The 3' terminal stem loop of the WNV minus-strand [WNV3'(-) SL] RNA was previously shown to bind the cell protein, T-cell intracellular antigen-1 (TIA-1), and the related protein, TIAR. These two proteins are known to bind AU-rich sequences in the 3' UTRs of some cellular mRNAs. AU stretches are located in three single-stranded loops (L1, L2, and L3) of the WNV3'(-) SL RNA. The RNA binding activity of both proteins was reduced when L1 or L2, but not L3, AU sequences were deleted or substituted with Cs. Deletion or substitution with Cs of the entire AU-rich sequence in either L1 or L2 in a WNV infectious clone was lethal for the virus while mutation of some of these nt decreased the efficiency of virus replication. Mutant viral RNAs with small plaque or lethal phenotypes had similar translational efficiencies to wildtype RNA, but showed decreased levels of plus-strand RNA synthesis. These results correlated well with the efficiency of TIA-1 and/or TIAR binding in in vitro assays. In normal cells, TIA-1 and TIAR are evenly distributed in the cytoplasm and nucleus. Between 6 and 24 hr after WNV infection, TIAR concentrated in the perinuclear region and TIA-1 localization to this region began by 24 hr. Similar observations were made in DV2 infected cells but at later times after infection. In infected cells, both proteins colocalized with dsRNA, a marker for viral replication complexes, and with viral non-structural proteins. Anti-TIAR or anti-TIA-1 antibody coimmunoprecipitated viral NS3 and possibly other viral nonstructural proteins. In response to different types stress, TIA-1 and TIAR recruit cell mRNA poly(A)+ into cytoplasmic stress granules (SG) leading to general translational arrest in these cells. SG were not induced by flavivirus infection and cells became increasingly resistant to arsenite induction of SG with time after infection. Processing Body (PB) assembly was also decreased beginning at 24 hr. These data suggest that the sequestration of first TIAR and then TIA-1 via their interaction with viral components in flavivirus infected cells inhibits SG formation and prevents the shutoff of host translation.

This thesis presents an investigation of fluorescence resonance energy transfer (FRET) as a reporting signal for protein-protein interactions. Quantitative optical assays to measure protein binding, conjugation and deconjugation are developed and results validated by conventional biochemical techniques. The optical techniques developed provide fast, cheap, quantitative and accurate alternatives to conventional methods. Fluorescent protein fluorophores ECFP and Venus-EYFP were chosen as they are a non-interfering FRET pair and provide an inexpensive and convenient cloning-based labelling method. The small ubiquitin-like modifier SUMO and the SUMOylation pathway leading to its conjugation to target proteins is investigated as a model system. These assays are hence particularly relevant to research on post-translational modification and ubiquitin systems. In protein-protein binding assays we utilise both steady-state and time-resolved FRET detection to measure the equilibrium binding constant of the well-characterised pair SUMO1 and Ubc9. An assay in multi-well plate format is also presented, which uniquely enables repeat measurements under varying conditions and under the addition of further substances. The multi-protein binding interactions of the SUMOylation pathway including RanBP2 are analysed in binding inhibition assays. Our results clarify the role of RanBP2: a covalent SUMO1-Ubc9 link is required for the formation of a trimeric complex, although mutual binding sites are present on all three proteins. Furthermore, the binding of SUMO1 and Ubc9 is disrupted by RanBP2, which may be an essential step in transferring SUMO1 to its target protein. A FRET-based kinetic study of this conjugation process to RanGAP1 is presented. An assay to monitor the deconjugation of SUMO1 by specific proteases is established using a doubly-tagged SUMO construct. This enables a quantitative analysis of protease and substrate specificity based on real-time kinetic data, a characterisation of crude cell extracts and a high-throughput screen for protease inhibitors using FRET. A screen of the National Cancer Institute (NIC) diversity set for SenP1 inhibition reveals nine suitable compounds, which are potential anti-cancer drugs. The results of two further projects, the study of protein-protein binding by measuring small refractive index changes and the autofluorescence of normal and neoplastic cervical tissue models are also presented. In the latter, principal component analysis was used to systematically identify emission regions of significant variation between samples, enabling discrimination between healthy and pre-cancerous tissue models.

Chiu, Wai Yin Vivien. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 151-162). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese.

La variabilité pharmacocinétique liée à une élimination des médicaments par glucuronoconjugaison a été peu étudiée. Nous avons donc choisi d’étudier les caractéristiques pharmacocinétiques de deux médicaments glucuronoconjugués, l’acide mycophénolique (MPA, prodrogue, mycophénolate mofétil ou MMF) et le raltégravir, dans certaines situations cliniques spécifiques. Deux études cliniques ont été réalisées avec le MMF. En transplantation hépatique pédiatrique, des AUC0-12 de MPA supérieures à 30 mg.h/L ont été obtenues chez tous les enfants avec une dose de 600 mg/m² de MMF administrée par voie orale deux fois par jour. L’estimation de l’AUC0-12 par méthode non compartimentale étant particulièrement contraignante en pédiatrie, nous avons développé une stratégie de prélèvements limités permettant une estimation à partir de seulement trois prélèvements. Chez des patients adultes transplantés rénaux, nos travaux ont permis de caractériser le polymorphisme génétique des transporteurs ABCC2 et ABCB1 et l’albuminémie comme étant des facteurs de variabilité inter et intra-individuelle de la pharmacocinétique du MPA. Les concentrations intracellulaires moyennes de MPA dans les cellules mononuclées du sang périphérique étaient élevées et largement supérieures à la concentration de MPA inhibant 50% de l’activité de l’IMPDH. Nos premiers résultats concernant le raltégravir montrent que ses paramètres pharmacocinétiques sont caractérisés par une variabilité inter-individuelle importante chez des patients infectés par le VIH. Nous avons établi que le raltégravir ne se fixe pas du tout sur l’alpha-1-glycoprotéine acide mais se fixe à 60% sur l’albumine, cette fixation étant dépendante du pH plasmatique. Cependant, cette forte liaison du raltégravir à l’albumine n’empêche pas une bonne diffusion du médicament dans le compartiment séminal. En conclusion, les études de pharmacocinétique clinique que nous avons menées montrent que la variabilité de la pharmacocinétique de ces deux médicaments glucuronoconjugués est aussi importante que pour des médicaments métabolisés par le cytochrome P450 3A4. L’identification des facteurs de variabilité de ces médicaments contribue à l’optimisation des traitements. / Pharmacokinetic variability was poorly studied for drugs eliminated by glucuronidation. We therefore chose to study the pharmacokinetic parameters of two glucuronidated drugs, mycophenolic acid (MPA, prodrug, mycophenolate mofetil or MMF) and raltegravir, in specific clinical situations. Two clinical studies were conducted with MMF. In pediatric liver transplantation, MPA AUC0-12 above the target AUC of 30 mg.h/L were obtained in all children with a MMF dosing regimen of 600 mg/m² administered orally twice a day. As extensive AUC monitoring is laborious, especially in children, we developed a limited sampling strategy to calculate MPA AUC0-12 with only three samples. In adult renal transplantation, our work allowed us to characterize genetic polymorphism of ABCC2 and ABCB1 genes and serum albumin as factors of inter and intraindividual variability in MPA pharmacokinetics. We demonstrated that MPA concentrations in peripheral blood mononuclear cells were high and well above the concentration of MPA responsible for a 50%-inhibition of the activity of IMPDH. Our first results show that the raltegravir pharmacokinetics is characterized by a wide interindividual variability in HIV-infected patients. Raltegravir does not bind to alpha-1-acid glycoprotein but binds to 60% to albumin and this binding is pH-dependent. Despite this high protein binding, a good penetration into the seminal compartment was evidenced. In conclusion, these clinical pharmacokinetic studies demonstrated that the variability in the pharmacokinetics of these glucuronidated drugs is as important as the one exhibited by drugs metabolized by cytochrome P450 3A4. Identifying factors of variability of these glucuronidated drugs contributes to optimizing patient care.

Atualmente a cucurbitacina E é considerada uma candidata a fármaco em razão de sua atividade anticâncer, reconhecimento de seus alvos moleculares e sinergismo com outros fármacos utilizados no tratamento do câncer. Porém, ainda não é possível seu uso na clínica devido a importantes lacunas na literatura relativas a ensaios de farmacocinética pré-clínicos e clínicos. A cucurbitacina E é hidrolisada a cucurbitacina I em plasma e em microssomas de fígado humano. O presente estudo visa avaliar a farmacocinética populacional e ligação as proteínas plasmáticas da cucurbitacina E e seu metabólito cucurbitacina I em plasma de ratos. O método de análise sequencial da cucurbitacina E e cucurbitacina I em plasma de ratos foi desenvolvido utilizando LCMS/ MS. Alíquotas de 50 ?L de plasma foram desproteinizadas com acetonitrila e os resíduos reconstituídos com acetonitrila:água (1:1, v/v) e adicionados do padrão interno clobazam. Os extratos foram injetados na coluna RP-18 com fase móvel constituída por mistura de acetonitrila:água:metanol (32:35:33, v/v/v). O método é preciso e exato com linearidade no intervalo de 1-100 ng de cucurbitacina E/mL de plasma e de 0,4-200 ng de cucurbitacina I/mL de plasma. O método foi aplicado na avaliação da farmacocinética da cucurbitacina E administrada a ratos machos Wistar em dose única oral (gavagem) e intravenosa de 1mg/kg dissolvida em DMSO e tampão fosfato salino pH 7,4 (5:95, v/v). As amostras seriadas de sangue foram coletadas até 24 h após a administração oral ou intravenosa. As concentrações plasmáticas de cucurbitacina E foram quantificadas até 16 h somente após a administração intravenosa, enquanto as concentrações plasmáticas de cucurbitacina I permaneceram abaixo dos valores de LIQ seguindo a administração oral ou intravenosa. O modelo de farmacocinética populacional foi desenvolvido para a cucurbitacina E administrada por via intravenosa com o auxílio do programa NONMEM com adequada qualidade de ajuste e desempenho preditivo. O perfil farmacocinético da cucurbitacina E administrada por via intravenosa foi descrito por modelo bicompartimental com distribuição e eliminação de primeira ordem com os seguintes parâmetros farmacocinéticos: tempo de liberação (D) de 0,45 h, volume de distribuição (Vd) de 27,22 L, clearance (Cl) de 4,13 L/h e meiavida de eliminação (t1/2) de 4,57 h. As interações da cucurbitacina E e cucurbitacina I com as albuminas séricas humana (HSA) e de rato (RSA) foram investigadas utilizando biossensor óptico baseado em ressonância de plasma de superfície (SPR) e espectroscopia de dicroísmo circular (CD). Os dados de ligação das cucurbitacinas a albuminas foram obtidos por experimentos de competição de CD com biliverdina. Os dados de SPR revelaram um evento de ligação inédito entre a cucurbitacina I e a HSA e as afinidades de ligação da cucurbitacina E e cucurbitacina I são maiores para a RSA do que para a HSA. A cucurbitacina E e a cucurbitacina I podem ser classificadas como substâncias de alta afinidade de ligação com a HSA e com a RSA. A análise de CD mostrou que a cucurbitacina E e a cucurbitacina I modificam a ligação da biliverdina as albuminas através de modulação alostérica oposta (positiva para HSA, negativa para RSA), confirmando a necessidade de cuidados na extrapolação de dados farmacocinéticos pré-clínicos para clínicos. / Cucurbitacin E is currently considered a drug candidate due to its anticancer activity, recognition of its molecular targets, and synergism with other drugs used for cancer treatment. However, the use of cucurbitacin E in clinical practice is not possible because of important research gaps regarding its preclinical and clinical pharmacokinetic characteristics. Cucurbitacin E is hydrolyzed to cucurbitacin I in plasma and in human liver microsomes. The aim of this study was to evaluate the population pharmacokinetics and plasma protein binding of cucurbitacin E and of its metabolite cucurbitacin I in rats. The method for the sequential analysis of cucurbitacins E and I in rat plasma was developed using LC-MS/MS. Plasma aliquots of 50 ?L were deproteinized with acetonitrile, the residues were reconstituted in acetonitrile:water (1:1, v/v), and clobazam was added as internal standard. The extracts were injected into an RP-18 column using a mobile phase consisting of a mixture of acetonitrile:water:methanol (32:35:33, v/v/v). The method was precise and accurate, showing linearities at a range of 1-100 ng cucurbitacin E/mL plasma and of 0.4-200 ng cucurbitacin I/mL plasma. The method was applied to the pharmacokinetic evaluation of cucurbitacin E administered to male Wistar rats at a single oral (gavage) or intravenous dose of 1 mg/kg dissolved in DMSO and phosphate-buffered saline, pH 7.4 (5:95, v/v). Serial blood samples were collected up to 24 h after oral or intravenous administration. The plasma concentrations of cucurbitacin E were quantified up to 16 h only after intravenous administration, while the plasma concentrations of cucurbitacin I remained below the limit of quantification after oral or intravenous administration. The population pharmacokinetic model was developed for administered intravenously cucurbitacin E using the NONMEM program, with adequate goodness of fit and predictive performance. The pharmacokinetic profile of intravenously administered cucurbitacin E was described by a two-compartment model with first-order distribution and elimination. The following pharmacokinetic parameters were obtained: release time (D) of 0.45 h, volume of distribution (Vd) of 27.22 L, clearance (Cl) of 4.13 L/h, and elimination half-life (t1/2) of 4.57 h. The interactions of cucurbitacin E and I with human (HSA) and rat (RSA) serum albumins were investigated using an optical biosensor by surface plasmon resonance (SPR) and circular dichroism (CD) spectroscopy. The binding data of the cucurbitacins to albumins were obtained by CD competition experiments with biliverdin. The SPR data revealed an undescribed binding event between cucurbitacin I and HSA and the binding affinities of cucurbitacin E and cucurbitacin I were higher for RSA than for HSA. Cucurbitacin E and cucurbitacin I can be classified as substances with high binding affinity for HSA and RSA. CD analysis showed that cucurbitacin E and cucurbitacin I modify the binding of biliverdin to albumins through opposite allosteric modulation (positive for HSA, negative for RSA), confirming that care should be taken when extrapolating the pharmacokinetic data between species.

Leung Ka-Kit. / Thesis submitted in: November 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 67-71). / Abstracts in English and Chinese. / Abstract / Chapter CHAPTER 1. --- INTRODUCTION --- p.1 / Chapter 1.1 --- Background of protein structures --- p.1 / Chapter 1.2 --- Background of protein-protein interaction (PPI) --- p.4 / Chapter 1.2.1 --- Quaternary structure and protein complex --- p.4 / Chapter 1.2.2 --- Previous related work --- p.4 / Chapter 1.2.3 --- The kinetic and thermodynamic formalism --- p.6 / Chapter CHAPTER 2. --- MATERIALS AND METHODS --- p.10 / Chapter 2.1 --- Amino acid composition representative power modeling --- p.10 / Chapter 2.1.1 --- Propensity level modeling --- p.10 / Chapter 2.1.2 --- Polar atoms visualization --- p.17 / Chapter 2.2 --- Rigid structure representative power modeling --- p.17 / Chapter 2.3 --- Electrostatic potential modeling --- p.17 / Chapter 2.3.1 --- Charge residence --- p.17 / Chapter 2.3.2 --- Minimum Ribbon (MR) --- p.19 / Chapter 2.4 --- Examination of interface --- p.23 / Chapter 2.5 --- Identification procedures of a binding site --- p.24 / Chapter 2.6 --- System requirements --- p.24 / Chapter CHAPTER 3. --- RESULTS AND DISCUSSIONS --- p.24 / Chapter 3.1 --- Polar atoms --- p.25 / Chapter 3.2 --- Minimum Ribbon (MR) --- p.27 / Chapter 3.3 --- "Charge complementarity, propensity level and rigid structure orientation" --- p.31 / Chapter 3.4 --- Identification of interacting site --- p.36 / Chapter CHAPTER 4. --- CONCLUSIONS --- p.64 / System requirements --- p.65 / Basic operation --- p.65 / Limitation --- p.66

by Peter, Wei Gong Chang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1997. / Includes bibliographical references (leaves 103-124). / ACKNOWLEDGEMENTS --- p.i / ABSTRACT --- p.ii / TABLE OF CONTENTS --- p.iv / ABBREVIATIONS --- p.viii / Chapter CHAPTER 1 --- INTRODUCTION / Chapter 1.1 --- General introduction --- p.1 / Chapter 1.2 --- Human genome project --- p.5 / Chapter 1.3 --- Human adult heart cDNA library --- p.7 / Chapter 1.4 --- Human fetal heart cDNA library --- p.8 / Chapter 1.5 --- Sequencing of a human heart cDNA clone --- p.9 / Chapter 1.6 --- Knowledge of the role of selenium --- p.13 / Chapter 1.7 --- Mouse 56kDa selenium binding protein and acetaminophen-binding protein --- p.16 / Chapter CHAPTER 2 --- MATERIALS AND METHODS / Chapter 2.1 --- Plating out the cDNA library --- p.20 / Chapter 2.1.1 --- "Mediums, buffers and solutions" --- p.20 / Chapter 2.1.2 --- Bacteriophage clones preparation --- p.21 / Chapter 2.2 --- cDNA clone amplification by PCR --- p.23 / Chapter 2.3 --- Cycle sequencing of PCR products --- p.25 / Chapter 2.3.1 --- "Media, buffers and solutions" --- p.25 / Chapter 2.3.2 --- Preparation of sequencing reaction --- p.25 / Chapter 2.4 --- Gel electrophoresis using an automated A.L.F sequencer --- p.27 / Chapter 2.5 --- DNA sequence analysis --- p.29 / Chapter 2.6 --- Preparation of competent E. coli for transformation --- p.30 / Chapter 2.7 --- Transformation of plasmid into competent E. coll --- p.31 / Chapter 2.8 --- Mini-preparation of plasmid DNA --- p.32 / Chapter 2.9 --- Large scale plasmid DNA preparation by QIAGEN --- p.34 / Chapter 2.10 --- Cloning the human 56 kDa selenium binding protein (hSP56) into the pAED4 vector --- p.36 / Chapter 2.10.1 --- Bacterial strains and vector --- p.36 / Chapter 2.10.2 --- "Media, buffers and solutions" --- p.38 / Chapter 2.10.3 --- Primers design and PCR --- p.42 / Chapter 2.10.4 --- Purification of PCR products by Geneclean --- p.43 / Chapter 2.10.5 --- Restriction digestion of purified PCR product and pAED4 --- p.44 / Chapter 2.10.6 --- Ligation and transformation of hSP56 --- p.45 / Chapter 2.10.7 --- Screening and purification ofpAED4hSP56. --- p.47 / Chapter 2.11 --- Expression of hsp56 --- p.50 / Chapter 2.11.1 --- Induction of hSP56 expression --- p.50 / Chapter 2.11.2 --- SDS-PAGE and protein detection --- p.51 / Chapter 2.12 --- Northern hybriddization of hSP56 --- p.53 / Chapter 2.12.1 --- Animals & human tissue --- p.53 / Chapter 2.12.2 --- "Mediums, buffers and solutions" --- p.53 / Chapter 2.12.3 --- Preparation of total RNA --- p.56 / Chapter 2.12.4 --- Formaldehyde agarose gel electrophoresis --- p.57 / Chapter 2.12.5 --- Preparation of radioactive probe --- p.58 / Chapter 2.12.6 --- RNA transfer and Northern hybridization --- p.59 / Chapter 2.13 --- Chromosomal mapping of the hSP56 gene --- p.62 / Chapter CHAPTER 3 --- RESULTS / Chapter 3.1 --- The sequencing results of 553 cDNA clones --- p.63 / Chapter 3.2 --- Catalogues of genes expressed --- p.65 / Chapter 3.3 --- Sequence analysis of hSP56 --- p.71 / Chapter 3.4 --- Northern hybridization of hSP56 --- p.84 / Chapter 3.5 --- Cloning of hSP56 into pAED4 --- p.87 / Chapter 3.6 --- Expression of the hSP56 in E. coli --- p.89 / Chapter 3.7 --- Chromosomal mapping of the hSP56 gene --- p.92 / Chapter CHAPTER 4 --- DISCUSSION / Chapter 4.1 --- General discussion --- p.94 / Chapter 4.2 --- The possible roles of hSP56 and mSP56 --- p.101 / Chapter 4.3 --- Future prospects --- p.102 / REFERENCES --- p.103 / APPENDIX 1 --- p.125 / APPENDIX.2 --- p.127

Abstract not available

L'oxydation spontanée de la dopamine en solution légèrement basique a été étudiée sur la base de la publication de Lee [Science, 318:426-430, 2007], et le produit de la réaction a été identifié comme de la mélanine. La capacité de la mélanine de lier des groupements amines de façon covalente a été confirmée par la quantification des sites de liaison correspondants. En outre il est possible de rédisperser des agrégats de mélanine dans des solutions fortement basiques. Les grains de mélanine ainsi obtenus ont été utilisés pour construire des films multicouches avec le poly(diallyldimethyl ammonium) (PDADMA). Différentes méthodes d'oxydation de la dopamine pour former des films de mélanine à l'interface solide-liquide ont été développées. Toutes les méthodes mènent à la formation de films continus de mélanine ayant des morphologies de surface similaires. Elles deviennent imperméables à des sondes électrochimiques à partir d'une épaisseur de l'ordre de 10 nm. Une plus grande perméabilité à des sondes chargées positivement ou neutres qu'à des sondes négatives a été confirmée. L'adsorption de protéines à des revêtements de mélanine a été expliquée par une combinaison d'interactions électrostatiques et covalentes. Pour arriver à cette explication le potentiel zêta de dépôts de mélanine a été mesuré en fonction du pH. La formation de la mélanine dans des films multicouches de poly(L-lysine) (PLL) et de hyaluronate (HA) a été étudiée: la mélanine est capable de remplir des films (PLL-HA)n de manière homogène, et les composés ainsi obtenus peuvent être détachés de leurs substrats comme membranes autosupportées préparées par une méthode biomimétique sous conditions douces.

Protein-protein and protein-ligand interactions are fundamental as many proteins mediate their biological function through these interactions. Many important applications follow directly from the identification of residues in the interfaces between protein-protein and protein-ligand interactions, such as drug design, protein mimetic engineering, elucidation of molecular pathways, and understanding of disease mechanisms. The identification of interface residues can also guide the docking process to build the structural model of protein-protein complexes. This dissertation focuses on developing computational approaches for protein-ligand and protein-protein binding site prediction and applying these predictions to improve protein-protein docking. First, we develop an automated approach LIGSITEcs to predict protein-ligand binding site, based on the notion of surface-solvent-surface events and the degree of conservation of the involved surface residues. We compare our algorithm to four other approaches, LIGSITE, CAST, PASS, and SURFNET, and evaluate all on a dataset of 48 unbound/bound structures and 210 bound-structures. LIGSITEcs performs slightly better than the other tools and achieves a success rate of 71% and 75%, respectively. Second, for protein-protein binding site, we develop metaPPI, a meta server for interface prediction. MetaPPI combines results from a number of tools, such as PPI_Pred, PPISP, PINUP, Promate, and SPPIDER, which predict enzyme-inhibitor interfaces with success rates of 23% to 55% and other interfaces with 10% to 28% on a benchmark dataset of 62 complexes. After refinement, metaPPI significantly improves prediction success rates to 70% for enzyme-inhibitor and 44% for other interfaces. Third, for protein-protein docking, we develop a FFT-based docking algorithm and system BDOCK, which includes specific scoring functions for specific types of complexes. BDOCK uses family-based residue interface propensities as a scoring function and obtains improvement factors of 4-30 for enzyme-inhibitor and 4-11 for antibody-antigen complexes in two specific SCOP families. Furthermore, the degrees of buriedness of surface residues are integrated into BDOCK, which improves the shape discriminator for enzyme-inhibitor complexes. The predicted interfaces from metaPPI are integrated as well, either during docking or after docking. The evaluation results show that reliable interface predictions improve the discrimination between near-native solutions and false positive. Finally, we propose an implicit method to deal with the flexibility of proteins by softening the surface, to improve docking for non enzyme-inhibitor complexes.