| Site-specific chemical tagging of proteins is a precursor to many structurally-focused biological studies by NMR and mass spectrometry. In particular, reductive methylation is a well-known approach to incorporate methyl groups onto lysine and N-terminal amines in proteins. Interestingly, the NMR spectra of reductively dimethylated lysine residues are often complex, due to methyl inequivalence and chemical exchange. Whereas prior studies on small molecules have eluded to some of the underlying exchange processes, the fundamental origins of methyl inequivalence for dimethyllysines have been largely neglected. Furthermore, prior to this thesis, no comprehensive model had been proposed which encapsulates all elements of the exchange phenomena, showing how they are interconnected and give rise to experimentally observed NMR spectra of reductively methylated proteins. The first part of this thesis addresses the methyl exchange for both small molecule substituted dimethylamines and for dimethylamino groups in proteins and should therefore be useful for better understanding methyl spectra of reductively methylated proteins as well as methyl NMR spectra in general.;The methodology described in this thesis extends the repertoire of techniques for designing new chemical tags for NMR applications, for site-specifically labeling proteins, and demonstrates NMR-based approaches to studying disease-relevant chemical exchange processes, characterizing conformational intermediates, and for understanding how biophysical characterization of side chain dynamics and kinetic processes can give insight into structure-function relationships in proteins.;The second half of this thesis is primarily concerned with the application of 19F NMR toward the study of protein chemical exchange as well as the design of novel 19F tags for site-specific labeling of amino acid side chains. The former pertains to a study of exchange between monomeric and oligomeric states of the toxic PrPSc form of the prion protein, which has implications for understanding the mechanisms responsible for aggregation and pathogenesis. The subsequent two chapters describe a computational method for the design of highly-sensitive 19F chemical tags and also introduce a new general bioconjugation strategy for chemically modifying amino groups with reactive indoles, with an emphasis on 19F NMR applications. The final chapters introduce a cross-saturation, spin-diffusion-based technique that allows for the detection of subtle conformational changes in proteins. |
