scholarly journals Time-gated detection of protein-protein interactions with transcriptional readout

2017 ◽  
Author(s):  
Min Woo Kim ◽  
Wenjing Wang ◽  
Mateo I. Sanchez ◽  
Robert Coukos ◽  
Mark Von Zastrow ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Time Window ◽  
High Specificity ◽  
Large Cell ◽  
Protein Protein Interactions ◽  
Signal Ratio ◽  
High Background ◽  
Tev Protease ◽  
Fast Light

AbstractTranscriptional assays such as yeast two hybrid, split ubiquitin, and Tango that convert transient protein-protein interactions (PPIs) in cells into stable expression of transgenes are powerful tools for PPI discovery, high-throughput screens, and analysis of large cell populations. However, these assays frequently suffer from high background and they lose all information about PPI dynamics. To address these limitations, we developed a light-gated transcriptional assay for PPI detection called PPI-FLARE (PPI-Fast Light- and Activity-Regulated Expression). PPI-FLARE requires both a PPI to deliver TEV protease proximal to its cleavage peptide, and externally-applied blue light to uncage the cleavage peptide, in order to release a membrane-tethered transcription factor (TF) for translocation to the nucleus. We used PPI-FLARE to detect the ligand-induced association of 12 different PPIs in living mammalian cells, with a temporal resolution of 5 minutes and a ±ligand signal ratio up to 37. By systematically shifting the light irradiation window, we could reconstruct PPI time-courses, distinguishing between GPCRs that engage in transient versus sustained interactions with the cytosolic effector arrestin. When combined with FACS, PPI-FLARE enabled >100-fold enrichment of cells experiencing a specific GPCR-arrestin PPI during a short 10-minute light window over cells missing that PPI during the same time window. Due to its high specificity, sensitivity, and generality, PPI-FLARE should be a broadly useful tool for PPI analysis and discovery.

scholarly journals Time-gated detection of protein-protein interactions with transcriptional readout

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Min Woo Kim ◽  
Wenjing Wang ◽  
Mateo I Sanchez ◽  
Robert Coukos ◽  
Mark von Zastrow ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
High Specificity ◽  
Specific Protein ◽  
Protein Protein Interactions ◽  
High Background ◽  
Specificity And Sensitivity ◽  
Time Courses ◽  
Rapid Kinetics ◽  
Two Hybrid

Transcriptional assays, such as yeast two-hybrid and TANGO, that convert transient protein-protein interactions (PPIs) into stable expression of transgenes are powerful tools for PPI discovery, screens, and analysis of cell populations. However, such assays often have high background and lose information about PPI dynamics. We have developed SPARK (Specific Protein Association tool giving transcriptional Readout with rapid Kinetics), in which proteolytic release of a membrane-tethered transcription factor (TF) requires both a PPI to deliver a protease proximal to its cleavage peptide and blue light to uncage the cleavage site. SPARK was used to detect 12 different PPIs in mammalian cells, with 5 min temporal resolution and signal ratios up to 37. By shifting the light window, we could reconstruct PPI time-courses. Combined with FACS, SPARK enabled 51 fold enrichment of PPI-positive over PPI-negative cells. Due to its high specificity and sensitivity, SPARK has the potential to advance PPI analysis and discovery.

IL-14 MAPPIT: a versatile METHOD to study protein-protein interactions in mammalian cells

2003 ◽  
Vol 16 (5) ◽  
pp. 577-577
Author(s):  
J. Tavernier ◽  
S. Eyckerman ◽  
I. Lemmens ◽  
S. Lievens ◽  
J. Vandekerckhove ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Protein Protein Interactions

scholarly journals β-Catenin is a pH sensor with decreased stability at higher intracellular pH

2018 ◽  
Vol 217 (11) ◽  
pp. 3965-3976 ◽  
Author(s):  
Katharine A. White ◽  
Bree K. Grillo-Hill ◽  
Mario Esquivel ◽  
Jobelle Peralta ◽  
Vivian N. Bui ◽  
...  
Keyword(s):  
Intracellular Ph ◽  
Protein Interactions ◽  
Mammalian Cells ◽  
Ph Sensor ◽  
Adherens Junction ◽  
Protein Protein Interactions ◽  
Adherens Junction Protein ◽  
Junction Protein ◽  
Evolutionarily Conserved ◽  
Ph Dependent

β-Catenin functions as an adherens junction protein for cell–cell adhesion and as a signaling protein. β-catenin function is dependent on its stability, which is regulated by protein–protein interactions that stabilize β-catenin or target it for proteasome-mediated degradation. In this study, we show that β-catenin stability is regulated by intracellular pH (pHi) dynamics, with decreased stability at higher pHi in both mammalian cells and Drosophila melanogaster. β-Catenin degradation requires phosphorylation of N-terminal residues for recognition by the E3 ligase β-TrCP. While β-catenin phosphorylation was pH independent, higher pHi induced increased β-TrCP binding and decreased β-catenin stability. An evolutionarily conserved histidine in β-catenin (found in the β-TrCP DSGIHS destruction motif) is required for pH-dependent binding to β-TrCP. Expressing a cancer-associated H36R–β-catenin mutant in the Drosophila eye was sufficient to induce Wnt signaling and produced pronounced tumors not seen with other oncogenic β-catenin alleles. We identify pHi dynamics as a previously unrecognized regulator of β-catenin stability, functioning in coincidence with phosphorylation.

scholarly journals TULP1 and TUB Are Required for Specific Localization of PRCD to Photoreceptor Outer Segments

2020 ◽  
Vol 21 (22) ◽  
pp. 8677
Author(s):  
Lital Remez ◽  
Ben Cohen ◽  
Mariela J. Nevet ◽  
Leah Rizel ◽  
Tamar Ben-Yosef
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Outer Segment ◽  
Protein Protein Interactions ◽  
Photoreceptor Outer Segment ◽  
Photoreceptor Outer Segments ◽  
Outer Segments ◽  
Yeast Two Hybrid System ◽  
Specific Localization ◽  
Recruitment System

Photoreceptor disc component (PRCD) is a small protein which is exclusively localized to photoreceptor outer segments, and is involved in the formation of photoreceptor outer segment discs. Mutations in PRCD are associated with retinal degeneration in humans, mice, and dogs. The purpose of this work was to identify PRCD-binding proteins in the retina. PRCD protein-protein interactions were identified when implementing the Ras recruitment system (RRS), a cytoplasmic-based yeast two-hybrid system, on a bovine retina cDNA library. An interaction between PRCD and tubby-like protein 1 (TULP1) was identified. Co-immunoprecipitation in transfected mammalian cells confirmed that PRCD interacts with TULP1, as well as with its homolog, TUB. These interactions were mediated by TULP1 and TUB highly conserved C-terminal tubby domain. PRCD localization was altered in the retinas of TULP1- and TUB-deficient mice. These results show that TULP1 and TUB, which are involved in the vesicular trafficking of several photoreceptor proteins from the inner segment to the outer segment, are also required for PRCD exclusive localization to photoreceptor outer segment discs.

scholarly journals Shaping the regulation of the p53 mRNA tumour suppressor: the co-evolution of genetic signatures

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Konstantinos Karakostis ◽  
Robin Fåhraeus
Keyword(s):  
Protein Interactions ◽  
Rna Structure ◽  
Mammalian Cells ◽  
Rna World ◽  
Genetic Diseases ◽  
Protein Protein Interactions ◽  
Activation Domain ◽  
Interacting Protein ◽  
Protein Motifs ◽  
Synonymous Mutations

Abstract Structured RNA regulatory motifs exist from the prebiotic stages of the RNA world to the more complex eukaryotic systems. In cases where a functional RNA structure is within the coding sequence a selective pressure drives a parallel co-evolution of the RNA structure and the encoded peptide domain. The p53-MDM2 axis, describing the interactions between the p53 tumor suppressor and the MDM2 E3 ubiquitin ligase, serves as particularly useful model revealing how secondary RNA structures have co-evolved along with corresponding interacting protein motifs, thus having an impact on protein – RNA and protein – protein interactions; and how such structures developed signal-dependent regulation in mammalian systems. The p53(BOX-I) RNA sequence binds the C-terminus of MDM2 and controls p53 synthesis while the encoded peptide domain binds MDM2 and controls p53 degradation. The BOX-I peptide domain is also located within p53 transcription activation domain. The folding of the p53 mRNA structure has evolved from temperature-regulated in pre-vertebrates to an ATM kinase signal-dependent pathway in mammalian cells. The protein – protein interaction evolved in vertebrates and became regulated by the same signaling pathway. At the same time the protein - RNA and protein - protein interactions evolved, the p53 trans-activation domain progressed to become integrated into a range of cellular pathways. We discuss how a single synonymous mutation in the BOX-1, the p53(L22 L), observed in a chronic lymphocyte leukaemia patient, prevents the activation of p53 following DNA damage. The concepts analysed and discussed in this review may serve as a conceptual mechanistic paradigm of the co-evolution and function of molecules having roles in cellular regulation, or the aetiology of genetic diseases and how synonymous mutations can affect the encoded protein.

scholarly journals Mass spectrometry-based methods for analysing the mitochondrial interactome in mammalian cells

2019 ◽  
Vol 167 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Takumi Koshiba ◽  
Hidetaka Kosako
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Mammalian Cells ◽  
Protein Complexes ◽  
Living Cells ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Protein Protein Interaction ◽  
Membrane Protein Complexes ◽  
Protein Protein Interaction Networks

Abstract Protein–protein interactions are essential biologic processes that occur at inter- and intracellular levels. To gain insight into the various complex cellular functions of these interactions, it is necessary to assess them under physiologic conditions. Recent advances in various proteomic technologies allow to investigate protein–protein interaction networks in living cells. The combination of proximity-dependent labelling and chemical cross-linking will greatly enhance our understanding of multi-protein complexes that are difficult to prepare, such as organelle-bound membrane proteins. In this review, we describe our current understanding of mass spectrometry-based proteomics mapping methods for elucidating organelle-bound membrane protein complexes in living cells, with a focus on protein–protein interactions in mitochondrial subcellular compartments.

Prion protein/protein interactions: fusion with yeast Sup35p‐NM modulates cytosolic PrP aggregation in mammalian cells

2007 ◽  
Vol 22 (3) ◽  
pp. 762-773 ◽  
Author(s):  
Carmen Krammer ◽  
Michael H. Suhre ◽  
Elisabeth Kremmer ◽  
Claudia Diemer ◽  
Simone Hess ◽  
...  
Keyword(s):  
Prion Protein ◽  
Protein Interactions ◽  
Mammalian Cells ◽  
Protein Protein Interactions

Split Luciferase as an Optical Probe for Detecting Protein−Protein Interactions in Mammalian Cells Based on Protein Splicing

2001 ◽  
Vol 73 (11) ◽  
pp. 2516-2521 ◽  
Author(s):  
Takeaki Ozawa ◽  
Asami Kaihara ◽  
Moritoshi Sato ◽  
Kazunari Tachihara ◽  
Yoshio Umezawa
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Optical Probe ◽  
Protein Splicing ◽  
Protein Protein Interactions ◽  
Split Luciferase

scholarly journals Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Stephanie Berger ◽  
Erik Procko ◽  
Daciana Margineantu ◽  
Erinna F Lee ◽  
Betty W Shen ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Human Cancer ◽  
High Specificity ◽  
Specific Protein ◽  
Biological Processes ◽  
Protein Protein Interactions ◽  
Human Cancer Cell Lines ◽  
Bcl2 Family ◽  
Bcl2 Protein

Many cancers overexpress one or more of the six human pro-survival BCL2 family proteins to evade apoptosis. To determine which BCL2 protein or proteins block apoptosis in different cancers, we computationally designed three-helix bundle protein inhibitors specific for each BCL2 pro-survival protein. Following in vitro optimization, each inhibitor binds its target with high picomolar to low nanomolar affinity and at least 300-fold specificity. Expression of the designed inhibitors in human cancer cell lines revealed unique dependencies on BCL2 proteins for survival which could not be inferred from other BCL2 profiling methods. Our results show that designed inhibitors can be generated for each member of a closely-knit protein family to probe the importance of specific protein-protein interactions in complex biological processes.

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