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| Approach |
Technique |
Summary |
|
| In vitro | Tandem affinity purification-mass spectroscopy (TAP-MS) | TAP-MS is based on the double tagging of the protein of interest on its chromosomal locus, followed by a two-step purification process and mass spectroscopic analysis |
|
Affinity chromatography |
Affinity chromatography is highly responsive, can even detect weakest interactions in proteins, and also tests all the sample proteins equally for interaction |
| Coimmunoprecipitation | Coimmunoprecipitation confirms interactions using a whole cell extract where proteins are present in their native form in a complex mixture of cellular components |
| Protein microarrays (H) | Microarray-based analysis allows the simultaneous analysis of thousands of parameters within a single experiment |
| Protein-fragment complementation | Protein-fragment complementation assays (PCAs) can be used to detect PPI between proteins of any molecular weight and expressed at their endogenous levels |
| Phage display (H) | Phage-display approach originated in the incorporation of the protein and genetic components into a single phage particle |
| X-ray crystallography | X-ray crystallography enables visualization of protein structures at the atomic level and enhances the understanding of protein interaction and function |
| NMR spectroscopy | NMR spectroscopy can even detect weak protein-protein interactions |
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| In vivo | Yeast 2 hybrid (Y2H) (H) | Yeast two-hybrid is typically carried out by screening a protein of interest against a random library of potential protein partners |
| Synthetic lethality | Synthetic lethality is based on functional interactions rather than physical interaction |
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| In silico | Ortholog-based sequence approach | Ortholog-based sequence approach based on the homologous nature of the query protein in the annotated protein databases using pairwise local sequence algorithm |
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Domain-pairs-based sequence approach |
Domain-pairs-based approach predicts protein interactions based on domain-domain interactions |
| Structure-based approaches | Structure-based approaches predict protein-protein interaction if two proteins have a similar structure (primary, secondary, or tertiary) |
| Gene neighborhood | If the gene neighborhood is conserved across multiple genomes, then there is a potential possibility of the functional linkage among the proteins encoded by the related genes |
| Gene fusion | Gene fusion, which is often called as Rosetta stone method, is based on the concept that some of the single-domain containing proteins in one organism can fuse to form a multidomain protein in other organisms |
| In silico 2 hybrid (I2H) | The I2H method is based on the assumption that interacting proteins should undergo coevolution in order to keep the protein function reliable |
| Phylogenetic tree | The phylogenetic tree method predicts the protein-protein interaction based on the evolution history of the protein |
| Phylogenetic profile | The phylogenetic profile predicts the interaction between two proteins if they share the same phylogenetic profile |
| Gene expression | The gene expression predicts interaction based on the idea that proteins from the genes belonging to the common expression-profiling clusters are more likely to interact with each other than proteins from the genes belonging to different clusters |
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