The development of new methods that provide mechanistic information on the structural dynamics of proteins represents a significant challenge in the field of biochemistry. Fluorescence spectroscopy is a highly sensitive technique that is ideally suited for monitoring protein movement in situ. However, the most commonly used fluorophores generally yield poor structural resolution, due to their relatively large size compared to the protein of interest. Research in our laboratory has demonstrated that a thioamide, a single atom-substitution of the peptide backbone, is capable of quenching a wide array of fluorophores in a distance-dependent fashion. We have shown that thioamide quenching of tyrosine and tryptophan can be used to monitor biological interactions, such as ligand binding to the protein Calmodulin (CaM). To expand the utility of the thioamide group as a spectroscopic probe, our laboratory has developed semi-synthesis techniques for its installation into full-length proteins. Having validated thioamide quenching of intrinsic protein fluorescence in our model system, we then applied this technique to monitoring the misfolding of the amyloidogenic protein α- synuclein (αS), implicated in the pathogenesis of Parkinson's Disease. In order to determine which of our spectroscopic pairs best behaves in accordance with our theoretical models, we also examined thioamide quenching of Cnf using our CaM model system. For intramolecular studies with Cnf/thioamide FRET pairs, we combined unnatural amino acid mutagenesis with native chemical ligation to access double-labeled αS using a minimum of chemical synthesis. We have also shown that we can combine unnatural amino acid mutagenesis with expressed protein ligation at methionine to incorporate the probe pair in an entirely traceless manner. Using thioamide/Cnf FRET of our constructs, we were able to monitor conformational changes of monomeric αS with unprecedented structural resolution. In addition to our work using thioamides, we have also developed efficient strategies for producing variants of singly and doubly-labeled αS containing red-shifted fluorophores for fluorescence polarization (FP) and other FRET based assays, respectively. Most recently, we have shown that we can use site specifically labeled αS in conjunction with FP to glean mechanistic insight into the processes of aggregation and disaggregation. Ultimately, these labeled constructs will allow us to study these processes in vivo.