Many protein-protein interactions are mediated by peptide recognition modules, compact domains that bind to short peptides and play a critical role ina wide array of biological processes.Recent experimental protein interaction data provide us with an opportunity to examine whether we may explain or even predict their interactions by computational sequence analysis.
The design of protein-peptide interactions has a wide array of practical applications and also reveals insight into the basis for molecular recognition.
The simplest method for identifying the binding partners of a peptide is to use it as bait in an affinity pull-down experiment, and then detect its binding proteins directly. Pull-down assays are useful both for confirming the protein-protein interactions that were predicted using other techniques (e.g., co-immunoprecipitation) and also as initial screening tools to identify novel protein-protein interactions. Synthetic peptides are commonly used to verify suspected protein-protein interactions by disrupting the binding competitively. Biotinylated peptides, which contain a specific functional domain, and their corresponding control native peptides are immobilized to avidin-conjugated resins. Samples are incubated with the resins. Then wash the resins to remove any unbound proteins. The bound proteins are eluted and analyzed using SDS-PAGE. The amount of modified versus unmodified bound peptide can then be compared to identify specific functions.
Related Journals of Protein Peptide Interactions
Bioengineering & Biomedical science Journals, Proteomics & Bioinformatics, Cell Science & Therapy, Cellular & Molecular Biology, Protein Engineering Design and Selection, Advances in Protein Chemistry, Amino Acids, Peptides and Proteins.