Structural Relay Methods for Functional Peptide Discovery

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DESCRIPTION (provided by applicant): Oligopeptides have many functions in biology, including providing binding selectivity that allows proteins to traffic to the proper place in the ell, between cells, within tissues, and throughout the organism. This trafficking function is becoming more and more important to the development of new therapeutic and diagnostic agents, as the requirements for the control of off-target effects are becoming ever more stringent and the delivered agents ever more expensive. However, trafficking is hard to do, mostly because it is a multivariate problem, and so is beyond our capabilities of rational design. We propose to bring powerful tools of molecular evolution to bear on the delivery of agents that do not carry genetic information. We will develop a new three-step method to identify peptides that carry desired cargoes into cells or to particular cellular organelles. The method relies on the ability of the SELEX technique (systematic evolution of ligands by exponential enrichment) to create DNA sequences that bind selectively to any particular peptide, and the ability of phage display to identify peptides that bind to any DNA molecule. With such tools in hand, we will prepare libraries of peptides bound to the cargo of interest, and incubate them with cells of interest. A very small fraction of that molecular population can be expected to traffic to the desired destination, such as the cytoplasm, mitochondria, or nucleus. Isolation of that cellular material accomplishes the separation of the desired peptide(s) from the rest of the candidates, but in very small amounts. No technique is currently available that will allow one to identify such peptides if the cargo does not code for the identity of the peptide. We hope that the sequential use of the SELEX and phage display techniques will allow the functional peptides to be detected and the information of their identities "amplified" so that they can be identified, resynthesized, and tested. If successful, these studies should lead to a general method to discover functional oligopeptides in a wide variety of settings and applications.