- Protein-protein interaction screening
Screening of Protein-protein interactions refer to identify protein interactions with
high throughput screeningmethods like computer and or robot assisted plate reading, flow cytometry analyzing etc.
The interactions between proteins are of central importance for virtually every process in a living cell. Information about these interactions improves our understanding of diseases and can provide the basis for new therapeutic approaches.
Methods to screen protein-protein interactions
Though there are many methods to detect protein-protein interactions, majority of them are not screening approaches. Methods like
Co-immunoprecipitation, Fluorescence resonance energy transfer(FRET) belong to this category.
Ex Vivo or In Vivo methods
Methods that screen protein-protein interactions in the living cells.
Bimolecular Fluorescence Complementation(BiFC) is a new technique in observing the interactions of proteins. Combining with other new techniques DERB, this method can be used to screen protein-protein interactions and their modulators [cite journal| author=Lu JP, Beatty LK, Pinthus JH. |date=2008 |title=Dual expression recombinase based (DERB) single vector system for high throughput screening and verification of protein interactions in living cells.|journal= Nature Precedings
yeast two-hybridscreen investigates the interaction between artificial fusion proteins inside the nucleus of yeast. This approach can identify binding partners of a protein in an unbiased manner. However, the method has a notorious high false-positive rate, which makes it necessary to verify the identified interactions by co-immunoprecipitation[cite journal| author= Fields S. |date= 2005 Nov;272(21):5391-9. |title=High-throughput two-hybrid analysis. The promise and the peril. .|journal= FEBS J. Review. PMID: 16262681] .
In Vitro methods
Tandem affinity purification(TAP) method allows high throughput identification of proteins interactions. In contrast to Y2H approach accuracy of the method can be compared to those of small-scale experiments (Collins et al., 2007) and the interactions are detected within the correct cellular environment as by co-immunoprecipitation. However, the TAP tag method requires two successive steps of protein purification and consequently it can not readily detect transient protein-protein interactions. Recent genome-wide TAP experiments were performed by Krogan et al., 2006 and Gavin et al., 2006 providing updated protein interaction data for yeast organism.
*Chemical crosslinking is often used to "fix" protein interactions in place before trying to isolate/identify interacting proteins. Common crosslinkers for this application include the non-cleavable [NHS-ester] crosslinker, ["bis"-sulfosuccinimidyl suberate] (BS3); a cleavable version of BS3, [dithiobis(sulfosuccinimidyl propionate)] (DTSSP); and the [imidoester] crosslinker [dimethyl dithiobispropionimidate] (DTBP) that is popular for fixing interactions in
ChIPassays. [cite journal| author=Chen CS, Zhu H.|date=2006 Apr;40(4):423, 425, 427 |title=Protein microarrays.|journal= Biotechniques. PMID: 16629388 ] .
Protein-protein interaction databases
* [http://hprd.org HPRD Human Protein Reference Database] a (manually) curated database of human protein information with visualization tools.
* [http://www.ebi.ac.uk/intact IntAct Interaction Database] is a public repository for manually curated molecular interaction data from literature.
* [http://dip.doe-mbi.ucla.edu/ DIP Database of Interacting Proteins] , a manual and automatic catalog of experimentally determined interactions between proteins.
* [http://mint.bio.uniroma2.it/mint/ MINT Molecular INTeraction Database] focuses on experimentally verified protein interactions mined from the scientific literature by expert curators.
* [http://mips.gsf.de/proj/ppi/ MIPS Mammalian Protein-Protein Interaction Database]
* [http://www.thebiogrid.org/ BioGRID]
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