Zhang, Yang. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 147-169). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

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Diss. (sammanfattning) Stockholm : Karol. inst., 2002. / Härtill 5 uppsatser.

Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 168-210). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

Les peptidyl-arginine désiminases (PADs) catalysent une modification post-traductionnelle, appelée désimination, qui correspond à la transformation des résidus arginine en résidus citrulline. À ce jour, leur rôle est encore mal compris, bien qu'elles aient été impliquées dans divers processus physiologiques et pathologiques. Dans l'épiderme et le follicule pileux, trois d'entre elles sont exprimées, les PAD1, 2 et 3. La désimination de la filaggrine (FLG), protéine essentielle de la différenciation épidermique, semble conduire à sa dissociation des filaments de kératines et permettre sa protéolyse totale. Les acides aminés libres ainsi générés sont nécessaires à la fonction de barrière que remplit la couche cornée, couche cellulaire la plus externe de l'épiderme. Dans le follicule pileux, la désimination de la trichohyaline (TCHH), protéine apparentée à la FLG, augmente sa solubilité et permet sa liaison covalente aux kératines par la transglutaminase 3 (TGase 3), ce qui participe à la formation de la tige pilaire. La description du rôle des PADs au cours de la différenciation des kératinocytes est cependant encore incomplète, et leurs implications dans les maladies de peau peu explorée. L'objectif de mon travail de thèse a été de mieux comprendre le rôle des PADs dans le métabolisme de la FLG et, plus généralement, dans l'homéostasie de l'épiderme et du follicule pileux. Tout d'abord, j'ai montré que la désimination de la FLG humaine par la PAD1 et/ou 3 est une étape majeure qui permet de réguler sa dégradation complète en fonction du taux d'humidité extérieure. Pour cela, j'ai utilisé comme modèle expérimental des épidermes reconstruits humains (ERHs). La diminution de l'humidité relative lors de leur production, de 95% à 30-50%, augmente la protéolyse de la FLG et la genèse des acides aminés correspondants. En parallèle, l'expression de la PAD1 et le taux de désimination de la FLG sont fortement accrus alors que ni l'expression ni l'activité des protéases impliquées dans cette protéolyse ne varient. De plus, le traitement d'ERHs pendant 24 heures avec un inhibiteur des PADs, le Cl-amidine, bloque en partie l'effet de la sécheresse sur le métabolisme de la FLG. J'ai ensuite recherché si la désimination joue un rôle plus global au cours de la différenciation des kératinocytes. J'ai traité des ERHs avec différentes concentrations de Cl-amidine pendant 48 heures et analysé l'effet du traitement sur leur morphologie. L'inhibition de la désimination est dose-dépendante et non toxique. À la plus forte concentration, le Cl-amidine entraîne un amincissement de la couche cornée, une augmentation importante du nombre de cellules transitionnelles, et l'accumulation de mitochondries et de vésicules dans le cytoplasme des kératinocytes granuleux. Ceci permet de proposer que la cornification, dernière étape de la différenciation kératinocytaire, est retardée. De plus, la protéine LC3B-II, marqueur des autophagosomes, étant plus fortement détectée dans les ERHs traités, les PAD1 et/ou 3 pourraient être impliquées dans le processus d'autophagie associé à la cornification.Enfin, j'ai participé à un nouveau projet collaboratif qui a permis de découvrir l'origine d'une maladie génétique rare, le syndrome des cheveux incoiffables. Des mutations des gènes de la TCHH, de la PAD3 ou de la TGase 3 ont été identifiées dans 11 familles et sont responsables de ce syndrome. La mutation non-sens du gène de la TCHH aboutit à la synthèse, si elle a lieu, d'une forme très courte, probablement incapable d'interagir avec les kératines. Les mutations des gènes de la PAD3 et de la TGase 3 induisent des changements structuraux et une quasi-absence de l'activité des enzymes correspondantes. De plus, les souris dont le gène de la Pad3 a été inactivé présentent des anomalies de la forme des poils. Ces résultats ont permis de comprendre la physiopathologie de cette maladie des cheveux et ont prouvé que la PAD3 est essentielle à leur morphogenèse. / Peptidylarginine deiminases (PADs) catalyze a post-translational modification, named deimination, corresponding to the transformation of arginine residues into citrulline. So far, their role is still poorly understood even if they have been associated with numerous physiological and pathological processes. In the epidermis and the hair follicle, three PADs are expressed, namely PAD1, 2 and 3. Deimination of filaggrin (FLG), a major protein of epidermal differentiation, would lead to its detachment from keratin filaments and allow its full proteolysis. The resulting free amino acids contribute to the barrier function of the cornified layer, the outmost cellular layer of the epidermis. In the hair follicle, deimination of trichohyalin (TCHH), a FLG-related protein, increases its solubility and improves its crosslinking by transglutaminase 3 (TGase 3) to keratins, contributing to the hair shaft formation. However, the function of PADs during keratinocyte differentiation is incompletely described and their involvements in skin diseases have been poorly investigated. The objective of my work was to better understand the role of PADs in the metabolism of FLG, and more generally in the epidermis and hair follicle homeostasis. First of all, I demonstrated that a major step in the metabolism of human FLG is its deimination by PAD1 and/or PAD3. This regulates its complete degradation according to the external humidity level. For this purpose, I used reconstructed human epidermis (RHEs) as an experimental model. Lowering relative humidity from 95 to 30-50% during RHE generation enhanced FLG proteolysis as well as the resulting amino acid amount. In parallel, PAD1 expression and FLG deimination were highly increased while the expression or activity of proteases known to target FLG did not vary. Moreover, treatment of RHEs during 24 hours with Cl-amidine, a PAD inhibitor, partially blocked the effect of dryness on FLG metabolism. Then, I investigated whether deimination could play a more general role during keratinocyte differentiation. I treated RHEs with various concentrations of Cl-amidine during 48 hours and I analyzed the effect of treatments on the epidermis morphology. The inhibition of deimination was dose-dependent and not cytotoxic. At the strongest concentration, Cl-amidine was shown to cause thinning of the cornified layer, to highly increase the number of transitional cells and to induce accumulation of mitochondria and vesicles in the cytoplasm of granular keratinocytes. This suggested that cornification, the ultimate stage of keratinocyte differentiation, is slowed down by Cl-amidine treatment. Besides, as the autophagosome marker LC3B-II was up-regulated in Cl-amidine treated RHEs, PAD1 and/or PAD3 could be involved in the cornification-associated process of autophagy. Finally, I participated in a new collaborative work that led to discover the cause of uncombable hair syndrome, a rare genetic disorder. Mutations of the genes encoding TCHH, PAD3 and TGase 3 were identified in 11 families and were shown to be responsible for the disease. The nonsense mutation in TCHH gene results in the synthesis, if any, of a very short protein, probably not able to interact with keratins. Mutations in PAD3 and TGase3 genes were shown to induce structural changes and almost total absence of activity of the corresponding enzymes. Moreover, examination of Pad3 deficient mice revealed alterations in the hair morphology. These results allowed a better understanding of this hair disease physiopathology and proved that PAD3 is essential for the hair shaft morphogenesis.

Protein synthesis is a process by which organisms manufacture their proteins that perform various cellular activities either alone or in combination with other similar or different molecules. In eubacteria, protein synthesis proceeds at a rate of around 15 amino acids per second. The ribosomes, charged tRNAs and mRNAs can be considered as the core components of protein synthesis system which, in addition, involves a panel of non-ribosomal proteins that regulate the speed, specificity and accuracy of the process. Peptidyl-tRNA hydrolase (Pth) and ribosome recycling factor (RRF) are two such non-ribosomal proteins involved in protein synthesis. These two proteins are essential for eubacterial survival and the work reported in this thesis involves structural characterization of these two proteins from the bacterial pathogen, Mycobacterium tuberculosis. The protein structures were solved using established techniques of protein crystallography. Hanging drop vapour diffusion method and crystallization under oil using microbatch plates were the methods employed for protein crystallization. X-ray intensity data were collected on a MAR Research imaging plate mounted on a Rigaku RU200 X-ray generator in all the cases. The data were processed using DENZO and MOSFLM. The structures were solved by molecular replacement method using the program PHASER. Structure refinements were carried out using programs CNS and REFMAC. Model building was carried out using COOT. PROCHECK, ALIGN, CHIMERA, and PYMOL were used for structure validation and analysis of the refined structures. Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA that has dropped off from ribosome before reaching the stop codon, in order to avoid the toxicity resulting from peptidyl-tRNA accumulation and to free the tRNA to make it available for further rounds in protein synthesis. To begin with, the structure of the enzyme from M. tuberculosis (MtPth) was determined in three crystal forms. This structure and the structure of the same enzyme from Escherichia coli (EcPth) in its crystal differ substantially on account of the binding of the C-terminus of the E.coli enzyme to the peptide binding site of a neighboring molecule in the crystal. A detailed examination of this difference led to an elucidation of the plasticity of the binding site of the enzyme. The peptide-binding site of the enzyme is a cleft between the body of the molecule and a polypeptide stretch involving a loop and a helix. This stretch is in open conformation when the enzyme is in the free state as in the crystals of MtPth. Furthermore, there is no physical continuity between the tRNA and the peptide-binding sites. The molecule in the EcPth crystal mimics the peptide-bound conformation of the enzyme. The peptide stretch involving a loop and a helix, referred to earlier, now closes on the bound peptide. Concurrently, a gate connecting the tRNA and the peptide-binding site opens primarily through the concerted movement of the two residues. Thus, the crystal structure of MtPth when compared with that of EcPth, leads to a model of structural changes associated with enzyme action on the basis of the plasticity of the molecule. A discrepancy between the X-ray results and NMR results, which subsequently became available, led to X-ray studies on new crystal forms of the enzyme. The results of these studies and those of the enzyme from different sources that became available, confirmed the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding site and tRNA binding site. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movement is not, however, observed in the NMR structure of MtPth. The discrepancy between the X-ray and NMR structures of MtPth in relation to the functionally important plasticity of the molecule, referred to earlier, also led to molecular dynamics simulations. The X-ray and the NMR studies along with the simulations indicated an inverse correlation between crowding and molecular volume. A detailed comparison of proteins for which X-ray and the NMR structures are available appears to confirm this correlation. In consonance with the reported results of the investigation in cellular components and aqueous solutions, the comparison indicates that the crowding results in compaction of the molecule as well as change in its shape, which could specifically involve regions of the molecule important for function. Crowding could thus influence the action of proteins through modulation of the functionally important plasticity of the molecule. After termination of protein synthesis at the stop codon, the ribosome remains as a post-termination complex (PoTC), consisting of the 30S and the 50S subunits, mRNA and a deacylated tRNA. This complex has to be disassembled so that the ribosome is available for the next round of translation initiation. Ribosome recycling factor (RRF) binds to ribosome and in concert with elongation factor G (EF.G), performs the recycling of ribosome that results in disassembly of PoTC. The structure of this L-shaped protein with two domains connected by a hinge, from Mycobacterium tuberculosis (MtRRF) was solved previously in our laboratory. The relative movement of domains lies at the heart of RRF function. Three salt bridges were hypothesized to reduce the flexibility of MtRRF when compared to the protein from E.coli (EcRRF), which has only one such salt bridge. Out of these three bridges, two are between domain 1 and domain 2, whereas the third is between the hinge region and the C-terminus of the molecule. These salt bridges were disrupted with appropriate mutations and the structure and activity of the mutants and their ability to complement EcRRF were explored. An inactive C-terminal deletion mutant of MtRRF was also studied. Major, but different, structural changes were observed in the C-terminal deletion mutant and the mutant involving the hinge region. Unlike the wild type protein and the other mutants, the hinge mutant complements EcRRF. This appears to result from the increased mobility of the domains in the mutant, as evidenced by the results of librational analysis. In addition to the work on PTH and RRF, the author was involved during the period of studentship in carrying out X-ray studies of crystalline complexes involving amino acids and carboxylic acids, which is described in the Appendix of the thesis. The complexes studied are that of tartaric acid with arginine and lysine.

In this project a number of peptidyl transferase antibiotics were studied, specifically a group of aminohexose cytosine nucleoside antibiotics and their interaction with a selected number of highly conserved ribonucleic acid (RNA) motifs, designed to represent their possible binding site within the ribosome. This group of antibiotics shows a wide range of interesting properties, including antiviral and anti-tumour activity, and as they bind to a particularly conserved region in the ribosome, they are likely to be difficult for microorganisms to develop resistance to. It is hoped that once the mechanism of action of these antibiotics is better understood, that modifications to the antibiotics can be effectively made to create new or hybrid antibiotics with more selective antibacterial, or indeed antiviral or anti-tumour properties. The nuclear magnetic resonance (NMR) structure of the RNA binding, peptidyl tranferase inhibitor antibiotics amicetin, blasticidin S and gougerotin, in their native solution states, have been successfully determined. The structures all exhibit a stable conformation, stabilised by intramolecular hydrogen bonds. Amicetin was observed to be folded, distinctly different from the linear, extended conformation of amicetin previously determined by X-ray crystallography. The structure of blasticidin S was found to be very similar to its X-ray crystal structure. Gougerotin was shown to form a similar conformation to blasticidin S, save that the end chain of gougerotin was bent at right angles to the rest of the molecule, forming a structure similar to that of the major bound X-ray crystal structure of blasticidin S. All the solution structures showed a similar conformation in the analogous regions of their chemical structure, suggesting that hybrid antibiotics could be produced.Two highly conserved RNA motifs of Halobacterium halobium (H. h.) and Escherichia coli (E. coli) 23S ribosomal RNAs were chosen to investigate their interaction with amicetin. The NMR structure of the H. h. and E. coli. 29-mer RNA motifs have been determined; the motifs both form well folded A-form RNA conformations. The E. coli NMR structure differs from the X-ray crystal structure of the motif contained within the ribosome, as a highly conserved adenine residue, which resides in a bulge strongly implicated with amicetin binding, folds into the helix as opposed to being flipped out. Instead, an adjacent cytosine residue partially flips out; whereas in the crystal structure, it is folded within the helix. The NMR stuctures of the H. h. motif differs from the X-ray crystal structure of the motif, contained within the ribosome, as none of the bases are flipped out and a number of non-canonical base pairs are formed in the solution structure. To continue this study, a fully 13C and 15N isotopically labelled version of the H. h. RNA sample has been partially assigned, and an initial structure determination has been performed, using ultra high field 1 GHz spectroscopy.Addition of amicetin to both the H. h. and E. coli 29-mer RNA samples were accompanied by discrete changes to the spectra, suggesting weak interaction between the two components. These can be qualitatively interpreted to changes induced in the local conformation of the RNA motifs and the amicetin arising from the formation of a complex, between the amicetin and the bulge region of the particular motif.

O polimorfismo de inserção/deleção (I/D) do gene da enzima de conversão da angiotensina I foi estudado em coorte de sobreviventes de 333 portadores de insuficiência cardíaca, de idades entre 13 e 68 (43,3 ± 10,5) anos, 262 (78,7%) dos quais eram homens e 71 (21,3%) mulheres. O grupo controle foi constituído de 807 doadores voluntários de sangue com idades entre 18 e 60 (31,5 ± 9,3) anos, 557 (69%) dos quais eram homens e 250 (31%) mulheres. A insuficiência cardíaca foi atribuída à cardiomiopatia dilatada idiopática em 125 (37,6%) pacientes. Nos demais pacientes as etiologias foram: a cardiomiopatia insquêmica em 63 (18,9%), a cadriomiopatia da doença de Chagas em 58 (17,4%), a cardiomiopatia hipertensiva em 41 (12,3%), a cardiomiopatia alcoólica 24 (7,2%), a cardiomiopatia valvar em 11 (3,3%) e a cardiomiopatia periparto em 11 (3,3%). A determinação dos genótipos associados ao polimorfismo I/D foi realizada pela reação em cadeia da polimerase. Foram estudadas a distribuição dos genótipos entre os indivíduos do grupo controle e os pacientes e as prováveis associações do polimorfismo I/D com diferentes variáveis clínicas e com a evolução. Essas análises foram realizadas de acordo com o padrão de herança genética atribuído ao alelo D (co-dominante, recessivo ou dominante). Na análise estatística foram utilizados o teste do qui-quadrado, o teste t-Student, a análise de variância (ANOVA), o método de Kaplan-Meier, o teste log-rank e a regressão de Cox. A freqüência do genótipo DD foi menor no grupo de pacientes, considerando-se o caráter recessivo atribuído ao alelo D (p=0,034). Os portadores do genótipo DD apresentaram maior média de valores do diâmetro sistólico do ventrículo esquerdo determinado pelo ecocardiograma, quando foi atribuído caráter recessivo ao alelo D (p=0,031). O intervalo decorrido do nascimento até o aparecimento dos sintomas foi menor nos portadores do genótipo DD com cardiomiopatia alcoólica, ao ser atribuído caráter recessivo ao alelo D (p=0,033). O intervalo entre o nascimento e o aparecimento dos sintomas foi menor nos portadores do genótipo DD com cardiomiopatia hipertensiva, quando foi atribuído caráter co-dominante (p=0,048) ou recessivo (p=0,024) ao alelo D. Os portadores do genótipo DD apresentaram maior mortalidade após os 50 anos, ao ser atribuído caráter co-dominante (p=0,007) ou recessivo (p=0,002) ao alelo D. As variáveis independentes relacionadas com a maior mortalidade após os 50 anos de idade, ao ser atribuído caráter recessivo ao alelo D, foram: a idade (p<0,001), o genótipo DD (p=0,003), o diabetes melito (p=0,003) e a doença de Chagas (p=0,005). Atribuindo-se caráter co-dominante ao alelo D, as variáveis independentes relacionadas com maior mortalidade foram: a idade (p<0,001), a doença de Chagas (p=0,004), o diabetes melito (p=0,005) e o genótipo DD (p=0,015). Os resultados obtidos permitem sugerir que o genótipo DD está associado com maior morbidade e mortalidade em determinados grupos de pacientes com insuficiência cardíaca. / Insertion/deletion (I/D) polymorphism of the angiotensin I- converting enzyme gene was studied in a cohort of survivors of 333 patients with heart failure of different etiologies and in a control group of 807 volunteer blood donors. The age of the patients ranged from 13 to 68 (43,3 ± 10,5) years, 262 (78.7%) were men and 71 (21.3%) women. The age of the control group ranged from 18 to 60 (31,5 ± 9,3) years, 557 (69%) were men and 250 (31%) women. Idiopathic dilated cardiomyopathy was diagnosed in 125 (37.6%), ischemic cardiomyopathy in 63 (18.9%), Chagas\' disease cardiomyopathy in 58 (17.4%), hypertensive cardiomyopathy in 41 (12.3%), alcoholic cardiomyopathy in 24 (7.2%), valvular cardiomyopathy in 11 (3.3%) and peripartum cadiomyopathy in 11 (3.3%). The genotypes associated with the I/D polymorphism were determined by polymerase chain reaction. The distribution of the genotypes was determined in the control and patient groups as well the possible associations of the I/D polymorphism with clinical variables and the evolution. The chi-square test, the t-Student test, the analysis of variance (ANOVA), the Kaplan-Meire method, the log-rank test and Cox regression were used in the statistical analysis. The DD genotype was less frequent in patients, assuming a recessive effect of the D allele (p=0,0034). The left ventricular en-systolic diameter by echocardiography was higher in patients with the DD genotype, .... And the DD genotype, assuming a recessive effect of the D allele (p=0,033). The time elapsed until the onset of symptoms was shorter in patients with hypertensive cardiomyopathy and the DD genotype, assuming a codominant (p=0,048) or recessive (p=0.024) effect of the D allele. Patients older than 50 years with the DD genotype showed increased mortality, assuming a codominant (p=0,007) or recessive (p=0,002) effect of the D allele. The independent variables associated with increased mortality in patients older than 50 years were: age (p<0,001), the DD genotype (p=0,003), diabetes mellitus (p=0,003) and Chagas\' disease (p=0,005), assuming a recessive effect of the D allele. Assuming a codominant effect of the D allele, the independent variables associated with increased mortality in patients older than 50 years were: age (p<0,001), Chagas\' disease (p=0,004), diabetes mellitus (p=0,005) and the Dd genotype (p=0,015). These results suggest that the DD genotype may be associated with higher morbidity and mortality in some groups of patients with heart failure.

Rhomboid intramembrane serine proteases cleave polypeptide chains within lipid bilayer. Rhomboid proteases were originally discovered in Drosophila melanogaster where they regulate ontogenesis of the fly, but they are present in all domains of life. Nowadays, various diseases, such as malaria, amoebiasis, Parkinson's disease, various tumour malignancies, and diabetes, have been linked with rhomboid proteases. However, natural substrates and function of most rhomboids remain elusive. Cell biology tools are needed for unravelling functions of rhomboids, as well as for potential pharmacological applications, and this together fuels the effort to develop specific rhomboid inhibitors. The inhibitors known to date always bear an electrophilic warhead attacking the nucleophilic serine of the atypical serine-histidine catalytic dyad of rhomboid. From the various developed inhibitors, peptidyl -ketoamides substituted at the ketoamide nitrogen by hydrophobic groups, discovered in our laboratory, hold the biggest potential. They are potent, reversible, selective, tunable, and are built around a pharmacophore already approved for medical use. Here, I set out to improve peptidyl -ketoamides by exploring the chemical space in the active site of rhomboid and testing substituents of the ketoamide nitrogen of increasing...

There is strong crystallographic evidence that the 23S rRNA is the only catalytic entity in the peptidyl transferase center. Various mechanisms for the catalysis of peptidyl transfer have been proposed. Recently, attention has been given to the idea that the 23S rRNA simply acts to position the tRNA for spontaneous peptidyl transfer and that chemical catalysis may play only a secondary role. Conserved nucleotides U2585 and U2506 are thought to be involved in positioning the 3’ ends of A- and P-site substrates based on the crystallographic evidence, and because mutagenesis at these sites severely impairs peptide bond formation. In this study, pure populations of ribosomes with either U2585A or U2506G mutations in the 23S rRNA were analyzed to test the hypothesis that substitutions at nucleotides U2585 and U2506 in the peptidyl transferase center impair peptide bond formation by altering the position of the 3’ end of P-site tRNA relative to the 23S rRNA. Pure populations of mutant or wild-type ribosomes were obtained by an affinity tagging system and probed with 32P-labeled [2N3A76]tRNAPhe to determine how the 3’ end of tRNA interacts with the ribosomal proteins and 23S RNA at the peptidyl transferase center. Some of the data for the ribosomes with a G at position 2506 are consistent with a model suggested by Schmeing and coworkers in which nucleotide U2506 breaks from its original wobble base pair with nucleotide G2583 during A-site tRNA binding and swings towards the 3’ end of P-site tRNA, while nucleotide U2585 simultaneously moves away from the 3’ end of P-site tRNA.