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Chlamydia pneumoniae is a Gram-negative, intracellular bacterium which utilizes a type III secretion system for virulence. This system injects virulence associated proteins into a host cell and ultimately hijacks host intracellular machinery required for the bacteria to propagate and reproduce. Chlamydia outer protein N or CopN (Cpn0324), is a member of a family of proteins found in pathogenic bacteria, which inhibits premature secretion of effector proteins by plugging the base of the injectisome. The lack of a genetic system to manipulate the bacteria hampers the identification of proteins within the T3S field. The work presented in this thesis establishes the role of CopN as the plug protein of Chlamydia pneumoniae, and examines protein interactions within the individual CopN domains. The structure of CopN was first explored by limited proteolysis to establish the domain boundaries. We found three domains, an N-terminal, central domain, and C-terminal domain. Next, we used the full length protein as well as a series of truncations to examine the interactions within each domain. Using a subset of the known protein interactions between CopN and other T3S proteins, we found that the proposed chaperones Scc1 and Scc4 bind in the N-terminal region. There were no apparent interactions in the central domain, whereas FliI, FliF, CopD1158-206 and Scc3 all bound within the C-terminal region of CopN. Finally the secretion of CopN in a HeLa cell model was addressed throughout the course of an infection. CopN was detected in the host cell immediately after infection, and then was not detectable again until late infection. Overall, I have characterized the individual domains of CopN and present data to support the role of CopN as the plug protein in the T3SS of Chlamydia pneumoniae. Master of Science (MSc)