Exploring the structural integrity of a picornavirus capsid
- Authors: Upfold, Nicole Sarah
- Date: 2020
- Subjects: Picornaviruses , Immunoglobulins , Capsids (Virology) , Viruses Morphology , RNA viruses
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/131837 , vital:36758 , DOI https://doi.org/10.21504/10962/131837
- Description: Picornaviruses are a diverse family of small RNA viruses that cause a broad range of human and veterinary diseases. Despite decades of research into the molecular biology of these pathogens, no antivirals and few vaccines are commercially available for the treatment and prevention of picornavirus infections. The capsids of these non-enveloped viruses are involved in many important aspects of the picornavirus lifecycle, such as cell attachment and entry, uncoating, and protection of the viral RNA. Although the structures of many picornavirus capsids have been solved, a broader understanding of the molecular determinants that are required for structural integrity and stability is imperative for an improved understanding of the basic biology of these viruses, and for designing effective control strategies. Collectively, this thesis aims to elucidate the molecular determinants of structural stability and integrity in the Theiler’s murine encephalomyelitis virus capsid (TMEV). To study the TMEV GDVII capsid using biochemical techniques, neutralising polyclonal antibodies were generated against GDVII particles. The antibodies recognised linear epitopes in the C-terminus of the VP1 protein, but not those present in VP2 or VP3. The VP1 C-terminal residues were mapped to a loop above the putative receptor binding pit on the capsid surface, which prompted an investigation into the potential binding site of the TMEV co-receptor, heparan sulphate. Molecular docking revealed that heparan interacts with residues of the receptor binding pocket, as well as residues of the adjoining VP1 C-terminal loop. These findings suggest that the antibodies neutralise virus infection by preventing attachment of the virus to the co-receptor and possibly the unknown primary receptor. Few studies have identified the specific residues and interactions at subunit interfaces that significantly contribute to picornavirus capsid stability, assembly, and function. A novel in-silico screen was developed for the prediction of hotspot residues at protein-protein interfaces of a virus capsid. This screen can be applied to elucidate the residues that contribute significantly to the intraprotomer, interprotomer and interpentamer interfaces of any picornavirus capsid, on condition that the structure of the virus is available. The screen was applied to TMEV GDVII resulting in the identification of hotspots, several of which correspond to residues that are known to be important for aspects of the virus lifecycle, such as those that contribute to pH stability or form part of receptor binding sites. This observation suggests that residues involved in specific capsid functions may also play a role in capsid stability. Many of the residues identified as hotspots in TMEV corresponded to those required for assembly, uncoating, and virus growth in representative picornaviruses from various genera, suggesting that the residues that regulate capsid stability may be somewhat conserved across the family. Hotspots identified at the interpentamer interfaces of TMEV were individually substituted to alanine to further explore their importance to the TMEV lifecycle. All the amino acid substitutions prevented completion of the virus lifecycle as no CPE was observed following transfection of susceptible cells. Immunofluorescence experiments demonstrated that virus protein synthesis and RNA replication were not inhibited by substitution of the hotspot residues, but that infectivity was severely impeded. This confirmed that the residues were required for some aspect of the virus lifecycle, such as capsid assembly, or were critical for maintaining the conformational stability of the TMEV particles. Virus capsids become unstable and are prone to dissociation under certain conditions such as extreme pH and non-physiological temperatures. The thermostability of TMEV was explored by selecting GDVII virions with improved thermal tolerance through serial passage and heat exposure. Thermostable virions that could tolerate temperatures above 57 °C had reduced infective titres compared to the wild type TMEV suggesting that the virus adapted to thermal stress at the expense of viral fitness. Sequencing the capsid encoding regions of the mutant virions revealed a pair of amino acid substitutions that were present in all mutants. Additional substitutions that were unique to viruses selected at different temperatures were also identified. Most of the substitutions were located within the intraprotomer interfaces of the virus, unlike previous studies on enteroviruses where mutations were mostly localised to the receptor binding pocket. This thesis provides the first analysis of the structural determinants of TMEV capsid stability. The generation of tools to further explore the capsid structures of TMEV and other picornaviruses provides an opportunity for future studies which may contribute to the development of novel control strategies against this important family of viruses. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2020
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- Date Issued: 2020
Analysis of the interaction between recombinant human Beta2 integrin I-domains and CD23
- Authors: Sprong, Kaitlin
- Date: 2014
- Subjects: Immune response -- Regulation , Immunoglobulins , CD23 antigen
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10362 , http://hdl.handle.net/10948/d1021078
- Description: In order to further elucidate the interaction between CD23 and β2 integrins (CD11b/CD18) the following objectives were established: Expression and purification of CD11b I-domain as a GST-fusion protein using Escherichia coli; Cloning, synthesis and expression of CD18 I-Like domain.CD11b I-domain has previously been expressed as a GST-fusion protein (Daniels, 2010) and consequently led to comparable expression of CD18 I-like domain as a GST-fusion protein; Preparation of two site-directed mutants of CD18 I-Like domain in order to study the function of the serine residue involved in the S116P mutation. The serine was mutated to proline, as in LAD patients, as well as alanine, a non-polar alternative, in order to contrast and compare binding characteristics. Expression, refolding and purification of sCD23, and a double mutatedsCD23 (RKΔAA) from E. coli; This was performed according to the method described by Daniels et al. (2005); Investigation of the CD23-CD11b I-like domain interaction through surface plasmon resonance spectroscopy.
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- Date Issued: 2014
Production of recombinant human CD21 and CD23 : towards a better understanding of their interaction
- Authors: Van Zyl, Dwain George
- Date: 2013
- Subjects: Immunoglobulins , Fc receptors
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:10365 , http://hdl.handle.net/10948/d10211135
- Description: The prevalence of allergic diseases has dramatically increased over the last three decades. Presently, it is estimated that 20-30 per cent of the developed world suffers from allergic diseases. The majority of allergic diseases are rooted in the activities of IgE; an immunoglobulin which exerts its effector functions by interacting with a network of proteins. This network includes its low affinity receptor CD23. Cross linking of membrane IgE and CD21 by soluble CD23 results in an increase in IgE synthesis. This marks the interaction between CD23 and CD21 as an attractive therapeutic target. However, details regarding this interaction are inadequate for rational drug design. To obtain a deeper understanding of the CD23-CD21 interaction recombinant human CD21 (SCR1-2 and SCR5-8) and CD23 (16 kD and 25 kDa) were produced. The cloning, expression and purification of recombinant proteins comprised a significant portion of this study. Recombinant CD23 was expressed as inclusion bodies, refolded by rapid dilution and purified by size exclusion chromatography. Conversely, recombinant CD21 was expressed as soluble MBP-fusions and purified with an amylose affinity resin. The interaction between recombinant CD23 and CD21 was analysed by flow cytometry and ELISA experiments. Flow cytometry showed that 16 kDa and 25 kDa CD23 interacted with SCR5-8 to the same extent. Semi-quantitative ELISA experiments showed that both SCR1-2 and SCR5-8 were able to interact with 16 kDa and 25 kDa CD23. This suggests that the binding sites of SCR1-2 and SCR5-8 occur on 16 kDa CD23. Furthermore, since proteins were expressed in E. coli it suggests that the CD23-CD21 interaction does not require glycosylation. Furthermore, considering what is known about the SCR1-2-CD23 interaction from previous NMR studies; i.e. that the C-terminal tail (residues residues 289-298) of CD23 is responsible for binding SCR1-2, indicates that SCR5-8 binds somewhere within the lectin domain of CD23. This indicates that the CD23-CD21 interaction involves C-terminal tail-SCR1-2 and lectin domain-SCR5-8 interactions.
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- Date Issued: 2013
Generation of polyclonal antibodies against Theiler's Murine Encephalomyelitis virus protein 2C, and their use in investigating localisation of the protein in infected cells
- Authors: Jauka, Tembisa Innocencia
- Date: 2010
- Subjects: Picornaviruses , RNA viruses , Immunoglobulins , Encephalomyelitis
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:3959 , http://hdl.handle.net/10962/d1004018 , Picornaviruses , RNA viruses , Immunoglobulins , Encephalomyelitis
- Description: The Picornavirus family of positive sense RNA viruses includes some significant human and animal pathogens including Poliovirus (PV), Foot-and-Mouth disease virus (FMDV) and Human Rhinovirus (HRV). The genome is translated within the host cell into a polyprotein that is proteolytically cleaved into the structural and nonstructural proteins. The highly conserved, non-structural protein 2C has numerous roles during the virus life cycle and is essential for virus replication. Although the protein has been well studied in the case of PV, its interactions with the host cell during picornavirus infection is poorly understood. Theiler’s Encephalomyelitis virus (TMEV) is a picornavirus that infects mice, and is being used in our laboratory as a model in which to study the 2C protein. In this study, polyclonal antibodies against the TMEV 2C protein were generated and used to localise the protein in infected cells by indirect immunofluorescence. To produce antigen for immunisation purposes, the TMEV-2C protein sequence was analysed to identify hydrophilic and antigenic regions. An internal region of the 2C representing amino acid residues 31-210 was selected, expressed in bacteria and purified by nickel NTA affinity chromatography. Time course analysis of 2C (31-210) showed that the peptide was maximally expressed at 5 hours post induction. The peptide was solubilised using a mild detergent and 1.5 mg of purified antigen was used for immunisation of rabbits. Western blot analysis confirmed that the antibodies could detect both bacteriallyexpressed antigen, and virally-expressed 2C. Examination of virus-infected baby hamster kidney cells by immunofluorescence and confocal microscopy using the antiserum (anti-TMEV 2C antibodies) showed that the protein had a diffuse distribution upon early infection and at later stages it was located in a large perinuclear structure representing the viral replication complex. Furthermore, 2C localised to the Golgi apparatus as revealed by dual-label immunofluorescence using anti-TMEV 2C antibodies and wheat germ agglutinin (WGA). Furthermore, it was shown that TMEV infection results in changes in cell morphology and a redistribution of the cytoskeletal protein, β-actin. The successful production of antibodies that recognise TMEV 2C opens the way for further studies to investigate interactions between 2C and hostencoded factors.
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- Date Issued: 2010
An investigation of the binding capacities of recombinant domain mutants of the human Polymeric Immunoglobulin Receptor (pIgR)
- Authors: Prinsloo, Earl Adin Gerard
- Date: 2006
- Subjects: Immunoglobulins
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:10307 , http://hdl.handle.net/10948/403 , Immunoglobulins
- Description: The membrane bound glycoprotein, polymeric immunoglobulin receptor (pIgR) is the primary transport molecule of the polymeric immunoglobulins, dimeric IgA and pentameric IgM, across epithelial cells. This process, known as transcytosis, is essential in order to establish immunity at mucosal surfaces. Typically, pIgR binds to the polymeric immunoglobulin at the basolateral surface of the epithelial cell, via five homologous immunoglobulin-like domains of the ectodomain. Binding is covalent to IgA and non-covalent to IgM; the IgM binding varying among species. The pIgR-bound complex is released at the apical surface of the cell after cleavage of pIgR at Arg585, thereafter referred to as secretory component (SC). SC confers protective and immunologic functions to the polymeric immunoglobulin. Free SC, i.e. not complexed with polymeric immunoglobulins, is also known to be released into mucosal secretions; and binds to pathogenic bacteria and bacterial products. It is known that domain I of the ectodomain is the primary domain in the interaction with polymeric immunoglobulins, while domain V is involved in a covalent linkage with IgA. However, little is known of domains II-IV and their role in immunoglobulin binding, particularly to IgM. This study aimed to characterize the binding of recombinant human pIgR domain mutants to polymeric IgM using immunological, biophysical and cell based techniques; thereby allowing greater insight into the contribution of each of the five domains. The unique domain structure allowed for selective amplification of single and multiple domain mutants from cloned human PIGR ectodomain cDNA. Mutants were cloned and expressed in Esherichia coli BL21 (DE3) as inclusion bodies. Recombinant mutant proteins were refolded in vitro by equilibrium gradient dialysis and purified to homogeneity. Equilibrium binding data show significant contributions to specific binding as a factor of domain presence. Binding kinetics determined by biophysical surface plasmon resonance measurements show the interplay between association and dissociation rates as defined by individual domains. In vitro competitive binding studies using the human intestinal carcinoma, HT29, known to constitutively express pIgR, show that the constructed recombinant domain mutants outcompete native pIgR. The level of competition is shown to be dependant on the domains downstream of domain I. The data also confirm the biological activity of the first in vitro refolded recombinant human SC.
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- Date Issued: 2006