Thesis (Ph. D.)--University of Texas at Austin, 2009. / Title from PDF title page (University of Texas Digital Repository, viewed on Sept. 15, 2009). Vita. Includes bibliographical references.

Thesis (Ph. D.)--Oregon Graduate Center, 1985.

Cellular redox homeostasis mediates a wide range of physiological and developmental processes. Various stresses trigger over-production of reactive oxygen/nitrogen species which leads to oxidative modifications of redox-sensitive proteins. Identification and characterization of redox-sensitive proteins are important steps toward understanding molecular mechanisms of stress responses. In the study, a high-throughput quantitative proteomic approach termed OxiTRAQ was developed for identifying proteins whose thiols undergo reversible oxidative modifications in Arabidopsis cells subjected to oxidative stress. In this approach, a biotinylated thiol-reactive reagent is used for differential labeling of reduced and oxidized thiols, and the biotin-tagged peptides are affinity-purified and labeled with iTRAQ reagents for quantitation. This approach allows identification of the specific redox-regulated cysteine residues in proteins and offers an effective tool for elucidation of redox proteomes. With this approach, we identified 195 cysteine-containing peptides from 179 proteins whose thiols underwent oxidative modifications in Arabidopsis cells following the treatment with hydrogen peroxide. A majority of those redox-sensitive proteins, including several transcription factors, were not identified by previous redox proteomics studies. Besides, this method was also used to identify proteins that underwent oxidative modifications in Arabidopsis cells subjected to 15 minute treatment of salicylate (a key signaling molecule in the plant defense pathway) or flg22 (a peptide from bacterial flagellin that induces pathogen associated molecular patterns-triggered immunity). In total, 127 peptides from 111 distinct proteins were identified as salicylate- and/or flg22-responsive redox-sensitive proteins. Among the identified redox sensitive proteins are many regulatory proteins including those involved in chromatin remodeling, transcription, nucleocytoplasmic shutting, and posttranslational regulation. Furthermore, in vivo 15N metabolic labeling method combined with a cysteine-containing peptide enrichment technique was applied to identify proteins that undergo oxidative modifications in plants in response to pathogen attack. The identification of redox-sensitive proteins provides a foundation from which further study can be conducted toward understanding the biological significance of redox signaling in plant stress response.

No description available.

The liquid phase autoxidation of 1,3-pentadiene to 2,4-pentadienoic acid utilizing gaseous oxygen at atmospheric pressure was investigated as a possible route for direct utilization of piperylene obtained during the cracking of naptha to ethylene. Catalyst system consisting of cobalt, manganese, and iron salts promoted by sodium, potassium and hydrogen bromides, were used under a variety of condition of catalyst concentration, temperature, oxygen flow and piperylene purity. Under all conditions studied, a large number of oxidation products were formed. Maximum yields of 2,4-pentadienoic acid were obtained using a cobalt acetate bromide catalyst at 85°C.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Electron transfer reactions between Clostridium pasteurianum flavodoxin semiquinone and various oxidants (horse heart cytochrome c, ferricyanide, and ferric EDTA) have been studied as a function of ionic strength using stopped-flow spectrophotometry. The cytochrome c reaction is complicated by the existence of two cytochrome species which react at different rates and whose relative concentrations are ionic strength dependent. Only the faster of these two reactions is considered here. At low ionic strength, complex formation between cytochrome c and flavodoxin is indicated by a levelling-off of the pseudo-first order rate constant at high cytochrome c concentration. This is not observed for either ferricyanide or ferric EDTA. For cytochrome c, the rate and association constants for complex formation were found to increase with decreasing ionic strength, consistent with negative charges on flavodoxin interacting with the positively charged cytochrome electron transfer site. Both ferricyanide and ferric EDTA are negatively charged oxidants and the rate data respond to ionic strength changes as would be predicted for reactants of the same charge sign. These results demonstrate that electrostatic interactions involving negatively charged groups are important in orienting flavodoxin with respect to oxidants during electron transfer. The effects of structural modifications of the FMN prosthetic group of C. pasteurianum flavodoxin on the kinetics of electron transfer to the oxidized form (from 5-deazariboflavin semiquinone produced by laser flash photolysis) and from the semiquinone form (to horse heart cytochrome c using stopped-flow spectrophotometry) have been investigated. The analogs used were 7,8-dichloroFMN, 8-chloroFMN, 7-chloroFMN and 5,6,7,8-tetrahydroFMN. The ionic strength dependence of cytochrome c reduction was not affected by chlorine substitution, although the specific rate constants for complex formation and decay were appreciably smaller. On the other hand, all of the chlorine analogs had the same rate constant for deazariboflavin semiquinone oxidation. The rate constants for tetrahydroFMN flavodoxin semiquinone reduction of cytochrome c were considerably smaller than those for the native protein. The results for the chlorine analogs indicate the important roles that the polarity of the exposed flavin edge and the substitution of the 8 position play in electron transfer. The data obtained with the tetrahydroFMN analog indicates that the (pi) electron system of the flavin is necessary for rapid electron transfer. These implications are discussed for the electron transfer mechanism of flavodoxin.

The axial ligands of the iron porphyrin in Cytochrome c, an electron transfer protein, are an imidazole group of a histidine residue and a methionine thioether. This ligand coordination sphere has been difficult to model and consequently the influence of these ligands on the properties of cytochrome c has been problematic. The electrochemical and spectroscopic study of a novel strapped porphyrin has been addressed toward this problem. Spectroscopic studies have demonstrated the ability of this porphyrin to hold a thioether ligand near the central metal atom. The influence of the thioether is not seen in the UV/visible spectrum of the iron complex of this porphyrin. The coordination of N-methyl imidazole to the iron complexes of several porphyrins has been studied by UV/visible spectroscopy. These studies indicate a reduced affinity of the strapped porphyrin for this ligand. Also, the oxidation products of several porphyrins were monitored by thin-layer spectroelectrochemistry. Cyclic voltammetry has been used to demonstrate the influence of the thioether on the Fe('+3)/Fe('+2) electron transfer reaction. It was found that the thioether stabilizes the lower oxidation state causing an anodic shift in the half-wave potential for the reaction. However, the stabilization seen with this model system is not sufficient to account for the large positive redox potential of Cytochrome c. The oxidations of a selected group of free base and metallo- porphyrins were also studied. It was found that the oxidation of strapped porphyrins was similar in many respects to those of non-strapped porphyrins. The notable acception to this generalization was the instability of the cation radical of the strapped porphyrins used in this work.

Redox chemistry is the basis for biological energy generation and anabolism. Redox conditions also serve as critical cues that modulate the development of many organisms. Roles for redox chemistry in the control of gene expression have been well characterized in multicellular eukaryotes, where oxygen availability in particular is a major developmental cue. As a gaseous metabolic substrate, oxygen becomes limiting as cellular communities grow, and can act as an indicator of aggregate size or developmental stage. In many of these cases, there are dedicated sensory and signal transduction networks that link oxygen and other redox signals to changes in gene expression and morphogenesis. The opportunistic pathogen Pseudomonas aeruginosa, like many species of microbes, forms multicellular structures called biofilms. Cells in biofilms can assume physiological states that differ from cells grown in well-mixed, homogeneous liquid cultures. They often exhibit increased resistance to environmental stresses and antibiotics, rendering biofilm physiology an important focus in the study of microbial pathogens. Biofilm development and architecture are tuned by environmental conditions. In turn, growth and survival in the community, and the specific structure of that community, give rise to internal microenvironments that are experienced by cells within a biofilm. Mechanisms that tune biofilm developmental programs in response to redox conditions are not well understood. This is due to challenges presented by most popular laboratory models of biofilm formation, which are not amenable to perturbation, characterization at the microscale, or high-throughput screening or analysis. In this thesis, I describe a standardized colony morphology assay for the study of P. aeruginosa PA14 biofilm development and use this model to address fundamental questions about the relationships between electron acceptor availability, biofilm cell physiology, and the regulation of biofilm morphogenesis. In the colony morphology assay, PA14 grows as ~1cm-diameter biofilms on agar-solidified media under controlled conditions, and displays a developmental pattern that is predictably influenced by changes in redox conditions. Microscale heterogeneity in chemical ecology can be profiled using microelectrodes, and the effects of specific mutations on development can be rigorously tested through high-throughput screening and the application of metabolic assays directly to biofilm samples. Prior to the work described here, application of the colony morphology assay had revealed that endogenous redox-active antibiotics called phenazines influence PA14 biofilm development such that defects in phenazine production promote colony wrinkling and the formation of a distinct wrinkle pattern. As phenazines can act as alternate electron acceptors for cellular metabolism, this provided an early clue to the role of redox conditions in determining biofilm architecture. The introduction to this thesis (Chapter 1) provides an overview of observations in P. aeruginosa and other microbes, drawing parallels between the physiology of colony biofilm development across phylogeny and highlighting specific preliminary studies that hint at redox-sensing mechanisms and signaling pathways that drive community morphogenesis. The associated Appendix A examines the effects of CORM-2, a synthetic compound that releases the respiratory poison carbon monoxide, on P. aeruginosa biofilm development. The inhibitory effects of CORM-2 are ameliorated by reducing agents and increased availability of electron donors for P. aeruginosa metabolism. Chapter 2 describes the foundational characterization of the P. aeruginosa PA14 colony morphology assay model, which showed that colony wrinkling is invoked under high intracellular NADH levels and electron acceptor-limiting conditions, suggesting that it is an adaptive strategy to increase access to electron acceptor. The associated Appendices B and C describe (i) a mathematical modeling approach demonstrating that wrinkle geometry is indeed optimized for efficient access to electron acceptors, and (ii) a study investigating the effects of phenazine antibiotics on the multicellular development of a eukaryotic microbe. Chapter 3 details the identification and characterization of a candidate mediator of the multicellular response to electron acceptor availability in PA14 called RmcA. RmcA contains domains that have been implicated in redox-sensitive developmental control in eukaryotic systems and domains that modulate intracellular levels of cyclic di-GMP (c-di-GMP). C-di-GMP is an important secondary messenger that controls social behaviors, including the secretion of factors required for colony biofilm structure formation, in diverse bacteria. RmcA thus bridges the gap between sensing of redox signals and colony morphogenesis. Appendix D outlines my approaches to purification and attempts to crystallize this and one other protein contributing to PA14 redox-driven colony morphogenesis. Finally, Appendix E describes the role of another protein that modulates c-di-GMP in response to metabolite-dependent signaling and physiological effects during interactions between P. aeruginosa and the fungus C. albicans. Together, the findings presented in this thesis have expanded our knowledge about the role that redox chemistry plays in biofilm development.

氧自由基曾被認為是有氧代謝过程的無用副產物。然而，在正常條件下，氧自由基也可以修飾蛋白質的結構與功能，同時能在多種細胞代謝過程中作為重要的信號分子。半胱氨酸的巰基極易被氧自由基、氮自由基以及其它的親電子分子所氧化，且其可逆的氧化反應對於與氧化還原相關的調控與信號傳遞是極其重要的。雖然僅有特定的一小部分半胱氨酸可以被氧化修飾，我們至今對於影響半胱氨酸對氧化還原敏感性的决定因素所知甚少。對於蛋白质半胱氨酸氧化修饰的比較分析及預測，不仅可以提高我們對半胱氨酸氧化還原敏感性的决定因素的認識，同時也能對後續关于重要的氧化還原敏感蛋白的實驗驗證起指導作用。 / 本研究中，本人主要做了如下三部分的工作：第一部分， RedoxDB數據庫的構建。这也是首個針對已被实验验证的蛋白氧化還原修飾的數據庫。第二部分，氧化還原敏感的半胱氨酸位點的特征分析及預測。本人分析了基於序列的各種可能與半胱氨酸氧化還原敏感性相關的特征，並發現其中三個特征可用於預測氧化還原敏感的半胱氨酸位點。基於這三個特征，我開發了RSCysPred 一个基於支持向量機且只依赖蛋白序列的預測氧化還原敏感的半胱氨酸位點的新方法。第三部分，可逆二硫鍵的分析。可逆二硫鍵的形成是蛋白質可逆氧化還原修飾的最主要的類型之一。我从RedoxDB中获取相关数据，然后針對功能位點標簽以及靜電特征等方面的特征，對可逆二硫鍵與結構二硫鍵進行了詳盡的比較分析。結果表明相比結構二硫鍵，可逆二硫鍵具有一些显著不同的特征。进一步的分析显示這些特征可用於可逆二硫鍵的預測。 / Reactive oxygen species (ROS) has been regarded as unwanted by-product of aerobic metabolism. However, under normal conditions, ROS can modify the structure and function of proteins and may also act as important signaling molecules in various cellular processes. Cysteine thiol groups of proteins are particularly susceptible to oxidation by ROS/RNS and other electrophilic molecules, and their reversible oxidation is of critical roles for redox regulation and signaling. Despite the fact that only a small fraction of cysteine residues undergone oxidative modification, the determinants of cysteine redox-sensitivity is poorly understood to date. Comparative analyses and computational prediction of protein cysteine oxidative modification will not only enhance our understanding about the determinants of cysteine redox-sensitivity, it may also facilitate further experimental investigation of important redox proteins. / This thesis includes the following three parts of work. Part I: Construction of RedoxDB - a curated database of protein oxidative modification. It is the first database for experimentally verified protein oxidative modification events. Part II: Feature analysis and computational prediction of redox-sensitive cysteines. I analyzed various sequence-based features potentially related to cysteine redox-sensitivity, and identified three features for efficient computational prediction of redox-sensitive cysteine. Based on these features, I developed RSCysPred, a SVM-based tool for predicting redox-sensitive cysteine using primary protein sequence only. Part III: Study on reversible disulfide formation, which is the major type of protein oxidative modification. By using data retrieved from RedoxDB, I performed extensive comparison between reversible disulfide-bonded cysteines and structural disulfide-bonded cysteines with regard to the functional site signatures and electrostatic properties. The results support that reversible disulfides show several remarkable differences compared with structural disulfides. Further analyses indicated that these features could be used for efficient prediction of reversible disulfide. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Sun, Mingan. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 77-89). / Abstract also in Chinese. / Thesis/Assessment Committee --- p.I / Statement: --- p.I / Abstract of thesis entitled --- p.II / 摘要 --- p.IV / Acknowledgements --- p.V / Table of contents --- p.VI / List of Tables --- p.IX / List of Figures --- p.X / List of Abbreviations --- p.XI / CHAPTER 1 --- p.1 / General Introduction --- p.1 / Chapter 1.1 --- Generation of ROS and oxidative stress --- p.2 / Chapter 1.2 --- Protein cysteine oxidative modification --- p.3 / Chapter 1.2.1 --- Protein oxidative modification --- p.3 / Chapter 1.2.2 --- Special properties of cysteine --- p.3 / Chapter 1.2.3 --- Reversible cysteine oxidation and its function --- p.4 / Chapter 1.2.4 --- Specificity of cysteine oxidative modification --- p.5 / Chapter 1.3 --- Experimental approaches for detecting protein oxidative modification --- p.6 / Chapter 1.4 --- Computational prediction of protein oxidative modification --- p.7 / Chapter 1.5 --- Project Objectives --- p.8 / CHAPTER 2 --- p.11 / RedoxDB: a Curated Database of Experimentally Verified Protein Oxidative Modification --- p.11 / Chapter 2.1 --- Introduction --- p.12 / Chapter 2.2 --- Database concept --- p.13 / Chapter 2.3 --- Database interface and tools --- p.15 / Chapter 2.4 --- Discussion --- p.16 / CHAPTER 3 --- p.23 / Computational Prediction of Redox-Sensitive Cysteines Using Sequential Distance and Other Sequence-based Features --- p.23 / Chapter 3.1 --- Introduction --- p.24 / Chapter 3.2 --- Methods and Materials --- p.26 / Chapter 3.2.1 --- Datasets --- p.26 / Chapter 3.2.2 --- Feature extraction --- p.28 / Chapter 3.2.3 --- Support vector machines (SVMs) implementation and parameter optimization --- p.29 / Chapter 3.2.4 --- Performance assessment --- p.30 / Chapter 3.2.5 --- Statistical analyses --- p.30 / Chapter 3.3.6 --- Webserver implementation --- p.30 / Chapter 3.3 --- Results --- p.31 / Chapter 3.3.1 --- Performance evaluation by 10-fold cross-validation --- p.31 / Chapter 3.3.2 --- Evaluation of the most efficient features --- p.33 / Chapter 3.3.3 --- Comparison with current structure-based method --- p.34 / Chapter 3.3.4 --- Performance evaluation using OSCTdb --- p.36 / Chapter 3.4 --- Discussion --- p.37 / CHAPTER 4 --- p.49 / Comparative Analysis of Reversible and Structural Disulfides to Reveal Their Distinct Characteristics --- p.49 / Chapter 4.1 --- Introduction --- p.50 / Chapter 4.2 --- Materials and methods --- p.52 / Chapter 4.2.1 --- Datasets --- p.52 / Chapter 4.2.2 --- Functional site signatures --- p.53 / Chapter 4.2.3 --- Electrostatic properties --- p.55 / Chapter 4.2.4 --- Support vector machines (SVMs) implementation and parameter optimization --- p.56 / Chapter 4.2.5 --- Performance assessment --- p.56 / Chapter 4.2.6 --- Statistical analyses --- p.56 / Chapter 4.3 --- Results --- p.56 / Chapter 4.3.1 --- General features of the functional site signatures for reversible-SS Cys and structural-SS Cys --- p.56 / Chapter 4.3.2 --- Differences in amino acid composition are related to several physical-chemical properties --- p.58 / Chapter 4.3.3 --- Electrostatic characteristics of disulfide-bonded Cys --- p.60 / Chapter 4.3.4 --- Comparison of S-S distance --- p.61 / Chapter 4.3.5 --- Predictive power of newly identified features --- p.62 / Chapter 4.4 --- Discussion --- p.63 / Chapter 4.4.1 --- Reversible disulfides show distinct characteristics compared with structural disulfides --- p.63 / Chapter 4.4.2 --- Chances and challenges for computational prediction of reversible disulfides --- p.64 / CHAPTER 5 --- p.79 / Conclusions and Perspectives --- p.79 / Chapter 5.1 --- Contributions and conclusions from this thesis research --- p.80 / Chapter 5.2 --- Future perspectives --- p.81 / Reference --- p.82 / List of Publications --- p.95