Thesis (Ph. D.)--University of Missouri--Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 103-117). Also issued on the Internet.

P. aerguinosa is a serious human bacterial pathogen. This thesis describes attempts to use structural biology to identify new starting points for drugs against P. aerguinosa .A number of fragment-based screening techniques were used in order to identify potential inhibitors to P. aerguinosa RmlA protein, the first enzyme in the L-Rhamnose pathway. A 500 “Rule of 3” Fragment Library (Maybridge) was investigated. The first approach was the application of Differential Scanning Fluorimetry (DSF) approach to detect ligands that bind and stabilize RmlA protein. The stabilisation of RmlA was determined by thermal unfolding in the presence of each of the 500 compounds. 21 of those compounds were found to increase the protein stability. The library was then screened by NMR spectroscopy for binding to RmlA. Two techniques were evaluated STD and WaterLOGSY. 106 compounds gave positive results in both NMR experiments. These hits were then tested by a simple STD competition binding with dTTP, a natural RmlA substrate, in order to identify those binding at the active or allosteric site. 21 out of the 106 compounds were observed to compete with dTTP. The results were compared to the results of the DSF screening. Compounds that tested positive in the dTTP competition binding STD experiment and in the DSF screening were tested for their ability to inhibit RmlA in a biological assay. A coupled enzyme assay was used to monitor RmlA activity. Only one compound, 3-pyridin-3-ylaniline, showed significant inhibition of the enzyme activity. The PA1645 protein from P. aerguinosa has been identified as essential. The protein was overexpressed, purified and crystallised. Data were collected at Diamond on beamline IO3 and phases were determined by S-SAD at a wavelength of 1.6Å. Final coordinates have been deposited in the protein data bank under entry code 2XU8. The structure has 3 molecules in the asymmetric unit. There is some ambiguity as to the validity of the proposed trimeric arrangement, with results from solution and crystal disagreeing. Fragment-based screening approach has been applied to RmlA protein, using the DSF technique, a number of ligand-based NMR experiments and a coupled enzyme biological assay. 3-pyridin-3-ylaniline was the only compound that showed significant inhibition of the enzyme activity. The structure of PA1645 from P. aerguinosa has been solved. This work will help to design new drugs to combat multi-drug resistant P. aerguinosa and MTB.

Spores of foodborne pathogens such as Clostridium botulinum, Clostridium perfringens and Bacillus cereus are widely distributed in nature. Presence of those spores in food products, particularly C. botulinum spores in vacuum packed, ready-to-eat low-acid products, is a great safety concern. The research here described is a first effort towards understanding the role of the spore coat proteins in the inactivation of bacterial spore using high pressure processing. This study proposes a coat protein solubilization methodology using non-ionic detergents minimizing protein damage and compatible with spectroscopy methods. The methodology developed here was compared with approaches proposed in the literature with respect to protein yield, protein fractions identified, amino acid composition and suitability with spectroscopy techniques for the further analysis of coat proteins. Bacillus subtilis ATCC 6633 spore coat proteins were solubilized (n=3) using octyl-β-D-glucopyranoside (OGP) at room temperature and urea/sodium dodecyl sulphate (UDS) at 37C and 70C. Analysis of variance (ANOVA) showed no significant (95% confidence) differences between the three repetitions of the three spore coat protein solubilization methods. Protein yield was significantly larger (95% confidence) when using UDS at 70C as compared to UDS at 37C. OGP gave the lowest protein yield but allowed circular dichroism (CD) analysis of the spore coat protein solution with minimum blank signal. SDS-PAGE revealed that the UDS-70C coat protein solutions consisted of five major and six minor proteins ranging 6 to 65 kD while the OGP solution appear to consist of four major and nine minor bands in the same mw range. Amino acid analysis of the protein extracted by the OGP method was conducted using reverse phase HPLC (RP-HPLC) and compared with published information. The OGP spore coat protein solution showed a higher proportion of aspartate, glutamate, alanine and tyrosine. Pressure, heat and time effects were studied on spore coat proteins obtained from untreated and pressure-treated B. subtilis ATCC 6633 spores. Pressure treatments of spores, and of extracted spore coat protein solutions, at 50 kpsi (345 mPa) and 85 kpsi (586 mPa) for 10 and 30 min at constant 85C along with appropriate heat- and pressure-only controls and untreated sample, were used to study the effect of pressure, heat and time on spore coat proteins. Both spore coat protein solubilization procedures showed a significant reduction in protein yield for pressure-only, heat-only and pressure/heat treated spores when compared with untreated spores. When OGP-solubilized proteins from untreated spores were pressure treated, SDS-PAGE profile showed an increasing overall band intensity with increasing pressure and time. In the case of protein solution obtained from pressure-treated spores the electrophoretic pattern showed the loss of higher molecular weight proteins. The significance of this study is that for the first time we have observed extensive changes on spore coat proteins caused by pressure, as well as heat treatments. Future studies will examine what is the probable physiological role of the proteins damaged by these physical treatments. An advantage of the protein solubilization here developed will allow the application of spectroscopy techniques to characterize changes in spore coat proteins. / Graduation date: 2003

Orientador: Manoel Victor Franco Lemos / Coorientador: Baltasar Escriche / Banca: Jackson Antonio Marcondes de Souza / Banca: Odair Aparecido Fernandes / Banca: Bergmann Morais Ribeiro / Banca: Norton Rodrigues Chagas Filho / Resumo: O presente trabalho objetivou avaliar a toxicidade de diferentes proteínas Cry1 e Vip3Aa de Bacillus thuringiensis em larvas de Diatraea saccharalis, verificar o modo de união dessas proteínas aos receptores do inseto alvo e analisar a interação dessas proteínas no controle larval, buscando informações para subsidiar o uso de plantas geneticamente modificadas com genes cry1 e vip3Aa de forma segura e duradoura. A análise de suscetibilidade larval revelou a proteína Cry1Ab como mais efetiva no controle, seguida das proteínas Cry1Ac, Vip3Aa, Cry1Ca e Cry1Fa. A população testada não foi suscetível à proteína Cry1Ea. A proteína Cry1Aa apresentou baixa toxicidade. Nos ensaios de união específica, as proteínas Cry1 ligaram-se a receptores presentes no intestino médio de D. saccharalis e um modelo com três diferentes receptores foi proposto com base nos ensaios de competição heteróloga. Um receptor comum para Cry1Aa, Cry1Ab e Cry1Ac, outro para Cry1Fa e Cry1Ab e um receptor diferente para a proteína Vip3Aa. Dentre as interações avaliadas por bioensaios, as combinações proteicas: Cry1Ab:Cry1Ca e Cry1Fa:Cry1Ca apresentaram efeito sinérgico; as demais combinações revelaram efeitos antagônicos / Abstract: The aim of this research was to evaluate the toxicity of different Cry1 and Vip3A proteins from Bacillus thuringiensis to Diatraea saccharalis, verify the proteins binding to receptors of the target insect and to analyze the protein interactions in larval control, seeking information to support safe and sustainable the use of transgenic Bt plants. The most toxic protein assayed was Cry1Ab followed by Cry1Ac, Vip3Aa, Cry1Ca and Cry1Fa. The population tested was not susceptible to Cry1Ea protein. Cry1Aa showed very low toxicity. Biotinylated Cry1 proteins showed specific binding to the midgut brush border membrane vesicles of the larvae. Heterologous competitive binding assays suggested a model of three receptors, a common receptor for Cry1Aa and Cry1Ab another one for Cry1Fa and Cry1Ab. Vip3Aa did not compete for binding with any of the Cry proteins tested. Among interactions bioassays, the combinations between Cry1Ab:Cry1Ca and Cry1Fa:Cry1Ca showed synergistic effect, whereas the other combinations showed antagonistic effects / Doutor

Fong, Yu Hang. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 102-107). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

Wong, Ho Chun. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 103-109). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

Mycobacterium avium subsp. hominissuis (MAH) is a pervasive environmental bacterium that can cause opportunistic infections in humans. Among the most robust and hardy members of the Mycobacterium genus, M. avium can persist and thrive in a range of challenging environments, including many which place it in direct contact with humans. Surface-exposed proteins are central to the bacterial processes involved in both environmental persistence and pathogenesis. These proteins also play a critical role in how the immune system of the host recognizes and responds to pathogens. Mycobacteria have evolved a specialized mechanism for protein export, a Type VII Secretion System (T7SS), in order to transport their proteins through their thick and impermeable cell envelope. This system is responsible for the export of several classes of proteins, many of which play an integral role in virulence. A central focus of this dissertation is the characterization of a conserved element of the T7SSs in pathogenic mycobacteria, a PPE family protein, whose deletion attenuates virulence in M. avium. Specifically, we examined the localization of this PPE protein (MAV_2928) within the bacterium, screened potential protein-protein interactions with other conserved elements in the adjacent T7SS loci and analyzed the transcriptional regulation of the gene in response to environmental changes. Seeking to more thoroughly characterize the surface-exposed proteome of M. avium, particularly in the context of early infection, we then developed a method, based on selective biotinylation and affinity purification, to profile the of surface-exposed proteome of the bacterium. We employed this method to analyze the surface-exposed proteomes of M. avium 109 that had been exposed to macrophages to those of M. avium 109 that had been cultured in media. This comparison detected several proteins whose presence at the bacterial surface appeared to be dependent on particular growth conditions. Lastly, in order to establish a more efficient method to isolate biotinylated surface proteins from complex mixtures, we developed a testing paradigm to identify modifications to the original method that might improve our coverage of identified proteins. Through this process, we developed a more robust methodology that yielded improved coverage and depth. We then utilized this technology to profile the surface-exposed proteome of another clinical isolate of M. avium subsp. hominissuis, M. avium 104. Beyond improving our understanding of the basic biology of M. avium, this new data provides independent evidence that PPE family proteins are indeed exported to the surface of M. avium, where they remain associated with the bacterial cell envelope. In total, this analysis represents the most comprehensive profile of the surface-exposed proteins of M. avium generated to date. / Graduation date: 2012

All blood vessels in the microvasculature are embedded in loose connective tissue, which regulates the transport of fluid to and from tissues. The intersti-tial fluid pressure (IFP) is one of the forces that control this transport. A lowering of IFP in vivo results in an increased transport of fluid from the circulation into the underhydrated connective tissues, resulting in edema formation. During homeostasis, contractile connective tissue cells exert a tension on the connective tissue fibrous network by binding with β1 in-tegrins, thereby actively controlling IFP. During inflammation, the IFP is lowered but platelet-derived growth factor (PDGF)-BB induces an IFP nor-malization dependent on integrin αVβ3. We demonstrate that extracellular proteins from Streptococcus equi subspecies equi modulated cell-mediated and integrin αVβ3-directed collagen gel contraction in vitro. One of these proteins, the collagen- and fibronectin binding FNE, stimulated contraction by a process dependent on fibronectin synthesis. This study identified a pos-sible novel virulence mechanism for bacteria based on the ability of bacteria to modulate the edema response. Another protein, the collagen-binding pro-tein CNE, inhibited contraction and this led to the identification of sites in collagen monomers that potentially are involved in connecting αVβ3 to the collagen network. PDGF-BB and prostaglandin E1 (PGE1) stimulate and inhibit collagen gel contraction in vitro and normalize and lower IFP, respec-tively. We showed that these agents affected both similar and different sets of actin-binding proteins. PDGF-BB stimulated actin cytoskeleton dynamics whereas PGE1 inhibited processes dependent on cytoskeletal motor and adhesive functions, suggesting that these different activities may partly ex-plain the contrasting effects of PGE1 and PDGF-BB on contraction and IFP. Mutation of the phosphatidylinositol 3’-kinase (PI3K), but not phospholipase C (PLC)γ activation site, rendered cells unable to respond to PDGF-BB in contraction and in activation of the actin binding and severing protein cofilin. Ability to activate cofilin after PDGF-BB stimulation correlated with ability to respond to PDGF-BB in contraction, suggesting a role for cofilin in this process downstream of PDGF receptor-activated PI3K. Many proteins can modulate contraction either by affecting the extracellular matrix and cell adhesions or by altering cytoskeletal dynamics. Knowledge on how these proteins might influence IFP is likely to be of clinical importance for treat-ment of inflammatory conditions including anaphylaxis, septic shock and also carcinoma growth.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 184-198).

Group A streptococcal disorders can result from autoantibodies generated against M proteins. These autoantibodies cross react with the basal ganglia resulting in movement disorders. Previously, we demonstrated binding of streptococcal mAb10F5, with CPu and phospholipids. To determine if mAb10F5 binding to basal ganglia and phospholipids is due to virulence of the antibody or antibody subtype, rats were injected with control IgG2 antibodies and euthanized after 24, 48, or 72 hours. Brains were harvested and immunofluorescence was used to analyze brain slices. Control IgG2 rats showed significantly less fluorescence in the CPu than mAb10F5 injected rats at every time point. These findings reaffirm 10F5 is an anti-basal ganglia antibody. To evaluate mechanism of antibody entry, mAb10F5 was examined for anti-phospholipid activity. MAb10F5 displayed greater affinity to phospholipids when compared to IgG2 controls. Our findings support mAb10F5 is an anti-basal ganglia and anti-phospholipid antibody due to its own virulence. / Access to thesis permanently restricted to Ball State community only / Department of Physiology and Health Science