What are the common methods used to analyze protein interactions?

Common methods used to analyze protein interactions include co-immunoprecipitation (Co-IP), label transfer, crosslinking, pull-down assays, and far-western blot analysis. 

1. Co-IP is a technique for protein interaction discovery. Its procedure is essentially the same as an immunoprecipitation of a single protein, except that the target protein precipitated by the antibody is utilized to co-precipitate a binding partner/protein complex from a lysate. In simpler terms, the interacting protein is bound to the target antigen, which is bound by the antibody which is immobilized to the support. These immunoprecipitated proteins and their ligands are typically detected by SDS-PAGE and western blot. 
2. Pull-down assays use beaded support to purify interacting proteins (like Co-IP does). The difference between these two techniques is that pull-down assays utilize a “bait” protein to purify any protein that binds to the bait. These assays are excellent for studying strong or stable interactions or those when no antibody is accessible for Co-IP.
3. Crosslinking interacting proteins is a method to stabilize or permanently adjoin the components of interaction complexes. Once the parts of an interaction are covalently crosslinked, other steps such as affinity purification, or cell lysis can be used to analyze the protein-protein interaction, while keeping the original interaction complex. 
4. In far-western blot analysis, protein-protein interactions are detected by incubating electrophoresed proteins with a tagged bait protein. This differs from a western blot analysis which uses a target protein-specific antibody instead. 
5. Label transfer involves crosslinking interacting molecules with a labeled crosslinking reagent and then cleaving the linkage between the two molecules so that the label remains attached to the prey protein. This technique is significant because of its capability to identify proteins which interact weakly with the target protein.