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Protein protein interaction lecture notes
 

Protein protein interaction lecture notes

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    Protein protein interaction lecture notes Protein protein interaction lecture notes Document Transcript

    • Proteinprotein interaction 1 Protein–protein interaction Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein components organised by their protein–protein interactions. Protein interactions have been studied from the perspectives of biochemistry, quantum chemistry, molecular dynamics, chemical biology, signal transduction and other metabolic or genetic/epigenetic networks. Indeed, protein–protein interactions are at the core of the entire interactomics system of any living cell. Interactions between proteins are important for the majority of biological functions. For example, signals from the exterior of a cell are mediated to the inside of that cell by protein–protein interactions of the signaling The horseshoe shaped ribonuclease inhibitor (shown as wireframe) forms a protein–protein interaction with the ribonuclease protein. molecules. This process, called signal transduction, The contacts between the two proteins are shown as coloured plays a fundamental role in many biological processes patches. and in many diseases (e.g. cancers). Proteins might interact for a long time to form part of a protein complex, a protein may be carrying another protein (for example, from cytoplasm to nucleus or vice versa in the case of the nuclear pore importins), or a protein may interact briefly with another protein just to modify it (for example, a protein kinase will add a phosphate to a target protein). This modification of proteins can itself change protein–protein interactions. For example, some proteins with SH2 domains only bind to other proteins when they are phosphorylated on the amino acid tyrosine while bromodomains specifically recognise acetylated lysines. In conclusion, protein–protein interactions 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 investigate protein–protein interactions As protein–protein interactions are so important there are a multitude of methods to detect them.[1] Each of the approaches has its own strengths and weaknesses, especially with regard to the sensitivity and specificity of the method. A high sensitivity means that many of the interactions that occur in reality are detected by the screen. A high specificity indicates that most of the interactions detected by the screen are also occurring in reality. Methods such as yeast two-hybrid screening can be used to detect novel protein–protein interactions. Structure The structures of many protein complexes have been unlocked by the technique of X-ray crystallography.[2] Whereas many high throughput techniques to investigate protein interactions can only tell you which protein interacts with which other proteins. Molecular structure can give fine details about which specific parts are interacting and what kinds of chemical bonds mediate that interaction. One of the earliest protein structures to be solved was that of haemoglobin by Perutz and colleagues, which is a complex of four proteins: two alpha chains and two beta chains.[3] As the number of structures available for protein complexes grew researchers began to investigate the underlying
    • Proteinprotein interaction 2 principles of protein-protein interactions. Based on just three structures of the insulin dimer, trypsin-pancreatic trypsin inhibitor complex and oxyhaemoglobin, Cyrus Chothia and Joel Janin found that between 1,130 and 1,720 Angstroms2 of surface area was removed from contact with water indicating that hydrophobicity was the major factor stabilising protein-protein interactions.[4] Later studies refined the buried surface area of the majority of interactions to be 1,600±350 Angstroms2. However, much larger interaction interfaces were observed that were associated with large changes in conformation of one of the interaction partners.[2] Visualization of networks Visualization of protein–protein interaction networks is a popular application of scientific visualization techniques.[5] Although protein interaction diagrams are common in textbooks, diagrams of whole cell protein interaction networks were not as common since the level of complexity made them difficult to generate. One example of a manually produced molecular interaction map is Kurt Kohns 1999 map of cell cycle control.[6] Drawing on Kohns map, in 2000 Schwikowski, Uetz, and Fields published a paper on protein–protein interactions in yeast, linking together 1,548 interacting proteins determined by two-hybrid testing. They used a layered graph drawing method to find an initial placement of the Network visualisation of the human interactome where nodes and then improved the layout using a force-based each point represents a protein and each blue line algorithm.[7][8][9] The Cytoscape software is a widely used between them is an interaction. application to visualise protein-protein interaction networks. Database collections Methods for identifying interacting proteins have defined hundreds of thousands of interactions. These interactions are collected together in specialised biological databases that allow the interactions to be assembled and studied further. The first of these databases was DIP, the database of interacting proteins.[10] Since that time a large number of further database collections have been created such as BioGRID, STRING and ConsensusPathDB. References [1] Phizicky EM, Fields S (March 1995). "Protein-protein interactions: methods for detection and analysis". Microbiol. Rev. 59 (1): 94–123. PMC 239356. PMID 7708014. [2] Janin J, Chothia C (September 1990). "The structure of protein-protein recognition sites". J. Biol. Chem. 265 (27): 16027–30. PMID 2204619. [3] PERUTZ MF, ROSSMANN MG, CULLIS AF, MUIRHEAD H, WILL G, NORTH AC (February 1960). "Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis". Nature 185 (4711): 416–22. PMID 18990801. [4] Chothia C, Janin J (August 1975). "Principles of protein-protein recognition". Nature 256 (5520): 705–8. PMID 1153006. [5] De Las Rivas J, Fontanillo C (June 2010). "Protein-protein interactions essentials: key concepts to building and analyzing interactome networks". PLoS Comput. Biol. 6 (6): e1000807. doi:10.1371/journal.pcbi.1000807. PMC 2891586. PMID 20589078. [6] Kurt W. Kohn (August 1, 1999). "Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems". Molecular Biology of the Cell 10 (8): 2703–2734. PMC 25504. PMID 10436023. [7] Benno Schwikowski1, Peter Uetz, and Stanley Fields (2000). "A network of protein−protein interactions in yeast" (http:/ / www. nature. com/ nbt/ journal/ v18/ n12/ full/ nbt1200_1257. html). Nature Biotechnology 18 (12): 1257–1261. doi:10.1038/82360. PMID 11101803. . [8] Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 17:1030-2. Rigaut, G; Shevchenko, A; Rutz, B; Wilm, M; Mann, M; Séraphin, B (1999). "A generic protein purification method for protein complex characterization and proteome exploration.". Nature Biotechnology 17 (10): 1030–2. doi:10.1038/13732. PMID 10504710. [9] Prieto C, De Las Rivas J (2006). APID: Agile Protein Interaction DataAnalyzer. Nucleic Acids Res. 34:W298-302. Prieto, C; De Las Rivas, J (2006). "APID: Agile Protein Interaction DataAnalyzer.". Nucleic Acids Research 34 (Web Server issue): W298–302. doi:10.1093/nar/gkl128.
    • Protein–protein interaction screening The screening of protein–protein interactions refers to the identification of protein interactions with high-throughput screening methods such as computer- and/or robot-assisted plate reading, flow cytometry analyzing. The interactions between proteins are central to virtually every process in a living cell. Information about these interactions improves understanding of diseases and can provide the basis for new therapeutic approaches.Methods to screen protein–protein interactionsThough there are many methods to detect protein–protein interactions, themajority of these methods—such as Co-immunoprecipitation, Fluorescenceresonance energy transfer (FRET) and dual polarisation interferometry—are notscreening approaches.Ex vivo or in vivo methods  Bimolecular Fluorescence Complementation (BiFC) is a new technique for observing the interactions of proteins. Combining it with other new techniques DERB can enable the screening of protein–protein interactions and their modulators.  The yeast two-hybrid screen investigates the interaction between artificial fusion proteins inside the nucleus of yeast. This approach can identify the binding partners of a protein without bias. However, the method has a notoriously high false-positive rate, which makes it necessary to verify the identified interactions co-immunoprecipitation.
    • In-vitro methods  The Tandem affinity purification (TAP) method allows the high- throughput identification of proteins interactions. In contrast with the Y2H approach, the 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 thus 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 organisms.  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 ChIP assays.
    • Two-hybrid screening 1 Two-hybrid screening Two-hybrid screening (also known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein–protein interactions[1] and [2][3] protein–DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of [1][2] transcription. The Y2H is thus a protein-fragment complementation assay. History Overview of two-hybrid assay, checking for interactions between two proteins, Pioneered by Stanley Fields and Song in called here Bait and Prey.A. Gal4 transcription factor gene produces two domain protein (BD and AD), which is essential for transcription of the reporter gene 1989, the technique was originally designed (LacZ).B,C. Two fusion proteins are prepared: Gal4BD+Bait and Gal4AD+Prey. to detect protein–protein interactions using None of them is usually sufficient to initiate the transcription (of the reporter the GAL4 transcriptional activator of the gene) alone.D. When both fusion proteins are produced and Bait part of the first yeast Saccharomyces cerevisiae. The GAL4 interact with Prey part of the second, transcription of the reporter gene occurs. protein activated transcription of a protein involved in galactose utilization, which formed the basis of selection.[4] Since then, the same principle has been adapted to describe many alternative methods including some that detect protein–DNA interactions, DNA-DNA interactions and use Escherichia coli instead of yeast.[3] Basic premise The key to the two-hybrid screen is that in most eukaryotic transcription factors, the activating and binding domains are modular and can function in proximity to each other without direct binding.[5] This means that even though the transcription factor is split into two fragments, it can still activate transcription when the two fragments are indirectly connected. The most common screening approach is the yeast two-hybrid assay.[6] This system often utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on media that lacks these nutrients, the yeast fail to survive. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids. In yeast two-hybrid screening, separate bait and prey plasmids are simultaneously introduced into the mutant yeast strain.
    • Two-hybrid screening 2 Plasmids are engineered to produce a protein product in which the DNA-binding domain (BD) fragment is fused onto a protein while another plasmid is engineered to produce a protein product in which the activation domain (AD) fragment is fused onto another protein. The protein fused to the BD may be referred to as the bait protein, and is typically a known protein the investigator is using to identify new binding partners. The protein fused to the AD may be referred to as the prey protein and can be either a single known protein or a library of known or unknown proteins. In this context, a library may consist of a collection of protein-encoding sequences that represent all the proteins expressed in a particular organism or tissue, or may be generated by synthesising random DNA sequences.[3] Regardless of the source, they are subsequently incorporated into the protein-encoding sequence of a plasmid, which is then transfected into the cells chosen for the screening method.[3] This technique, when using a library, assumes that each cell is transfected with no more than a single plasmid and that, therefore, each cell ultimately expresses no more than a single member from the protein library. If the bait and prey proteins interact (i.e., bind), then the AD and BD of the transcription factor are indirectly connected, bringing the AD in proximity to the transcription start site and transcription of reporter gene(s) can occur. If the two proteins do not interact, there is no transcription of the reporter gene. In this way, a successful interaction between the fused protein is linked to a change in the cell phenotype.[1] The challenge of separating cells that express proteins that happen to interact with their counterpart fusion proteins from those that do not, is addressed in the following section. Fixed domains In any study, some of the protein domains, those under investigation, will be varied according to the goals of the study whereas other domains, those that are not themselves being investigated, will be kept constant. For example in a two-hybrid study to select DNA-binding domains, the DNA-binding domain, BD, will be varied whilst the two interacting proteins, the bait and prey, must be kept constant to maintain a strong binding between the BD and AD. There are a number of domains from which to choose the BD, bait and prey and AD, if these are to remain constant. In protein–protein interaction investigations, the BD may be chosen from any of many strong DNA-binding domains such as Zif268.[2] A frequent choice of bait and prey domains are residues 263–352 of yeast Gal11P with a N342V mutation[2] and residues 58–97 of yeast Gal4,[2] respectively. These domains can be used in both yeast- and bacterial-based selection techniques and are known to bind together strongly.[1][2] The AD chosen must be able to activate transcription of the reporter gene, using the cells own transcription machinery. Thus, the variety of ADs available for use in yeast-based techniques may not be suited to use in their bacterial-based analogues. The herpes simplex virus-derived AD, VP16 and yeast Gal4 AD have been used with success in yeast[1] whilst a portion of the α-subunit of E. coli RNA polymerase has been utilised in E. coli-based methods.[2][3] Whilst powerfully activating domains may allow greater sensitivity towards weaker interactions, conversely, a weaker AD may provide greater stringency. Construction of expression plasmids A number of engineered genetic sequences must be incorporated into the host cell to perform two-hybrid analysis or one of its derivative techniques. The considerations and methods used in the construction and delivery of these sequences differ according to the needs of the assay and the organism chosen as the experimental background. There are two broad categories of hybrid library: random libraries and cDNA-based libraries. A cDNA library is constituted by the cDNA produced through reverse transcription of mRNA collected from specific cells of types of cell. This library can be ligated into a construct so that it is attached to the BD or AD being used in the assay.[1] A random library uses lengths of DNA of random sequence in place of these cDNA sections. A number of methods exist for the production of these random sequences, including cassette mutagenesis.[2] Regardless of the source of the
    • Two-hybrid screening 3 DNA library, it is ligated into the appropriate place in the relevant plasmid/phagemid using the appropriate restriction endonucleases.[2] E. coli-specific considerations By placing the hybrid proteins under the control of IPTG-inducible lac promoters, they are expressed only on media supplemented with IPTG. Further, by including different antibiotic resistance genes in each genetic construct, the growth of non-transformed cells is easily prevented through culture on media containing the corresponding antibiotics. This is particularly important for counter selection methods in which a lack of interaction is needed for cell survival.[2] The reporter gene may be inserted into the E. coli genome by first inserting it into an episome, a type of plasmid with the ability to incorporate itself into the bacterial cell genome[2] with a copy number of approximately one per cell.[7] The hybrid expression phagemids can be electroporated into E. coli XL-1 Blue cells which after amplification and infection with VCS-M13 helper phage, will yield a stock of library phage. These phage will each contain one single-stranded member of the phagemid library.[2] Recovery of protein information Once the selection has been performed, the primary structure of the proteins which display the appropriate characteristics must be determined. This is achieved by retrieval of the protein-encoding sequences (as originally inserted) from the cells showing the appropriate phenotype. E. coli The phagemid used to transform E. coli cells may be "rescued" from the selected cells by infecting them with VCS-M13 helper phage. The resulting phage particles that are produced contain the single-stranded phagemids and are used to infect XL-1 Blue cells.[2] The double-stranded phagemids are subsequently collected from these XL-1 Blue cells, essentially reversing the process used to produce the original library phage. Finally, the DNA sequences are determined through dideoxy sequencing.[2] Controlling sensitivity The Escherichia coli-derived Tet-R repressor can be used in line with a conventional reporter gene and can be controlled by tetracycline or doxicycline (Tet-R inhibitors). Thus the expression of Tet-R is controlled by the standard two-hybrid system but the Tet-R in turn controls (represses) the expression of a previously mentioned reporter such as HIS3, through its Tet-R promoter. Tetracycline or its derivatives can then be used to regulate the sensitivity of a system utilising Tet-R.[1] Sensitivity may also be controlled by varying the dependency of the cells on their reporter genes. For example, this effected by altering the concentration of histidine in the growth medium for his3-dependent cells and altering the concentration of streptomycin for aadA dependent cells.[2][3] Selection-gene-dependency may also be controlled by applying an inhibitor of the selection gene at a suitable concentration. 3-Amino-1,2,4-triazole (3-AT) for example, is a competitive inhibitor of the HIS3-gene product and may be used to titrate the minimum level of HIS3 expression required for growth on histidine-deficient media.[2] Sensitivity may also be modulated by varying the number of operator sequences in the reporter DNA.
    • Two-hybrid screening 4 Non-fusion proteins A third, non-fusion protein may be co-expressed with two fusion proteins. Depending on the investigation, the third protein may modify one of the fusion proteins or mediate or interfere with their interaction.[1] Co-expression of the third protein may be necessary for modification or activation of one or both of the fusion proteins. For example S. cerevisiae possesses no endogenous tyrosine kinase. If an investigation involves a protein that requires tyrosine phosphorylation, the kinase must be supplied in the form of a tyrosine kinase gene.[1] The non-fusion protein may mediate the interaction by binding both fusion proteins simultaneously, as in the case of ligand-dependent receptor dimerization.[1] For a protein with an interacting partner, its functional homology to other proteins may be assessed by supplying the third protein in non-fusion form, which then may or may not compete with the fusion-protein for its binding partner. Binding between the third protein and the other fusion protein will interrupt the formation of the reporter expression activation complex and thus reduce reporter expression, leading to the distinguishing change in phenotype.[1] Split-ubiquitin yeast two-hybrid One limitation of classic yeast two-hybrid screens is that they are limited to soluble proteins. It is therefore impossible to use them to study the protein–protein interactions between insoluble integral membrane proteins. The split-ubiquitin system provides a method for overcoming this limitation.[8] In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35–76) and an N-terminal ubiquitin moiety ("Nub", residues 1–34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait–prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes. One-, three- and one-two-hybrid variants One-hybrid The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain. The binding domain in this case however is not necessarily of fixed sequence as in two-hybrid protein–protein analysis but may be constituted by a library. This library can be selected against the desired target sequence, which is inserted in the promoter region of the reporter gene construct. In a positive-selection system, a binding domain that successfully binds the UAS and allows transcription is thus selected.[1] Note that selection of DNA-binding domains is not necessarily performed using a one-hybrid system, but may also be performed using a two-hybrid system in which the binding domain is varied and the bait and prey proteins are kept constant.[2][3]
    • Two-hybrid screening 5 Three-hybrid RNA-protein interactions have been investigated through a three-hybrid variation of the two-hybrid technique. In this case, a hybrid RNA molecule serves to adjoin together the two protein fusion domains—which are not intended to interact with each other but rather the intermediary RNA molecule Overview of three-hybrid assay. (through their RNA-binding domains).[1] Techniques involving non-fusion proteins that perform a similar function, as described in the non-fusion proteins section above, may also be referred to as three-hybrid methods. One-two-hybrid Simultaneous use of the one- and two-hybrid methods (that is, simultaneous protein–protein and protein–DNA interaction) is known as a one-two-hybrid approach and expected to increase the stringency of the screen.[1] Host organism Although theoretically, any living cell might be used as the background to a two-hybrid analysis, there are practical considerations that dictate which is chosen. The chosen cell line should be relatively cheap and easy to culture and sufficiently robust to withstand application of the investigative methods and reagents.[1] Yeast S. cerevisiae was the model organism used during the two-hybrid techniques inception. It has several characteristics that make it a robust organism to host the interaction, including the ability to form tertiary protein structures, neutral internal pH, enhanced ability to form disulfide bonds and reduced-state glutathione among other cytosolic buffer factors, to maintain a hospitable internal environment.[1] The yeast model can be manipulated through non-molecular techniques and its complete genome sequence is known.[1] Yeast systems are tolerant of diverse culture conditions and harsh chemicals that could not be applied to mammalian tissue cultures.[1] A number of yeast strains have been created specifically for Y2H screens, e.g. Y187[9] and AH109,[10] both produced by Clontech. Proteins from as small as eight to as large as 750 amino acids have been studied using yeast.[1] E. coli E. coli-based methods have several characteristics that may make them preferable to yeast-based homologues. The higher transformation efficiency and faster rate of growth lends E. coli to the use of larger libraries (in excess of 108).[2] A low false positive rate of approximately 3x10−8, the absence of requirement for a nuclear localisation signal to be included in the protein sequence and the ability to study proteins that would be toxic to yeast may also be major factors to consider when choosing an experimental background organism.[2] It may be of note that the methylation activity of certain E. coli DNA methyltransferase proteins may interfere with some DNA-binding protein selections. If this is anticipated, the use of an E. coli strain that is defective for a particular methyltransferase may be an obvious solution.[2]
    • Two-hybrid screening 6 Applications Determination of sequences crucial for interaction By changing specific amino acids by mutating the corresponding DNA base-pairs in the plasmids used, the importance of those amino acid residues in maintaining the interaction can be determined.[1] After using bacterial cell-based method to select DNA-binding proteins, it is necessary to check the specificity of these domains as there is a limit to the extent to which the bacterial cell genome can act as a sink for domains with an affinity for other sequences (or indeed, a general affinity for DNA).[2] Drug and poison discovery Protein–protein signalling interactions pose suitable therapeutic targets due to their specificity and pervasiveness. The random drug discovery approach uses compound banks that comprise random chemical structures, and requires a high-throughput method to test these structures in their intended target.[1] The cell chosen for the investigation can be specifically engineered to mirror the molecular aspect that the investigator intends to study and then used to identify new human or animal therapeutics or anti-pest agents.[1] Determination of protein function By determination of the interaction partners of unknown proteins, the possible functions of these new proteins may be inferred.[1] This can be done using a single known protein against a library of unknown proteins or conversely, by selecting from a library of known proteins using a single protein of unknown function.[1] Zinc finger protein selection To select zinc finger proteins (ZFPs) for protein engineering, methods adapted from the two-hybrid screening technique have been used with success.[2][3] A ZFP is itself a DNA-binding protein used in the construction of custom DNA-binding domains that bind to a desired DNA sequence.[11] By using a selection gene with the desired target sequence included in the UAS, and randomising the relevant amino acid sequences to produce a ZFP library, cells that host a DNA-ZFP interaction with the required characteristics can be selected. Each ZFP typically recognises only 3–4 base pairs, so to prevent recognition of sites outside the UAS, the randomised ZFP is engineered into a scaffold consisting of another two ZFPs of constant sequence. The UAS is thus designed to include the target sequence of the constant scaffold in addition to the sequence for which a ZFP is selected.[2][3] A number of other DNA-binding domains may also be investigated using this system.[2] Strengths • Two-hybrid screens are low-tech; they can be carried out in any lab without sophisticated equipment. • Two-hybrid screens can provide an important first hint for the identification of interaction partners. • The assay is scalable, which makes it possible to screen for interactions among many proteins. Furthermore, it can be automated, and by using robots many proteins can be screened against thousands of potentially interacting proteins in a relatively short time. • Yeast two-hybrid data can be of similar quality to data generated by the alternative approach of coaffinity purification followed by mass spectrometry (AP/MS).[12]
    • Two-hybrid screening 7 Weaknesses • The main criticism applied to the yeast two-hybrid screen of protein–protein interactions is the possibility of a high number of false positive (and false negative) identifications. The exact rate of false positive results is not known, but earlier estimates were as high as 70%.[13] The reason for this high error rate lies in the characteristics of the screen: • Certain assay variants overexpress the fusion proteins which may cause unnatural protein concentrations that lead to unspecific (false) positives. • The hybrid proteins are fusion proteins; that is, the fused parts may inhibit certain interactions, especially if an interaction takes place at the N-terminus of a test protein (where the DNA-binding or activation domain is typically attached). • An interaction may not happen in yeast, the typical host organism for Y2H. For instance, if a bacterial protein is tested in yeast, it may lack a chaperone for proper folding that is only present in its bacterial host. Moreover, a mammalian protein is sometimes not correctly modified in yeast (e.g., missing phosphorylation), which can also lead to false results. • The Y2H takes place in the nucleus. If test proteins are not localized to the nucleus (because they have other localization signals) two interacting proteins may be found to be non-interacting. • Some proteins might specifically interact when they are co-expressed in the yeast, although in reality they are never present in the same cell at the same time. However, in most cases it cannot be ruled out that such proteins are indeed expressed in certain cells or under certain circumstances. Each of these points alone can give rise to false results. Due to the combined effects of all error sources yeast two-hybrid have to be interpreted with caution. The probability of generating false positives means that all interactions should be confirmed by a high confidence assay, for example co-immunoprecipitation of the endogenous proteins, which is difficult for large scale protein–protein interaction data. Alternatively, Y2H data can be verified using multiple Y2H variants[14] or bioinformatics techniques. The latter test whether interacting proteins are expressed at the same time, share some common features (such as gene ontology annotations or certain network topologies), have homologous interactions in other species.[15] References [1] Young K (1998). "Yeast two-hybrid: so many interactions, (in) so little time." (http:/ / www. biolreprod. org/ cgi/ reprint/ 58/ 2/ 302). Biol Reprod 58 (2): 302–11. doi:10.1095/biolreprod58.2.302. PMID 9475380. . [2] Joung J, Ramm E, Pabo C (2000). "A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions" (http:/ / www. pnas. org/ cgi/ content/ full/ 97/ 13/ 7382). Proc. Natl. Acad. Sci. U.S.A. 97 (13): 7382–7. doi:10.1073/pnas.110149297. PMC 16554. PMID 10852947. . [3] Hurt J, Thibodeau S, Hirsh A, Pabo C, Joung J (2003). "Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection" (http:/ / www. pnas. org/ cgi/ content/ full/ 100/ 21/ 12271). Proc. Natl. Acad. Sci. U.S.A. 100 (21): 12271–6. doi:10.1073/pnas.2135381100. PMC 218748. PMID 14527993. . [4] Fields S, Song O (1989). "A novel genetic system to detect protein-protein interactions" (http:/ / www. nature. com/ nature/ journal/ v340/ n6230/ abs/ 340245a0. html;jsessionid=2F9E056F57E5547D17D2D6658C9B0437) (abstract). Nature 340 (6230): 245–6. Bibcode 1989Natur.340..245F. doi:10.1038/340245a0. PMID 2547163. . Abstract is free; full-text article is not. [5] Verschure P, Visser A, Rots M (2006). "Step out of the groove: epigenetic gene control systems and engineered transcription factors". Adv Genet 56: 163–204. doi:10.1016/S0065-2660(06)56005-5. PMID 16735158. [6] Gietz R.D., Triggs-Raine Barbara, Robbins Anne, Graham Kevin, Woods Robin (1997). "Identification of proteins that interact with a protein of interest: Applications of the yeast two-hybrid system" (http:/ / www. springerlink. com/ content/ t5w6u8667583641p/ ?p=163f5ecf5cff441b940a429da9d83187& pi=0). Mol Cel Biochem 172 (1–2): 67–79. doi:10.1023/A:1006859319926. PMID 9278233. . [7] Whipple F (1998). "Genetic analysis of prokaryotic and eukaryotic DNA-binding proteins in Escherichia coli". Nucleic Acids Res 26 (16): 3700–6. doi:10.1093/nar/26.16.3700. PMC 147751. PMID 9685485. [8] Stagljar I, Korostensky C, Johnsson N, te Heesen S (April 1998). "A genetic system based on split-ubiquitin for the analysis of interactions between membrane proteins in vivo" (http:/ / www. pnas. org/ cgi/ pmidlookup?view=long& pmid=9560251). Proc. Natl. Acad. Sci. U.S.A. 95 (9): 5187–92. doi:10.1073/pnas.95.9.5187. PMC 20236. PMID 9560251. . [9] Fromont-Racine, Micheline; Rain, Jean-Christophe, Legrain, Pierre (1997). "Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens". Nature Genetics 16 (3): 277–282. doi:10.1038/ng0797-277.
    • Two-hybrid screening 8 [10] Lu, L; Horstmann, H, Ng, C, Hong, W (2001 Dec). "Regulation of Golgi structure and function by ARF-like protein 1 (Arl1).". Journal of Cell Science 114 (Pt 24): 4543–55. PMID 11792819. [11] Gommans W, Haisma H, Rots M (2005). "Engineering zinc finger protein transcription factors: therapeutic relevance of switching endogenous gene expression on or off at command" (http:/ / www. rug. nl/ farmacie/ onderzoek/ basiseenheden/ therapeuticgenemodulation/ publicaties/ publicaties2004/ !find?path=/ farmacie/ onderzoek/ basisEenheden/ THErapeuticGeneModulation/ publicaties/ publicaties2004/ 2005_6. pdf& params=as=pdf). J Mol Biol 354 (3): 507–19. doi:10.1016/j.jmb.2005.06.082. PMID 16253273. . [12] Haiyuan Yu et al. (2008). "High-Quality Binary Protein Interaction Map of the Yeast Interactome Network". Science 322 (5898): 104–110. doi:10.1126/science.1158684. PMC 2746753. PMID 18719252. [13] Deane C, Salwiński Ł, Xenarios I, Eisenberg D (2002). "Protein interactions: two methods for assessment of the reliability of high throughput observations" (http:/ / www. mcponline. org/ cgi/ content/ full/ 1/ 5/ 349). Mol Cell Proteomics 1 (5): 349–56. doi:10.1074/mcp.M100037-MCP200. PMID 12118076. . [14] Chen, Y. C.; Rajagopala, S. V.; Stellberger, T.; Uetz, P. (2010). "Exhaustive benchmarking of the yeast two-hybrid system". Nature Methods 7 (9): 667–668; author 668 668. doi:10.1038/nmeth0910-667. PMID 20805792. [15] Koegl, M.; Uetz, P. (2008). "Improving yeast two-hybrid screening systems". Briefings in Functional Genomics and Proteomics 6 (4): 302–312. doi:10.1093/bfgp/elm035. PMID 18218650. External links • Complete Yeast Two-Hybrid Protocol (http://www.singerinstruments.com/index.php?option=com_content& task=view&id=181&Itemid=980) • Detail on sister technique two-hybrid system (http://www.biochem.arizona.edu/classes/bioc568/ two-hybrid_system.htm) • Science Creative Quarterlys overview of the yeast two hybrid system (http://www.scq.ubc.ca/?p=246) • Gateway-Compatible Yeast One-Hybrid Screens (http://www.cshprotocols.org/cgi/content/full/2006/28/ pdb.prot4590) • Video animation of the Yeast Two-Hybrid System (http://www.sumanasinc.com/webcontent/animations/ content/yeasttwohybrid.html) • Two-Hybrid+System+Techniques (http://www.nlm.nih.gov/cgi/mesh/2011/MB_cgi?mode=& term=Two-Hybrid+System+Techniques) at the US National Library of Medicine Medical Subject Headings (MeSH)
    • Article Sources and Contributors 9 Article Sources and Contributors Two-hybrid screening  Source: http://en.wikipedia.org/w/index.php?oldid=508304163  Contributors: A.bit, Alansohn, Alboyle, Anna K., Arcadian, Ariliand, Boku wa kage, Bubbachuck, DChetkovich, DabMachine, Dai mingjie, Danshil, Dekimasu, Drdaveng, Eahd201, Element16, Fixthatspelling, Flyguy649, Gregjohnso, Ilia Kr., Jebus989, Jeffw245, Jesse V., John Broughton, Jopept1, Katieh5584, Lotje, Luna Santin, Medibio, Miguel Andrade, Narayanese, O RLY?, Pbogomiakov, Peteruetz, Pixie, Plindenbaum, RDBrown, Rich Farmbrough, Rjwilmsi, RogerDodger88, Safflle, Seans Potato Business, Serephine, Several Times, Sintaku, Tassedethe, TestPilot, Tide rolls, Tinz, Tobycat, Tony1, Trey314159, Whosasking, Zeyaraun, 70 anonymous edits Image Sources, Licenses and Contributors Image:Two hybrid assay.svg  Source: http://en.wikipedia.org/w/index.php?title=File:Two_hybrid_assay.svg  License: Creative Commons Attribution-Sharealike 3.0,2.5,2.0,1.0  Contributors: Anna Image:Three-hybrid-system.svg  Source: http://en.wikipedia.org/w/index.php?title=File:Three-hybrid-system.svg  License: Creative Commons Attribution-Sharealike 2.5  Contributors: Ilia Kr. License Creative Commons Attribution-Share Alike 3.0 Unported //creativecommons.org/licenses/by-sa/3.0/