Epitope mapping protein-peptide interactions

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Peptides, for example, are needed for the production of antibodies and for epitope mapping proteins can be produced in radioactively labelled forms by in vitro translation for studies of protein-protein interactions and other applications. In vitro protein synthesis is a technique that can be readily carried out in any biochemistry laboratory, whereas peptide synthesis, like peptide sequencing, is a specialist technique using dedicated equipment, which is nowadays routinely automated. 

Another simple approach for the detection of noncovalent interactions is to compare the peptide maps produced by proteolysis of the target protein and its complex with other ligands. This approach, also known as epitope mapping, relies on the fact that the two maps differ qualitatively because the contact regions of the interacting proteins are shielded from the protease s activity in the complex. An illustrative example is the detection of protein-protein interaction between a protein representing the kinase inhibitory domain of the cell cycle regulatory protein (p21-B) and cyclin-dependent kinase 2 (cdk).164... 

Bialek, K., Swistowski, A., and Frank, R. (2003) Epitope-targeted proteome analysis towards a large-scale automated protein-protein-interaction mapping utilizing synthetic peptide arrays. Anal. Bioanal. Chem. 376, 1006-1013. 

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