Biomolecular recognition is one of the cornerstones of biotechnology, and though the importance of binding strength (affinity) is appreciated, the interplay of molecular specificity in biological systems (e.g., protein interaction networks) is not well understood. The primary objectives of the proposed research are to develop new methodologies that enable discovery and engineering of highly-specific biomolecular recognition elements, and to elucidate mechanisms through which biomolecules achieve high specificity interactions. A new framework for investigating and engineering specificity is proposed that uses two new biotechnologies developed by the PI. First, an in vitro approach utilizing bacterial display peptide library technology in conjunction with cell sorting instrumentation will be developed and applied to generate protein-binding peptides with optimal specificity. Second, a mammalian cell two-hybrid system will be developed using Forster resonance energy transfer, and applied to detect and screen for specific recognition inside living cells. The peptides resulting from these approaches will be investigated in a protein-detecting microarray format. Such technology is likely to extend current capabilities in systems biology, medical diagnostics and proteomics, and basic research. The educational component of this work aims to disseminate molecular specificity concepts and current research to young students through integration into graduate curriculum via "Biomolecular Science and Engineering," and through a new first-year undergraduate student colloquium entitled "Biotechnology Controversies." The colloquium aims to augment students' scientific literacy, communications skills, and awareness of controversial issues in biotechnology.
