Pseudomonas aeruginosa ᴅ-arginine dehydrogenase (PaDADH) is a flavin-dependent enzyme. The enzyme catalyzes the oxidative deamination of a broad range of ᴅ-amino acids to their corresponding imino-acids, which are non-enzymatically hydrolyzed to α-keto-acids and ammonia. A46, S45 and I335 residues are located in flexible loops, which form a flask-like substrate-binding pocket. In this study, I335, A46, and S45 were mutated to histidine, glycine, and alanine, respectively and individually, through site-directed mutagenesis, to investigate their role in binding and catalysis in PaDADH. The results showed that A46 and S45 residues participate in the optimal orientation of the substrate α-amino group and I335 modulate the active site flexibility.

A novel approach of using near infrared region (NIR) dyes is applied to elucidate the binding interaction between human serum albumin (HSA) and mangiferin (MGF). HSA is a blood carrier protein used for drug delivery, while mangiferin is a natural polyphenol found in mangoes that possesses numerous beneficial health properties. The NIR dyes are used as a probe to investigate MGF binding interaction with HSA via monitoring fluorescence of Trp-214 residue. Molecular modeling is used for docking and semi-empirical analysis. The investigation of the binding interaction between Trp-214 and MGF is significant, for it may offer broader pharmacological insight and applications for the polyphenol. Mangiferin in proposed to bind with a 2:1 stoichiometric ratio with HSA to the Trp-214 residue in subdomain IIA and another possible binding site to be determined in future studies. Spectral changes suggest a stabilized protein conformation upon mangiferin binding with the addition of NIR dye E-06 and MHI-06.

Transient change of cytosolic calcium level leads to physiological actions, which are modulated by the intracellular calcium stores, and gated by membrane calcium channels/pumps. To closely monitor calcium dynamics there is a pressing need to develop calcium sensors that are targeted to high calcium environment such as the ER/SR with relatively low binding affinity and fast kinetic properties to complement the current calcium indicator toolkits. In this dissertation, the development of fast red florescent calcium binding protein using the protein design is reported. The results show the calcium dependent fluorescence increase of mCherry mutant MCD1 (RapidER) and MCD15 (RapidER’) is able to monitor the ER calcium release in several cell lines responding to perturbations of extracellular calcium signaling. The specific targeting to the ER membrane was achieved by fusing the ryanodine receptor 1 transmembrane domains for the spatio-temporal calcium imaging. To understand the underlying mechanism of calcium binding induced fluorescence increase in the designed calcium sensor CatchER, the fluorescence lifetime of CatchER was determined in calcium free and bound forms using time resolved florescence spectroscopy. The results suggest that calcium binding inhibits the geminate quenching, resulting in a longer lifetime when the anionic form is indirectly excited at 395 nm. It is believed that such unique calcium-induced lifetime change can be applied to monitor calcium signaling in cell imaging. NMR spectroscopy was used to investigate the protein-protein/ligand interaction in this dissertation. The residual dipolar coupling and T1, T2, NOE dynamic study were carried out to understand the binding mode of CaM and the N-terminal intracellular loop of connexin 43. The results show that both N and C terminal domains of Ca2+-CaM contact with the peptide, leading to a partially unwound and bending central helix of CaM. The ligand binding induced conformational change was demonstrated by selectively labeled proteins including extracellular domain of calcium sensing receptor and the bacterial membrane protein SecA fragments C34 and N68.

Phenazines and heterocyclic N-oxides have proven to be interesting classes of antitumoral as well as antibiotic agents . The natural product myxin (1-hydroxy-6-methoxyphenazine- N5, N10-dioxide) which belongs to both of these unique classes of molecules, has been found to cause bio-reductively activated, radical-mediated DNA strand cleavage via a de-oxygenative mechanism, making it a potential anti-tumoral as well as anti-bactierial candidate. In order to investigate as well as improve the bioactive properties of myxin, the following study was designed to synthesize glycosylated myxin analogs. A small catalog of these compounds were synthesized, some of them exhibiting comparable biological activity to that of myxin.

The function of the metalloenzymes is mainly determined by four structural features: the metal core, the metal binding motif, the second sphere residues in the active site and the electronic statistics. Cysteamine dioxygenase (ADO) and cysteine dioxygenase (CDO) are the only known enzymes that oxidize free thiol containing molecules in mammals by inserting of a dioxygen molecue. Both ADO and CDO are known as non-heme iron dependent enzymes with 3-His metal binding motif. However, the mechanistic understanding of both enzymes is obscure. The understanding of the mechanistic features of the two thiol dioxygenases is approached through spectroscopic and metal substitution in this dissertation. Another focus of the dissertation is the understanding of the function of a second sphere residue His228 in a 3-His-1-carboxyl zinc binding decarboxylase α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD). ACMSD catalyzes the decarboxylation through a hydrolase-like mechanism that is initialized by the deprotonation of metal bounded water molecule. Our study reveled that the second sphere residue His228 is responsible for the water deprotonation through hydrogen bonding. The spectroscopic and crystallographic data showed the H228Y mutation binds ferric iron instead of native zinc metal and the active site water is replaced by the Tyr228 residue ligation. Thus, we concluded that, H228Y not only plays a role of stabilizing and deprotonating the active site water but also is an essential residue on metal selectivity.

Protein translocation is essential for bacterial survival and the most important translocation mechanism in bacteria is the secretion (Sec) pathway. Thus targeting Sec pathway is a promising strategy for developing novel antibacterial therapeutics. We report the design, syntheses, mechanistic studies and structure-activity relationship studies using HQSAR and 3-D QSAR Topomer CoMFA analyses of 4-oxo-5-cyano thiouracil derivatives. In summary, introduction of polar group such as –N3 and linker groups such as –CH2-O- enhanced the potency as well as logP and logS several fold. We also report the discovery, optimization and structure-activity relationship study of 1,2,4-triazole containing pyrimidines as novel, highly potent antimicrobial agents. A number of inhibitors have been found to inhibit microbial growth at high nanomolar concentrations.

The interaction of small molecules with DNA has been extensively studied and has produced a large catalogue of molecules that non-covalently bind to DNA though groove binding, intercalation, electrostatics, or a combination of these binding modes. Anthracene, acridine, and carbocyanine-based chromophores have been examined for their DNA binding properties and photo-reactivities. Their planar aromatic structures make them ideal chromophores that can be used to probe DNA structural interactions and binding patterns. We have studied DNA binding and photocleavgage properties of a bisacridine chromophore joined by a 2,6-bis(aminomethyl)pyridine copper-binding linker (Chapter II), a series of 9-aminomethyl anthracene chromophores (Chapters III and IV), both under conditions of high and low ionic strength, as well as a series of pentamethine linked symmetrical carbocyanine dyes (Chapter V). In Chapter II we present data showing that high ionic strength efficiently increases copper(II)-dependent photocleavage of plasmid DNA by the bisacridine based chromophore (419 nm, pH 7.0). In Chapters III and IV, using an pyridine N-substituted 9-(aminomethyl)anthracene (Chapter III), a bis-9-(aminomethyl)anthracene, and its mono 9-(aminomethyl)anthracene analogue (Chapter IV), pUC19 plasmid DNA was photo-converted to highly diffuse DNA fragments (350 nm, pH 7.0) in the presence of 150 mM NaCl and 260 mM KCl. Spectroscopic analyses suggest that the combination of salts promotes a change in DNA helical structure that initiate a switch in anthracene binding mode from intercalation to an external or groove binding interactions. The alteration in DNA structure and binding mode leads to an increase in the anthracene-sensitized production of DNA damaging reactive oxygen species. Finally, in Chapter V, pUC19 plasmid DNA is converted to its nicked circular and linear forms following irradiation of a series of pentamethine linked symmetrical carbocyanines (red light, pH 7.0). The data suggest that the relative levels of photocleavage arise from the different substituents on the nitrogen alkyl side chain and the pentamethine linker.

Kinetic studies determining the second order rate constants for the monoepoxidation of cyclic dienes, 1,3-cyclohexadiene and 1,3-cyclooctadiene, and the epoxidation of cis-/trans-2-hexenes by dimethyldioxirane (DMDO) were carried out using UV methodology. Consistent with published results, the kinetics of cis-/trans-2-hexenes by DMDO showed greater reactivity of the cis-isomer compared to that of the trans-compound. Molecular modeling studies for the epoxidation of a series of cis-/trans-alkenes, by DMDO were carried out using the DFT approach. The mechanism of epoxidation by DMDO was modeled by determining the transition state geometry and calculating the electronic activation energies and relative reactivities. The calculations were consistent with a concerted, electrophilic, exothermic process with a spiro-transition state for all cases. Kinetic studies for the monoepoxidation of the cyclic dienes showed a greater reactivity for 1,3-cyclohexadiene compared to that for 1,3-cyclooctadiene. The DFT method was employed to successfully model the transition state for the monoepoxidation of the cyclic dienes by DMDO and successfully predict the relative reactivities. Student misconceptions, at the high school and/or middle school level involving energy changes and chemical reactions have been prevalently noted in literature (by ACS and AAAS). Two examples of these misconceptions are: 1) heat is always needed to initiate a chemical reaction and 2) all chemical reactions create or destroy energy. In order to address these types of misconceptions, an educational module detailing the influence of energy changes on chemical reactions has been developed in conjunction with the Bio-bus program for middle and high school students. Visual aids and hands-on activities were developed in the module to potentially help students overcome/deal with the common misconceptions. Surveys were designed to access the situations (determine the extent of the misconceptions) and the effectiveness of the educational module, before and immediately after the module and one-month later to determine retention. The educational module has been presented to approximately 100 high school students from underrepresented communities. Pre-survey data confirmed the presence of the common misconceptions reported in the literature. Data from the post-survey indicated the new instructional module enhanced the student’s interest of science and expanded their content knowledge and laboratory skills. The post-survey data (immediately following the module) showed a significant difference in two out of five misconceptions when compared to the pre-survey data. However, this significance decreased when the 1-month post-survey data were compared to the pre-survey data.

The use of cyanine dyes in bioanalytical applications has become a widely explored topic of interest in chemistry. Their ability to absorb and fluoresce in the UV-visible and near-infrared region of the electromagnetic spectrum benefits their use as imaging probes and fluorescent labels due to the reduced auto-fluorescence from biological molecules. The behavior of these dyes lies in their structure which consists of two nitrogen containing heterocycles joined by an electron deficient polymethine bridge that allows specific energy transitions to occur. The first portion of this work aims to explore dye functionality for analytical applications regarding the non-covalent labeling of bovine serum albumin. The second portion of the work explores dye interactions with human serum albumin in biological membrane mimetic environments using the ternary system of sodium dioctyl sulfosuccinate (AOT) in water and n-heptane.

The 5-HT7 receptor is the most recent addition to the 5-HT receptor family and has been linked to a variety of physiological and pathophysiological processes. Well established antide-pressant pharmaceuticals have recently been found to activate the 5-HT7 receptor, supporting the role of the 5-HT7 receptor in the antidepressant mechanism. The synthesis of potent selec-tive 5-HT7 receptor antagonists could afford a greater understanding of the 5-HT7 receptor function as well as lead to potential drug candidates. The synthesis of unfused biheteroaryl derivatives as 5-HT7 receptor ligands has been de-scribed within. These compounds have been tested for biological activity on the 5-HT6 and 5-HT7 receptors. 4-(3’-Furyl)-2-(N-substituted-piperazino)pyrimidines were found to be potent 5-HT7 receptor ligands. 4-(2’-Furyl)-2-(N-substituted-piperazino)pyrimidines have shown high se-lectivity for the 5-HT7 receptor over the 5-HT6 receptor.