scholarly journals High throughput flow cytometry based yeast two-hybrid array approach for large-scale analysis of protein-protein interactions

2011 ◽  
Vol 81A (1) ◽  
pp. 90-98 ◽  
Author(s):  
Jun Chen ◽  
Mark B. Carter ◽  
Bruce S. Edwards ◽  
Hong Cai ◽  
Larry A. Sklar
Keyword(s):  
Flow Cytometry ◽  
High Throughput ◽  
Protein Interactions ◽  
Large Scale ◽  
Scale Analysis ◽  
Protein Protein Interactions ◽  
Yeast Two Hybrid ◽  
Large Scale Analysis ◽  
Two Hybrid

scholarly journals Yeast Two-Hybrid Systems and Protein Interaction Mapping Projects for Yeast and Worm

Yeast ◽  
2000 ◽  
Vol 1 (2) ◽  
pp. 88-94 ◽  
Author(s):  
Albertha J. M. Walhout ◽  
Simon J. Boulton ◽  
Marc Vidal
Keyword(s):  
Hybrid Systems ◽  
High Throughput ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Protein Interactions ◽  
Yeast Two Hybrid ◽  
Systematic Analysis ◽  
Technical Features ◽  
Two Hybrid

The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput experimental settings. Such approaches are collectively referred to as ‘functional genomics’. One approach to investigate the properties of a proteome of interest is by systematic analysis of protein–protein interactions. So far, the yeast two-hybrid system is the most commonly used method for large-scale, high-throughput identification of potential protein–protein interactions. Here, we discuss several technical features of variants of the two-hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeastSaccharomyces cerevisiaeand the nematodeCaenorhabditis elegans.

scholarly journals Yeast Two-Hybrid Systems and Protein Interaction Mapping Projects for Yeast and Worm

Yeast ◽  
2000 ◽  
Vol 1 (2) ◽  
pp. 88-94 ◽  
Author(s):  
Albertha J. M. Walhout ◽  
Simon J. Boulton ◽  
Marc Vidal
Keyword(s):  
Hybrid Systems ◽  
High Throughput ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Protein Interactions ◽  
Yeast Two Hybrid ◽  
Systematic Analysis ◽  
Technical Features ◽  
Two Hybrid

The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput experimental settings. Such approaches are collectively referred to as ‘functional genomics’. One approach to investigate the properties of a proteome of interest is by systematic analysis of protein–protein interactions. So far, the yeast two-hybrid system is the most commonly used method for large-scale, high-throughput identification of potential protein–protein interactions. Here, we discuss several technical features of variants of the two-hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans.

On the structure of protein–protein interaction networks

2003 ◽  
Vol 31 (6) ◽  
pp. 1491-1496 ◽  
Author(s):  
A. Thomas ◽  
R. Cannings ◽  
N.A.M. Monk ◽  
C. Cannings
Keyword(s):  
Power Law ◽  
Protein Interactions ◽  
Large Scale ◽  
Underlying Structure ◽  
Protein Protein Interactions ◽  
Yeast Two Hybrid ◽  
Protein Protein Interaction ◽  
Human Proteins ◽  
Approximate Power ◽  
Two Hybrid

We present a simple model for the underlying structure of protein–protein pairwise interaction graphs that is based on the way in which proteins attach to each other in experiments such as yeast two-hybrid assays. We show that data on the interactions of human proteins lend support to this model. The frequency of the number of connections per protein under this model does not follow a power law, in contrast to the reported behaviour of data from large-scale yeast two-hybrid screens of yeast protein–protein interactions. Sampling sub-graphs from the underlying graphs generated with our model, in a way analogous to the sampling performed in large-scale yeast two-hybrid searches, gives degree distributions that differ subtly from the power law and that fit the observed data better than the power law itself. Our results show that the observation of approximate power law behaviour in a sampled sub-graph does not imply that the underlying graph follows a power law.

scholarly journals Reliable identification of protein-protein interactions by crosslinking mass spectrometry

2020 ◽  
Author(s):  
Swantje Lenz ◽  
Ludwig R. Sinn ◽  
Francis J. O’Reilly ◽  
Lutz Fischer ◽  
Fritz Wegner ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Complexes ◽  
Estimation Procedure ◽  
Scale Analysis ◽  
Protein Protein Interactions ◽  
False Discovery ◽  
Large Scale Analysis ◽  
False Discovery Rate Estimation

Crosslinking mass spectrometry is widening its scope from structural analyzes of purified multi-protein complexes towards systems-wide analyzes of protein-protein interactions. Assessing the error in these large datasets is currently a challenge. Using a controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate a reliable false-discovery rate estimation procedure for protein-protein interactions identified by crosslinking mass spectrometry.

scholarly journals A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities

2019 ◽  
Author(s):  
David Cluet ◽  
Ikram Amri ◽  
Blandine Vergier ◽  
Jérémie Léault ◽  
Clémence Grosjean ◽  
...  
Keyword(s):  
Flow Cytometry ◽  
Hybrid System ◽  
Protein Interactions ◽  
Technological Advancement ◽  
Protein Protein Interactions ◽  
Yeast Two Hybrid ◽  
High Throughput Analysis ◽  
Expression Levels ◽  
Yeast Two Hybrid System ◽  
Two Hybrid

AbstractWe present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on PPIs with different affinities. After only two hours of reaction, expression of the reporter can easily be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflects the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated high-throughput analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.

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