Thesis advisor: Steven D. Bruner / Thesis advisor: Larry W. McLaughlin / Nonribosomal peptides are therapeutically important natural products produced through pathways that utilize large multimodular enzymes, termed nonribosomal peptide synthetases (NRPSs). Central to the assembly line methodology, the monomer building blocks and the growing polymer chain are covalently linked to dedicated peptidyl carrier protein domains as phosphopantetheinyl thioesters. Although structures of multidomain NRPS fragments have been solved recently, the active conformation of the carrier domains with their attached phosphopantetheinyl arms has not been determined. Significant conformational changes in carrier domains are likely to occur as the domains shuttle peptidyl phosphopantetheinyl thioesters between the active sites of the partner domains. This thesis focuses on the application of the synthetic isosteric non-hydrolyzable CoA analogs to manipulate carrier domain geometry of NRPS assemblies through. The synthetic conjugates are designed to deliver an inhibitor moiety to a domain of interest. Using this strategy, various complexes have been designed to direct the phosphopantetheinyl arm to active sites of adenylation domains and thioesterase domains in catalytically relevant conformations. The structurally restrained multidomain NRPS assemblies are useful for elucidating the complex structure and mechanism of NRPSs. An X-ray crystal structure of a peptidyl carrier-thioesterase NRPS didomain fragment from enterobactin synthetase has been solved with a phosphopantetheinyl analog which forms a cross-link between the two domains. This structure provides, for the first time, detailed insights into the phosphopantetheinyl arm interaction with an NRPS partner domain, as well as an active confirmation of a mutidomain NRPS in the holo-form. In addition, the hydrolytically stable CoA analogs have been successfully used as probes in the structural and mechanistic study of a CoA-utilizing enzyme DpgC, a unique cofactor-independent dioxygenase involved in vancomycin biosynthesis. / Thesis (PhD) — Boston College, 2009. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.