The hydrophobic effect and hydrogen bonding interactions have long been considered to be the dominant forces in protein folding. However, the contribution of hydrogen bonds to stabilizing proteins has been difficult to clarify. As the intramolecular hydrogen bonds are formed in place of hydrogen bonds with solvent during folding, measures of stability fail to give a significant change in free energy. Previous studies on hydrogen bonding interactions have shown that they are only marginally important. Three long-range side chain-main chain hydrogen bonds have been found in the alpha subunit of tryptophan synthase (αTS), a (βα)8TIM barrel protein. These long-range noncovalent interactions connect either the N-terminus of one β-strand with the C-terminus of the succeeding and anti-parallel α-helix (F19-D46 and I97-D124) or the N-terminus of an α-helix with the C-terminus of the succeeding β-strand (A103-D130). By analogy, these interactions are designated as βα- or αβ-hairpin clamps. Surprisingly, the removal of any one of these clamp interactions, by replacement of the aspartic acid with alanine, results in significantly decreased thermodynamic stability for the native state and a substantial loss of secondary structure. When compared to several other side chain-side chain and short-range side chain-main chain interactions in αTS, these hairpin clamps clearly play a unique role in the structure and stability of αTS. The generality of these observations for βα-hairpin clamps in TIM barrel proteins was tested by experimental analysis of the clamps in a pair of homologous indole-3-glycerol phosphate synthase (IGPS) TIM barrels of low sequence identity. The results suggest that only the subset of conserved βα-hairpin clamps with hydrogen bond length less than 2.80 Å make substantive contributions to stability and/or structure. Those clamps with longer hydrogen bonds make modest contributions to stability and structure, similar to other types of side chain-main chain or side chain-side chain hydrogen bonds. The role of these clamps in defining the structures of the super-family of TIM barrel proteins was examined by a survey of 71 TIM barrel proteins from the structural database. Conserved features of βα-hairpin clamps are consistent with a 4-fold symmetry, with a predominance of main chain amide hydrogen bond donors near the N-terminus of the odd-number β-strands and side chain hydrogen bond acceptors in the loops between the subsequent α-helices and even-numbered β-strands. In this configuration, the clamps provide an N-terminal cap to odd-number β- strands in the β-barrel. Taken together, these findings suggest that βα-hairpin clamps are a vestigial signature of the fundamental βαβ building block for the (βα)8 motif and an integral part of the basic TIM barrel architecture. The relative paucity of βα-hairpin clamps remaining in TIM barrel structures and their variable contributions to stability imply that other determinants for structure and stability of the barrel have evolved to render a subset of the clamp interactions redundant. Distinct sequence preferences for the partners in the βα-hairpin clamps and the neighboring segments may be useful in enhancing algorithms for structure prediction and for engineering stability in TIM barrel proteins.

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RNAs have become increasingly recognized as possible drug targets due to their involvement in important biochemical functions, as well as their unique but well-defined structures. Recently published crystal structures depict the binding of a series of aminoglycosides- or more specifically- 2-deoxystretamine (2-DOS), the most preserved central scaffold of aminoglycosides, to a conserved 5'-GU-3'region on their target RNAs. A novel unnatural γ-amino acid, 1, has been synthesized using 2-deoxystreptamine as a template through structure-based rational design. The unnatural amino acid has been designed to replace a glycosidic linkage with an amide bond, which may limit the promiscuous binding characteristics of aminoglycosides through increased rigidity of the ligands and additional hydrogen bonding. The binding selectivity and affinity will be studied in the future through a fluorescence assay.

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Ion exchange chromatography (IC) is an analytical technique used to separate charged molecules including ions, proteins, small nucleotides, and amino acids. It can function in anion or cation mode. In this dissertation, anion exchange chromatography was used, and column materials were made in our lab with resorcinarene-based compounds called cavitands. Cavitands create cavities to bind to molecules because of their three-dimensional structure. Two new gradient IC methods were established to identify and quantify perrhenate and perfluoroalkyl substances (PFAS) by customized resorcinarene-based column, zinc cyclen resoecinarene (ZCR) and arginine methyl ester (RUE) columns. The ZCR column accomplished outstanding separation of perrhenate from other anions such as chloride and sulfate by using a gradient elution of 2-60 mM NaOH. There was a logarithmic relationship between the perrhenate concentration and its retention time. In addition to separating anions, the ZCR column was able to preconcentrate perrhenate with over 90% recovery in different conditions. RUE was successfully synthesized and attached to polystyrene resin and used in IC to separate the PFAS, perfluorobutanoic acid (PFBA), perfluoropentanoic acid (PFPeA), perfluorobutanesulfonic acid (PFBS), perfluorohexanoic acid (PFHxA), perfluorohexanesulphonic acid (PFHxS), and perfluorooctanoic acid (PFOA). The sample preparation for the PFAS was simple and only needed filtration. A gradient method starting with 70 mM NaOH and going to pure water was necessary to separate the PFAS. There was no detectable PFAS in Provo tap water and Utah Lake water by our method. Although the LOD and LOQ of PFAS were not as low as the existing methods, the IC method does not require complicated sample preparation steps to separate and quantify PFAS. Binding studies of RUE and RUA were done with organic acids, including citric, malic, and succinic acid, and PFAS including PFBA, and PFHxA. The strongest binding was for L-malic acid followed by succinic acid, D-malic acid, pentanoic acid, citric acid, and dimethyl L-malate. RUE displayed some chiral recognition between L-malic acid and D-malic acid. Unfortunately, it did not show significant differences in binding between the different PFAS even though RUE had been able to separate them by IC.

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