Fundamentals of protein interaction network mapping

Snider, Jamie; Kotlyar, Max; Saraon, Punit; Yao, Zhong; Jurišica, Igor; Štagljar, Igor

doi:10.15252/msb.20156351

Cited by 250 publications

(193 citation statements)

References 224 publications

(281 reference statements)

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“…This method would thereby generate a dataset that is complementary to those constructed using binary PPI mapping methods. However, AP-MS is limited in its ability to detect transient associations, low-abundance complexes, and interactions occurring in particular cell types [21]. In addition, PPAs identified by AP-MS indicate only co-complex associations.…”

Section: Affinity Purification and Mass Spectrometry (Ap-ms)mentioning

confidence: 99%

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

Cafarelli

Desbuleux

Wang

et al. 2017

Current Opinion in Structural Biology

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Section: Affinity Purification and Mass Spectrometry (Ap-ms)mentioning

confidence: 99%

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

Cafarelli

Desbuleux

Wang

et al. 2017

Current Opinion in Structural Biology

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“…In responses to different disturbances and circumstances, the physical binding of two or more proteins is referred as Protein-protein interaction (PPI) that provides considerable adaptability for biological cells to adapt to the changing environmental conditions. [5] Based on the PPIs, more systematic protein networks were established gradually, known as the protein-protein interaction network (PIN). Similar to most biological networks, PIN are scale-free and small-world properties.…”

Section: Introductionmentioning

confidence: 99%

Untitled

2017

RJLBPCS

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ABSTRACT:The Universal stress protein appears to belong to all stress and starvation stimulons under the inclusive regulation of gene expression. It has been suggested that Usp proteins have different physiological functions that reprogram the cell towards defense and escape during cellular stress. In this study Protein interaction network (PIN) analysis was used to predict its mechanism of molecular action. The PIN of Universal stress protein was constructed by Cytoscape and the function modules identified by gene ontology (GO) enrichment analysis based on molecular complex detection (MCODE). The PIN of Universal stress protein has scale-free, small world and modular properties.Based on analysis of these function modules, the mechanism of Universal stress protein is proposed.The protein-protein interactions information of Universal stress protein is connected to the protein secretion pathway, apoptosis, cell division, cell shape and gene regulation. These results will serve as a distinctive resource to present a physical map of protein profile of bacteria under stress condition, drug targeting and the development of novel therapeutics.

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“…We aimed to tackle this problem from the perspective of proteinprotein interaction (PPI). 2,3 However, the fact that RTKs are integral transmembrane proteins makes it extremely difficult to study RTK-phosphatase interactions in a systems fashion using traditional PPI methods, due to the special physical and chemical features of the membrane environment. To overcome this problem, we developed a unique Membrane Yeast Two-Hybrid (MYTH) system to study membrane protein PPIs (Fig.…”

mentioning

confidence: 99%

Multiple functions of protein phosphatases in receptor tyrosine kinase signaling revealed by interactome analysis

Yao

Štagljar

2017

Molecular & Cellular Oncology

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To obtain a global picture of how protein phosphatases are involved in receptor tyrosine kinase (RTK) signaling, we mapped the RTK-phosphatase interactome. Analyses of selected interactions revealed detailed mechanisms of their actions. This study provides new knowledge to better understand cancer development and to identify novel therapeutic targets. Receptor tyrosine kinases (RTKs) receive multiple extracellular signals, and process and transmit them into intracellular space. They operate through the activation of their tyrosine kinase domains upon ligand engagement, and the following tyrosine phosphorylation. These phosphorylated tyrosines recruit signaling molecules containing SRC homology 2 (SH2) or phosphotyrosine-binding (PTB) domains and relay the signal to downstream pathways. KEYWORDS1 Malfunction of RTKs is involved in several disorders. Self-sufficient activation derived from overexpression or mutation of RTKs or related regulated molecules is one of the driving causes of various types of cancer. In addition, mutations in RTKs also contribute to resistance to anti-cancer drugs.Protein tyrosine phosphatases (PTPs) are a group of enzymes that remove phosphate from tyrosine residues and thereby are the major means of terminating RTK signal and maintaining control of RTK signaling. An oversimplified model describes that PTPs function as signal erasers. However, accumulating data have demonstrated that PTPs behave in a complex manner; besides terminating signals, some PTPs actually potentiate RTK signaling, and some play controversial roles depending on different cellular and RTK context. In addition to tyrosine phosphorylation, serine/theronine phosphorylation also plays certain roles in fine-tuning RTK signaling, although most of these roles are unknown. Therefore, theoretically all protein phosphatases, including protein Ser/Thr phosphatases (PSPs), are involved in RTK signaling.To fully understand RTK function, it is necessary to comprehensively examine the RTK-phosphatase relationship. We aimed to tackle this problem from the perspective of proteinprotein interaction (PPI).2,3 However, the fact that RTKs are integral transmembrane proteins makes it extremely difficult to study RTK-phosphatase interactions in a systems fashion using traditional PPI methods, due to the special physical and chemical features of the membrane environment. To overcome this problem, we developed a unique Membrane Yeast Two-Hybrid (MYTH) system to study membrane protein PPIs (Fig. 1A), which utilizes split ubiquitin to sense PPIs. 4 It should be noted that the MYTH system detects PPIs in a yeast environment instead of in mammalian cells for mammalian PPIs, but MYTH is still a valuable system since it maximally eliminates the interference of endogenous mammalian interactors and regulators. Recently, we also developed a mammalian version of MYTH, the Mammalian Membrane Two-Hybrid (MaMTH) system, to complement the MYTH assay. 5 We performed a RTK-phosphatase interactome screen using MYTH and MaMTH assays. 6 The MYTH ass...

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Fundamentals of protein interaction network mapping

Cited by 250 publications

References 224 publications

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

Untitled

Multiple functions of protein phosphatases in receptor tyrosine kinase signaling revealed by interactome analysis

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