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Thesis (Ph. D.)--University of Washington, 2004. / Vita. Includes bibliographical references (p. 184-192).

The concerns of the present study were to determine 1) the conditions necessary to measure displaceable [³H] L-aspartate binding to membrane fractions of the rat brain, 2) whether the binding demonstrated the charcteristics of the site which is active in vivo, and 3) whether the acidic amino acid neurotransmitters aspartate and glutamate bind to identical or different sites by comparing the pharmacological specificities of the [³H] L-aspartate binding with that of [³H] L-glutamate. The conditions of the [³H] L-aspartate binding assay were determined in synaptosomal and total particulate fractions of whole rat brain. The reaction mixture which included the membrane fraction suspended in Tris-HCl buffer (pH 7.4) in the presence or absence of the compound under test, was incubated at 37°C for 30 minutes. The reaction was stopped by centrifugation and the radioactivity in the pellet counted by liquid scintillation spectrometry. The [³H] L-aspartate binding was characterized in total particulate fractions of rat cerebellum. The apparent dissociation constant (K[sub=D]) and maximum binding (Bmax), as determined by Scatchard analysis, are 1.64 ± 0.34 μM and 7711 ± fmol/mg protein respectively. The displaceable binding is reversible, saturable, independent of the presence of NA⁺, has an affinity in the range where the neurotransmitter is active in vivo, and demonstrates a pharmacological specificity which includes stereospecificity. The compounds tested to demonstrate the pharmacological specificity were L-aspartate (IC[sub=50] = 1.81 μM), D-aspartate (IC[sub=50] = 46.6 μM), L-glutamate (IC[sub=50] = 1.24 μM), N-methyl-DL-aspartate (inactive), kainate (inactive), D-alpha-aminoadipate (inactive), and L-alpha-aminoadipate (IC[sub=50] =7.12 μM). The pharmacological specificity of [³H] L-aspartate binding was different from that of [³H] L-glutamate. When the binding data only are considered, therefore, separate receptors for aspartate and glutamate are indicated. The pharmacological specificity of the [³H] L-aspartate binding, that is the affinity of the binding site for N-methyl-DL-aspartate, D- and L-alpha-aminoadipate, however, does not correlate with the potency of these compounds derived from iontophoretic studies. L-alpha-aminoadipate is very effective while N-methyl-DL-aspartate and D-alpha-aminoadipate do not displace the [³H] L-aspartate binding. In iontophoretic studies, N-methyl-D-aspartate and D-alpha-aminoadipate are very potent as compared to aspartate while L-alpha-aminoadipate Is inactive. The [³H] L-aspartate binding then may not represent the site which is active in vivo. The characteristics of the aspartate site in vivo, however, may not be truely represented in iontophoretic studies because of, for example, uptake of the compounds. The aspartate binding site, therefore, must be identified as that which is activated in vivo. The question of separate receptors for aspartate and glutamate then must still be resolved. / Science, Faculty of / Zoology, Department of / Graduate

published_or_final_version / Physiology / Doctoral / Doctor of Philosophy

published_or_final_version / Biochemistry / Master / Master of Philosophy

The binding of low concentrations of actinomycin D (Act D) to fixed human metaphase chromosomes was studied using both autoradiographic and immunofluorescent techniques. At the concentration range of 0.001 - 0.1 μg/ml Act D is known to selectively inhibit rRNA synthesis. Although it was previously suggested that at these low concentrations Act D would selectively bind to the ribosomal cistrons, evidence also exists that the drug binds to non-ribosomal DNA, and inhibits rRNA transcription in an indirect fashion. Because of the conflicting data on Act D binding and a lack of focus on biologically relevant concentrations of drug, it was decided to systematically investigate the distribution of the drug binding in low concentrations to chromosomes from 72-hr human lymphocyte cultures. Autoradiographic detection of [³H]Act D bound to chromosomes showed no selective binding of the drug at concentrations that maximally inhibit rRNA synthesis. A new technique was employed using Formvar and potassium chromium sulfate as a pretreatment to autoradiography. This technique permitted simultaneous detection of silver grains and chromosome identification by G-banding. With autoradiographic exposure times of 1 and 7 days, there was a positive correlation of autoradiographic grains with chromosome length. To increase sensitivity in detection of Act D bound to chromosomes, a specific anti-Act D antibody was generated in rabbits. Antibody avidity was evaluated on the basis of a rapid charcoal assay. This charcoal assay was then used in development of a radioimmunoassay for Act D which is sensitive in quantitating the drug down to 0.005 μg/ml. The anti-Act D antibody was characterized to be IgG, and was shown to be specific for the pentapeptide lactone portion of the Act D molecule. Indirect immunofluorescence of Protein A-purified IgG containing anti-Act D was used to detect drug bound to fixed human chromosomes. The antibody was shown to be specific for drug bound to chromatin. When 0.1 μg/ml Act D was bound to chromosomes, the drug was observed bound throughout the genome, with no selective binding at the ribosomal cistrons. This confirms the autoradiographic data and supports the model of extranucleolar regulation of rRNA synthesis. Preliminary results suggest that Act D binds to GC-rich DNA, since an R-banding pattern was observed in 5% of the immunofluorescent metaphases examined.

To determine the antigenic relatedness of the different developmental stages of Cryptosporidium parvum, monoclonal IgG3 antibody (mAb), Cmg-3, was produced by immunizing mice with partially purified merozoites. The monoclonal Cmg-3 reacted with a 3.5 kDa antigen of sporozoites in western blots and appeared to react with cell surface antigens of air-dried merozoites and sporozoites using immunofluorescence (IF). Additional mAbs, C6B6 (IgG1) and C4A1 (IgM), which react with a 20 kDa and multiple sporozoite antigens, respectively, were employed for immunoelectron microscopic studies with Cmg-3. These mAbs showed similar (surface/cytoplasmic) immunoelectron microscopic colloidal gold labeling patterns with all C. parvum life cycle stages. The three mAbs were also examined for potential modulation of cryptosporidial infections in vivo by daily oral mAb administration to oocyst-inoculated neonatal mice. Monoclonal-treated neonatal mice were sacrificed four and eight days post infection (pi). Differences in infection rates were observed among the treatment groups (p < .05). Suckling mice treated daily with orally administered mixtures of mAbs (ascitic fluids) showed significantly reduced parasite loads compared to control mice at four and eight days pi, while suckling mice receiving mAb Cmg-3 alone showed significant differences only at four days pi. Passive transfer of immunity using hyperimmune bovine colostrum was performed to determine the therapeutic and prophylactic efficacy of daily oral administration of anti-C. parvum antibody on the manifestation of cryptosporidial disease in neonatal mice as a model for treating cryptosporidiosis in immunocompromised patients. Hyperimmune colostrum was found to provide therapeutic and prophylactic efficacy against cryptosporidiosis in neonatal mice. Significantly fewer (p < 0.05) stages of C. parvum were found in mice that received hyperimmune skim colostrum (HSC) or hyperimmune original colostrum (HC) than in those treated with control colostrum (CC) or saline. Using IF, antigen-specific IgG in HSC and HC to C. parvum was 35 times greater than that of CC. There was no significant difference between groups treated with HSC or HC (p < .05), which suggests that the immunoglobulins, other biologically active factors such as cytokines, or both, might be active factors of immunity against cryptosporidiosis.

A HEp-2 cell culture model was used to investigate the invasive properties of Campylobacter species. Two of twenty-five Campylobacter isolates did not invade HEp-2 cells, and one of these isolates did not adhere to the epithelial cells. Penetration of HEp-2 epithelial cells by C. jejuni was significantly (P < 0.05) inhibited with C. jejuni lysates and a MAb (1B4) in competitive inhibition studies. Immunogold electron microscopic studies revealed that the 1B4 MAb bound to the flagella and cell surface of low passage (invasive) C. jejuni M 96, whereas only the flagella of high passage (non-invasive) C. jejuni were labelled. Western blot analysis revealed that the 1B4 MAb identified an epitope on antigens ranging in size from 66 to 44 kDa in invasive and non-invasive organisms. Antigens were also recognized in lysates prepared only from invasive strains from 42 to 38 kDa. Sodium meta-periodate chemical treatment of C. jejuni lysates significantly (P < 0.05) affected its inhibitory capacity. Additionally, proteinase K and sodium meta-periodate treatment of lysates changed the mobility of antigens recognized by the 1B4 MAb. This suggests that the antigens required for epithelial cell penetration by C. jejuni may be glycoprotein in nature and that the functional binding site is dependent upon an intact carbohydrate moiety. Co-infection of HEp-2 epithelial cells with coxsackievirus B3, echovirus 7, polio virus (LSc type 1), porcine enterovirus and Campylobacter isolates was performed to determine if a synergistic effect could be obtained. The invasiveness of C. jejuni was significantly increased for HEp-2 cells pre-infected with echovirus 7, coxsackievirus B3, and UV-inactivated (non-infectious) coxsackievirus B3 particles. Polio and porcine enterovirus had no effect on C. jejuni adherence and invasiveness. C. hyointestinalis and C. mucosalis, two non-invasive isolates, did not invade virus-infected HEp-2 cells. The increase of invasiveness of C. jejuni appears to be the result of specific interactions between the virus and the HEp-2 cell membrane. The data suggest that the invasiveness of Campylobacter is dependent upon the inherent properties of the organism. Virus-induced cell alterations can potentiate the invasiveness of virulent Campylobacter but are not sufficient to allow internalization by non-invasive bacteria.

The number of three-dimensional structures of potential protein targets available in several platforms such as the Protein Data Bank is subjected to a constant increase over the last decades. This observation should be an additional motivation to use structure-based methodologies in drug discovery. In the recent years, different success stories of Structure Based Drug Design approach have been reported. However, it has also been shown that a lack of druggability is one of the major causes of failure in the development of a new compound. The concept of druggability can be used to describe proteins with the capability to bind drug-like compounds. A general consensus suggests that around 10% of the human genome codes for molecular targets that can be considered as druggable. Over the years, the protein druggability was studied with a particular interest to capture structural descriptors in order to develop computational methodologies for druggability assessment. Different computational methods have been published to detect and evaluate potential binding sites at protein surfaces. The majority of methods currently available are designed to assess druggability of a static structure. However it is well known that sometimes a few local rearrangements around the binding site can profoundly influence the affinity of a small molecule to its target. The use of techniques such as molecular dynamics (MD) or Metadynamics could be an interesting way to simulate those variations. The goal of this thesis was to design a new computational approach, called JEDI, for druggability assessment using a combination of empirical descriptors that can be collected ‘on-the-fly’ during MD simulations. JEDI is a grid-based approach able to perform the druggability assessment of a binding site in only a few seconds making it one of the fastest methodologies in the field. Agreement between computed and experimental druggability estimates is comparable to literature alternatives. In addition, the estimator is less sensitive than existing methodologies to small structural rearrangements and gives consistent druggability predictions for similar structures of the same protein. Since the JEDI function is continuous and differentiable, the druggability potential can be used as collective variable to rapidly detect cryptic druggable binding sites in proteins with a variety of MD free energy methods.

Poon Kwok Man. / Thesis submitted in: December 1999. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (leaves 118-123). / Abstracts in English and Chinese. / ABSTRACT --- p.ii / 摘要 --- p.iv / DECLARATION --- p.vi / ACKNOWLEDGEMENTS --- p.vii / TABLE OF CONTENTS --- p.viii / LIST OF FIGURES --- p.xii / LIST OF TABLES --- p.xv / ABBREVIATIONS --- p.xvi / Chapter CHAPTER 1: --- INTRODUCTION / Chapter 1.1. --- Antibody structure and diversity --- p.1 / Chapter 1.2. --- Antibody genes --- p.5 / Chapter 1.3. --- The antibody response to phosphorylcholine --- p.10 / Chapter 1.3.1. --- Group I antibodies --- p.11 / Chapter 1.3.2. --- Group II antibodies --- p.14 / Chapter 1.3.3. --- Fine specificity of group I antibodies --- p.14 / Chapter 1.4. --- Anti-phosphorylcholine antibody structure --- p.15 / Chapter 1.5. --- Recombinant antibody --- p.22 / Chapter 1.5.1. --- Phage biology --- p.24 / Chapter 1.5.2. --- Phage-displayed antibodies --- p.29 / Chapter 1.5.3. --- Helper phage --- p.32 / Chapter 1.6. --- Objectives and scope of study --- p.34 / Chapter CHAPTER 2 --- METHODOLGY / Chapter 2.1. --- Antibody --- p.41 / Chapter 2.1.1. --- Hybridoma culture --- p.41 / Chapter 2.1.2. --- Production of antibody by induction of ascitic fluid --- p.41 / Chapter 2.1.3. --- Antibody purification --- p.41 / Chapter 2.1.3.1. --- Ammonium sulfate precipitation --- p.42 / Chapter 2.1.3.2. --- Affinity purification by Protein A-sepharose --- p.42 / Chapter 2.1.4. --- Production of Fab fragment by papain digestion --- p.43 / Chapter 2.2. --- Antigens --- p.43 / Chapter 2.2.1. --- Preparation of TsAg form infected ICR mouse --- p.44 / Chapter 2.2.2. --- Purification of Trichinella spairalis PC antigen --- p.44 / Chapter 2.2.2.1. --- Preparation of Mab2 affinity column --- p.44 / Chapter 2.2.2.2. --- Purification of TsAg --- p.45 / Chapter 2.2.3. --- Preparation of PC-HSA --- p.45 / Chapter 2.2.3.1. --- Preparation of p-diazonium phenylphosphorylcholine (DPPC) --- p.45 / Chapter 2.2.3.2. --- Conjugation of PC to HSA --- p.45 / Chapter 2.2.4. --- Commercial available antigens --- p.46 / Chapter 2.2.4.1. --- Pneumovax® 23 --- p.46 / Chapter 2.2.4.2. --- Lipopolysaccharide --- p.46 / Chapter 2.2.5. --- Standardization of PC-antigens --- p.46 / Chapter 2.3. --- Cloning of Mab2-scFv into phage display form --- p.47 / Chapter 2.3.1. --- Total RNA extraction --- p.50 / Chapter 2.3.2. --- cDNA synthesis --- p.50 / Chapter 2.3.3. --- Heavy chain variable region gene amplification --- p.51 / Chapter 2.3.4. --- Light chain variable region gene amplification --- p.51 / Chapter 2.3.5. --- Joining of heavy and light chain gene with linker --- p.52 / Chapter 2.3.6. --- Ligation of scFv gene with pCANTAB-5E vector --- p.52 / Chapter 2.3.7. --- Transformation --- p.53 / Chapter 2.3.7.1. --- E.coli strains --- p.53 / Chapter 2.3.7.2. --- E.coli cell preparation for electroporation --- p.54 / Chapter 2.3.7.3. --- Electroporation --- p.54 / Chapter 2.3.7.4. --- Competent E.coli preparation by CaCl2 --- p.55 / Chapter 2.3.7.5. --- Heat shock --- p.55 / Chapter 2.4. --- Expression of phage display scFv --- p.55 / Chapter 2.5. --- Enrichment and screening of Mab2-scFv phage --- p.56 / Chapter 2.5.1. --- Biopanning --- p.56 / Chapter 2.5.2. --- Restricition fragment analysis --- p.58 / Chapter 2.5.3. --- PCR screening --- p.58 / Chapter 2.5.4. --- DNA sequencing --- p.58 / Chapter 2.5.4.1. --- Manual sequencing --- p.58 / Chapter 2.5.4.2. --- Auto sequencing --- p.59 / Chapter 2.6. --- Mutagenesis --- p.59 / Chapter 2.6.1. --- Preparation of Uracil containing ssDNA --- p.60 / Chapter 2.6.2. --- Phosphorylation of mutagenic oligonucleotide --- p.60 / Chapter 2.6.3. --- Hybridization and secondary strand synthesis...…… --- p.60 / Chapter 2.6.4. --- Transfection and screening of mutants --- p.61 / Chapter 2.7. --- Expression of soluble scFv-E-tag --- p.61 / Chapter 2.7.1. --- SDS-PAGE analysis --- p.62 / Chapter 2.7.2. --- Anti-E-tag ELISA --- p.62 / Chapter 2.8. --- ELISA binding assay --- p.63 / Chapter 2.8.1. --- Specificity of Mab2 antibody Fab --- p.63 / Chapter 2.8.1.1. --- Carrier specifcity assay --- p.63 / Chapter 2.8.1.2. --- Free hapten inhibition assay --- p.64 / Chapter 2.8.2. --- Specificity of the scFv --- p.64 / Chapter 2.8.2.1. --- Antigen binding assay --- p.65 / Chapter 2.8.2.2. --- Free hapten inhibition assay --- p.65 / Chapter 2.8.2.3. --- Inhibition on Ts2 and Mab2 antibody assay --- p.65 / Chapter 2.9. --- Affinity assay --- p.66 / Chapter 2.10. --- Mutants analysis --- p.66 / Chapter CHAPTER 3 --- RESULTS / Chapter 3.1. --- Cloning VH and VL gene of Mab2 into scFv --- p.67 / Chapter 3.1.1. --- Amplification of variable region of H and L chain --- p.67 / Chapter 3.1.2. --- Biopanning --- p.70 / Chapter 3.1.3. --- Genetic composition of isolated clones --- p.70 / Chapter 3.2. --- Mutagenesis --- p.84 / Chapter 3.3. --- Expression and characterisation of wild-type scFv --- p.88 / Chapter 3.3.1. --- ScFv soluble protein --- p.88 / Chapter 3.3.2. --- Phage displayed scFv --- p.91 / Chapter 3.3.3. --- Standardization of PC antigens --- p.91 / Chapter 3.3.4. --- Binding acticity of scFv --- p.94 / Chapter 3.3.4.1. --- Influence of the avidity on carrier specificity binding --- p.96 / Chapter 3.4. --- Antigen specificity --- p.99 / Chapter 3.4.1. --- Free hapten inhibiton --- p.99 / Chapter 3.4.2. --- Inhibition on the binding of Ts2 --- p.102 / Chapter 3.4.3. --- Binding affinity --- p.104 / Chapter 3.5. --- Binding activities of mutants --- p.106 / Chapter CHAPTER 4 --- GENERAL DISCUSSION --- p.109 / REFERENCE --- p.118