Following initiation of protein synthesis, the nascent polypeptide must journey through the exit tunnel of the ribosome. Although this has typically been deemed a passive process, it is established that certain peptide sequences interact with rRNA components and ribosomal proteins lining the walls of the tunnel to bring protein synthesis to a complete halt. In many cases, translational arrest is dependent upon the presence of a small cofactor – such as an amino acid or an antibiotic – acting in concert with the specific peptide being synthesized.In order to gain a deeper insight into the process of nascent chain-mediated translational arrest, I propose to focus on two complementary objectives:First, I will obtain high-resolution structures of ribosome nascent chain (RNC) complexes by X-ray crystallography in order to understand the mechanistic aspects of this process. Current strategies for preparing RNC complexes rely on cell-free expression systems and produce samples of varying quality and unknown stoichiometry. Here, I propose to prepare peptidyl-tRNAs by attaching chemically synthesized peptides onto tRNAs expressed in vivo, using small RNA enzymes known as a flexizymes. Peptidyl-tRNAs obtained in this manner will be added to the ribosome in trans to obtain RNC complexes, thereby sidestepping some of the problems that result from ribosomal peptide synthesis in cis.Second I will explore the functional diversity of nascent chain-mediated arrest by developing an in vitro selection/evolution method that will enable the identification of cis-regulatory nascent peptides capable of inhibiting the ribosome with the help of small molecules. By integrating the structure and sequence data obtained from our studies, we will develop a predictive algorithm for identifying regulatory peptide sequences within genomic data and we will begin to assess the biological extent and distribution of nascent chain-mediated events in a systematic manner.