Cell-based arrays for the identification of interacting polypeptide domains or epitopes

The specific regions on proteins which are responsible for protein-protein interaction are called interacting domains, or epitopes in case of antigen-antibody binding. These domains are one feature to characterize proteins and are important in clinical diagnostics and research. For the mapping of such domains the use of protein/peptide arrays has become popular. Regardless of which kind of array, the major requirements are a high number of candidates arranged in the array, high quality, ease of use, and cost-effectiveness. Here, the authors describe a general protocol for mapping the interacting domains of proteins demonstrated by a high affinity protein interaction, the interaction of an antibody to an antigen. The chapter describes a stepwise protocol from library production to the verification of the domain by the use of an automated cell-based polypeptide array, which comprises the named requirements of a good array.