Interactions between proteins can be classified into the following groups:
Based on affinity protein-protein interactions can be called either obligate or non-obligate:
Obligate are unstable unless they are reacting and forming protein complexes and non-obligate where the protein is sufficient and can exist individualistically.
Non-obligate interactions can further be divided based on the complex stability they form into permanent and transient. The majority of the obligate interactions fall under the permanent category and most of the non-obligate interactions fall under the transient category.
Transient interactions are further divided into strong and weak interactions.
Protein-protein interaction detection:
Protein-protein interactions can be detected by various methods that can be classified into three groups such as in vitro techniques, in vivo techniques, and in silico techniques.
In vitro techniques:
In in-vitro techniques, the procedure is carried outside the cell in a condition where all the parameters are controlled. The common techniques involved in in-vitro detection of protein interactions are affinity chromatography, co-immunoprecipitation, microarray, and so on.
1. Affinity chromatography:
This method is considered to be highly accurate as it can detect even the slightest of interactions and also checks the protein interaction with the protein present in the column. Due to its high specificity, it can give false results at times as a result of protein interaction inside the column although the protein does not take part in the cell mechanism. It can be carried out along with SDS-PAGE and mass spectroscopy for better results.
2. Co-immunoprecipitation:
This technique uses an entire cell extract to confirm protein interactions and the proteins exist in their native structure along with other cell constituents that are required to carry out protein interactions successfully. If eukaryotic cells are used, it will allow post-translational modifications that may be significant in interactions.
3. Microarrays:
Protein microarray analysis is a powerful technique for protein detection, monitoring protein expression, and investigating the interaction of protein and its function. The apparatus of the protein microarray consists of a piece of glass that has different protein molecules attached to it at different locations in a particular order.
In vivo techniques:
In vivo techniques make use of yeast two-hybrid methods (Y2H and Y3H) and it determines the protein-protein interactions. To perform its function, Y2H needs to have two domains of proteins that will perform their designated functions. The first domain is the binding domain for DNA that will facilitate DNA binding and the second domain is responsible for the activation of DNA transcription.Y2H recognizes any protein-protein interactions directly between any pair of protein.
In silico techniques:
There are various in silico techniques that help us establish the interactions determined by different experiments. In silico techniques involves various methods of prediction such as based on sequence, based on structure, phylogenetic analysis, the proximity of chromosomes, and so on.
1. Based on structure:
This method helps us in protein-protein interaction prediction if the proteins in question have the same structure. For example, if there are two interacting proteins A and B, there might be some other two proteins with structural similarity with proteins A and B; this can imply that these two proteins can also interact with each other just like proteins A and B do. The main step in this is to determine the structure of the protein of interest as many proteins may not have already known structures.
2. Based on the sequence:
In this method, protein-protein interactions are predicted based on the interactions already known according to their homology of sequence. This method is based on the hypothesis that if an interaction is observed in one species, the same interaction can be expected in other species too.
3. Phylogenetic analysis:
This method is useful in determining the evolutionary pattern of a protein. Based on the mirror tree approach, it can be said that the proteins interacting with each other appear to be similar in a phylogenetic tree as a result of coevolution through various interactions.
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