His-Asp signaling systems are ubiquitous in bacteria, archaea, and certain plants and fungi. Little structural information is known about the protein-protein interactions within these signaling pathways, leaving an incomplete picture of how these essential systems operate. In this dissertation, the focus of my work in the West laboratory was the receiver domain of the fungal response regulator protein Ssk1, and its interaction with the histidine phosphotransfer protein Ypd1. In Saccharomyces cerevisiae (Sc), Ypd1 interacts with receiver domains from upstream Sln1 and downstream Ssk1 on a common hydrophobic docking site. The main portion of this thesis presents the co-crystal complex of Ypd1 and Ssk1-R2W638A and the accompanying analysis to explain key differences in the physiological functions of Ssk1-R2 and Sln1-R1. Protein-protein interactions were characterized using a newly developed fluorescence binding assay and in vitro 32P-phosphotransfer experiments. In addition, the co-crystallization of Ssk1-R2W638A and a point mutant of Ypd1 (Ypd1-G68Q) is described. Ssk1 protein constructs from the human pathogen Cryptococcus neoformans (Cn) were designed in order to biochemically characterize interactions with C. neoformans Ypd1, but these proteins were either insoluble or inactive. Lastly, my work in the Cichewicz laboratory describes the discovery of three new secondary metabolites from a previously uncharacterized microbial mat fungus (clearanols C, D and E).