Disulfide bond formation is an essential process for the folding and biological activity of most extracellular proteins; however, it may become the limiting step when the production of these proteins is attempted in heterologous hosts such as Escherichia coli. The rearrangement of incorrect disulfide bonds between cysteines that do not normally interact in the native structure of a protein is carried out by disulfide isomerase enzymes. The disulfide isomerase present in the bacterial secretory compartment (the periplasmic space) is the homodimeric enzyme DsbC. The objective of this dissertation was to understand the key features of how DsbC catalyzes disulfide bond isomerization. Chimeric disulfide isomerases comprising of protein domains that share a similar function, or are homologous to domains of DsbC were constructed in an effort to understand the effect of the domain orientation in the dimeric protein, and the need for a substrate binding region in disulfide isomerases. We successfully created a series of fusion enzymes, FkpA-DsbAs, which catalyze in vivo disulfide isomerization with comparable efficiency to DsbC. These enzymes comprise of the peptide binding region of the periplasmic chaperone FkpA, which is functionally and structurally similar to the binding domain of DsbC but share no amino acid homology with it, fused to the bacterial oxidase DsbA. In addition, these chimeric enzymes were shown to assist in the initial formation of disulfide bonds, a function that is normally exhibited only by DsbA. Directed evolution of the FkpA-DsbA proteins conferred improved resistance to CuCl₂, a phenotype dependent on disulfide bond isomerization and highlighted the importance of an optimal catalytic site. The bacterial disulfide isomerase DsbC is a homodimeric V-shaped enzyme that consists of a dimerization domain, two α-helical linkers and two opposing catalytic domains. The functional significance of the existence of two catalytic domains of DsbC is not well understood yet. The fact that identical subunits naturally dimerize to generate DsbC has so far limited the study of the individual catalytic sites in the homodimer. In chapter 3 we discuss the engineering, in vivo function, and biochemical characterization chapter 3 we discuss the engineering, in vivo function, and biochemical characterization of DsbC variants covalently linked via (Gly3Ser) flexible linkers. We have either inactivated one of the catalytic sites (CGYC), or entirely removed one of the catalytic domains while maintaining the putative binding area intact. Our results support the hypotheses that dual catalytic domains in DsbC are not necessary for disulfide bond isomerization, but are important in terms of increasing the effective concentration of catalytic equivalents, and that the availability of a substrate binding region is a determining feature in isomerization. Finally, we have carried out initial studies to map the residues and sequence motifs that are recognized in substrate proteins that interact with DsbC. Although the main putative binding region of DsbC has been localized within the limits of the hydrophobic cleft that emerges from the interaction of the N-terminal domains of this enzyme, and, a few native substrates have already been identified, no information on the features of substrate proteins that are recognized by the enzyme has been reported. To address this problem, we have screened two different, 15 amino-acid random peptide libraries for binding to DsbC. We have successfully isolated several peptides with high affinity for the enzyme. Possible consensus binding motifs were identified and their significance in substrate recognition will be examined in future studies. / text

Protein disulfide isomerase (PDI), a member of the thioredoxin superfamily, contains two domains with significant sequence homology to the active sites in thioredoxin. PDI facilitates the folding of nascent proteins in the endoplasmic reticulum (ER), binds hormones and Ca�����, catalyzes the glutathione dependent reduction of dehydroascorbate, serves as a major chaperone molecule in the ER and serves as a subunit for prolyl-4-hydroxylase and microsomal triglyceride transferase. Because of its abundance in the ER and association with disease and chemically induced toxicity, the goal of this research was to investigate the relative susceptibility of PDI thiols to alkylation. The sensitivity of PDI to 1-chloro-2,4-dinitrobenzene (CDNB), iodoacetamide (IAM) and biotinoylated iodoacetamide (BIAM) was explored. The relative susceptibility of the thiolate anions present in the two active sites of PDI each containing the -CGHC- sequence was investigated with mass spectrometric techniques. PDI was inactivated by CDNB but was not found as sensitive as thioredoxin reductase as shown by Amer and coworkers (1995). IAM and BIAM were used as model alkylating agents to explore the two active sites of PDI and determine the residues most susceptible to alkylation. Alkylation by IAM and BIAM was first detected at the N-terminal cysteine in each active site (-C*GHC-) followed by alkylation at the second cysteine residue (-C*GHC*-) as shown by tandem mass spectrometry. Mass spectroscopy showed that the episulfonium ion derived from the glutathione conjugate of 1,2-dichloroethane, S-(2-chloroethyl)glutathione (CEG), decreased activity and protein thiols of PDI. CEG produced two protein adducts at very low excesses of CEG over PDI; however, higher concentrations resulted in several protein adducts. Only one modification in each active site at the N-terminal cysteine residue can be identified, indicating that while these thiolate anions of PDI are susceptible, it would appear that the episulfonium ion may present itself to other sites as well. This may have important toxicologic significance regarding the mechanism of 1,2-dichloroethane toxicity and the role of PDI in the redox status of the cell. / Graduation date: 2003

Coatings are often used on critical components in machines and engines to reduce wear and to provide low friction in order to reduce energy losses and the environmental impact. A triboactive coating not only provides this desired performance, it also actively maintains the low friction by a structural or chemical change in a very thin top layer of these already micrometer thin coatings. This so-called tribofilm is often 5-50 nm thick and can be formed either from the coating itself or by a reaction with the counter surface or the surrounding atmosphere, i.e. gas, fuel, oil, etc. The tribofilm will maintain the wanted performance for as long as the system is not chemically disturbed. This thesis provides a detailed overview of the functionality of triboactive low-friction coatings, in many different systems. The majority of the tribofilms discussed, formed in very different environments, are built up by tungsten disulfide (WS2), which is a material similar to graphite, with a lamellar structure where strongly bonded atomic planes may slip over each other almost without resistance. The major difference is that WS2 is an intrinsically triboactive material, while graphite is not. However, graphite and other carbon-based materials can be made triboactive in certain atmospheres or by addition of other elements, such as hydrogen. The remarkable affinity and driving force to form such WS2 low-friction tribofilms, regardless of the initial states of the sulfur and tungsten, and even when the forming elements are present only at ppm levels, is a recurrent observation in the thesis. Addition of an alloying element to sputtered coatings of WS2 can improve its mechanical and frictional properties significantly. Several promising attempts have been made to find good candidates, out of which a few important ones are investigated in this thesis. Their achievable potential in friction reductions is demonstrated. By reducing friction, energy losses can be avoided, which also results in lower particle and exhaust emissions, which directly reduces the environmental impact. Triboactive coatings are shown to be a promising route to significantly improve tribological applications and allow more environmental friendly and energy efficient vehicles.

Disulfide bonds are special covalent cross links between two cysteines in a protein. This kind of bonding state plays an important role in protein folding and stabilization. For connectivity pattern prediction, it is a very difficult problem because of the fast growth of possible patterns with respect to the number of cysteines. In this thesis, we propose a new approach to address this problem. The method is based on hybrid models with SVM. Via this strategy, we can improve the prediction accuracies by selecting appropriate models. In order to evaluate the performance of our method, we apply the method by 4-fold cross-validation on SP39 dataset, which contains 446 proteins. We achieve accuracies with 70.8% and 65.9% for pair-wise and pattern-wise prediction respectively, which is better than the previous works.

Disulfide bond information can help the prediction of protein secondary structure, tertiary structure and all-atom coordinates. Most of previous works focused on either state classification or connectivity prediction with some assumption that some constraints were added to make the problem solvable in reality. In this thesis, we propose a multi-phase approach to solve the problem. Our method can export the number of bonds and achieve 90.7% accuracy in the state classification. For the connectivity prediction problem, we use the number of bonds we predict as a base to decide bond pairs. For overcoming the ratio imbalance of samples, we propose a down-sampling method to reducing processing time. Finally, we perform the weighted graph matching algorithm to obtain the bonding pattern, which achieves 63.5% accuracy. We also achieve 48% accuracy for the thorough prediction. Our method is validated by the datasets derived from SWISS-PROT and PDB. The results are better than the previous works.

Thesis (M.S.)--University of Missouri, School of Mines and Metallurgy, 1928. / The entire thesis text is included in file. Typescript. Title from title screen of thesis/dissertation PDF file (viewed December 7, 2009) Includes bibliographical references (p. 25-26).

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 143-154).

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Tetramethylthiuram disulfide (42-S Thiram), a carbamate fungicide was studied for its mutagenic potential on the germ cell stages of wild-type male Drosophila melanogaster. The mutagenicity was tested using the sex-linked recessive lethal assay (SLRL). Any lethals induced in the F2 generation were evidenced by the absence of wild-type males. Although there was an increase in mutation rates in the 42-S Thiram treated wild-type males over the control wild-type males, it was not significantly higher. According to the laboratory conditions in this preliminary study, tetramethylthiuram disulfide failed to produce mutagenic effect.