Technologies of protein interactomics: A review
- BiologyRussian Journal of Bioorganic Chemistry
A brief description and a comparative evaluation of the most widely used methods of protein interactomics are given in the present review.
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases
- BiologyPLoS Comput. Biol.
This review describes different experimental techniques of protein interaction identification together with various databases which attempt to classify the large array of experimental data and presents several approaches to verify and validate the diverse experimental data produced by high-throughput techniques.
Protein‐protein interaction screening with the Ras‐recruitment system
The RRS is proposed as a valuable alternative interaction screening method that can widely be used among protein classes and that has been further developed by this group into a high-throughput screening system.
Systematic identification of SH3 domain‐mediated human protein–protein interactions by peptide array target screening
Compared to protein interactions listed in the online predicted human interaction protein database (OPHID), the majority of interactions identified by PATS are novel, suggesting that, when extended to the large number of peptide interaction domains encoded by the human genome, PATS should aid in the mapping of the human interactome.
Interactome network analysis identifies multiple caspase-6 interactors involved in the pathogenesis of HD.
- BiologyHuman molecular genetics
Characterization of the interaction network provides important new information regarding key pathways of interactors of CASP6 and highlights potential novel therapeutic targets for HD, AD and cerebral ischemia.
Dynamics of Protein Complexes Tracked by Quantitative Proteomics
Deciphering the dynamics of these protein interaction networks by assembling sets of various interactomes that echo different cellular conditions, rather than simply draw a comprehensive map of a static protein interactome, remains one of the key challenges in cell biology.
Visualization of Multiprotein Complexes by Flow Cytometry
- BiologyCurrent protocols in immunology
Analysis of coimmunoprecipitation of protein complexes by flow cytometry (IP‐FCM, or “the fly‐p” method) provides a sensitive means to measure these interactions in the native/nondenatured state without requiring genetic engineering or large sample sizes.
Learning of protein interaction networks
- Computer Science
A systematic study of the efficacy of using supervised learning methods to integrate direct and indirect biological evidence for predicting pairwise protein interactions and proposed algorithms provide strong computational tools for predicting and analyzing protein-protein interaction networks.
Charting the Landscape of Tandem BRCT Domain–Mediated Protein Interactions
- BiologyScience Signaling
Bioinformatics analysis of the BRCT protein-protein interaction network revealed biological processes and protein complexes that integrate the DDR with cell cycle regulation and transcription and signaling subnetworks that may aid in understanding the involvement of tBRCT in disease and DNA repair.
Detection of protein complexes from affinity purification/mass spectrometry data
- Computer ScienceBMC Systems Biology
This study highlights the significance of taking co-complex relations into account when extracting protein complexes from AP-MS data and can be easily extended to the analysis of other biological networks which can be conveniently represented by bipartite graphs such as drug-target networks.
SHOWING 1-10 OF 16 REFERENCES
A Map of the Interactome Network of the Metazoan C. elegans
A large fraction of the Caenorhabditis elegans interactome network is mapped, starting with a subset of metazoan-specific proteins, and more than 4000 interactions were identified from high-throughput, yeast two-hybrid screens.
Comparative assessment of large-scale data sets of protein–protein interactions
Comprehensive protein–protein interaction maps promise to reveal many aspects of the complex regulatory network underlying cellular function and are compared with each other and with a reference set of previously reported protein interactions.
A comprehensive two-hybrid analysis to explore the yeast protein interactome
- BiologyProceedings of the National Academy of Sciences of the United States of America
The comprehensive analysis using a system to examine two-hybrid interactions in all possible combinations between the budding yeast Saccharomyces cerevisiae is completed and would significantly expand and improve the protein interaction map for the exploration of genome functions that eventually leads to thorough understanding of the cell as a molecular system.
A Protein Interaction Map of Drosophila melanogaster
This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans, and recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components.
A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome
Functional proteomics mapping of a human signaling pathway.
- BiologyGenome research
An integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway is presented, validating this integrated functional proteomics approach.
High-Throughput Mapping of a Dynamic Signaling Network in Mammalian Cells
LUMIER (for luminescence-based mammalian interactome mapping), an automated high-throughput technology, is developed and applied to the transforming growth factor–β (TGFβ) pathway and it is shown that Occludin regulates TGFβ type I receptor localization for efficient TGF β-dependent dissolution of tight junctions during epithelial-to-mesenchymal transitions.
Interaction network containing conserved and essential protein complexes in Escherichia coli
Insight is provided into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.
Dynamic Complex Formation During the Yeast Cell Cycle
It is shown that additional regulation through targeted degradation and phosphorylation by Cdc28p (Cdk1) specifically affects the periodically expressed proteins.
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.