we develop a minimally disruptive optical approach to toggle the activity of protein tyrosine phosphatase 1B (PTP1B)-an important regulator of receptor tyrosine kinases and a therapeutic target for the treatment of diabetes, obesity, and cancer-and we use that approach to probe both the structure and intracellular function of this enzyme. Our conservative architecture for photocontrol, which consists of a protein-based light switch fused to an allosteric regulatory element, preserves the native structure, activity, and subcellular localization of PTP1B, affords changes in activity that match those elicited by post-translational modifications inside the cell, and permits experimental analyses of the molecular basis of optical modulation. This work provides a framework for using optogenetic systems to examine both the biophysical basis and spatial context of cell signaling. 3 The enzymatic phosphorylation of tyrosine residues is centrally important to cellular function. It controls the location and timing of cellular differentiation, movement, proliferation, and death 1-4 ; its misregulation can cause cancer, diabetes, and neurodegenerative diseases, among other disorders 5-7 . Methods to toggle the activity of phosphorylation-regulating enzymes without interfering with their native structure or cellular organization could, thus, enable detailed analyses of the mechanisms by which cells process essential chemical signals 8,9 .Optogenetic actuators-genetically encoded proteins that undergo light-induced changes in conformation-provide a powerful means of controlling enzyme activity over time and space.As protein fusion partners, they have enabled optical manipulation of biomolecular transport, binding, and catalysis with millisecond and submicron resolution 10,11 . Common strategies to integrate optogenetic actuators into enzymes include (i) attachment near an active site, where they control substrate access 12,13 , (ii) insertion within a catalytic domain, where they afford activity-modulating structural distortions 14 , and (iii) fusion to N-or C-termini, where they direct subcellular localization 15 or guide domain assembly 16 . These approaches have generated powerful tools for stimulating phosphorylation-mediated signaling networks; their reliance on disruptive structural modifications, however, has precluded their use in both (i) biophysical analyses of native intra-domain control systems (allosteric networks) and (ii) biochemical studies of native regulatory effects-that is, changes in activity that match, rather than artificially exceed, those caused by post-translational modifications of an enzyme under study.Protein tyrosine phosphatase 1B (PTP1B) is an important regulatory enzyme for which minimally disruptive architectures for photocontrol could prove particularly informative. This enzyme catalyzes the hydrolytic dephosphorylation of tyros...

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“…docking motifs or different subunit combinations) provides substantial specificity. 158 There has been some success in examining phosphatase interaction partners with a mammalian two-hybrid system 159 or cross-linking mass spectrometry, 160 but because these studies indicate what proteins simply associate with phosphatase complexes, additional work is needed to verify their identities as substrates. Another strategy involves mutation of the phosphatase catalytic domain so that it binds tightly to potential substrates.…”

Section: Kinase-substrate Mappingmentioning

confidence: 99%

Recent advances in phosphoproteomics and application to neurological diseases

Arrington

Hsu

Elder

et al. 2017

Analyst

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Phosphorylation has an incredible impact on the biological behavior of proteins, altering everything from intrinsic activity to cellular localization and complex formation. It is no surprise then that this post-translational modification has been the subject of intense study and that, with the advent of faster, more accurate instrumentation, the number of large-scale mass spectrometry-based phosphoproteomic studies has swelled over the past decade. Recent developments in sample preparation, phosphorylation enrichment, quantification, and data analysis strategies permit both targeted and ultra-deep phosphoproteome profiling, but challenges remain in pinpointing biologically relevant phosphorylation events. We describe here technological advances that have facilitated phosphoproteomic analysis of cells, tissues, and biofluids and note applications to neuropathologies in which the phosphorylation machinery may be dysregulated, much as it is in cancer.

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A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome

Cited by 127 publications

References 53 publications

Variant Interpretation: Functional Assays to the Rescue

Variant Interpretation: Functional Assays to the Rescue

Minimally disruptive optical control of protein tyrosine phosphatase 1B

Recent advances in phosphoproteomics and application to neurological diseases

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