An understanding of the mechanical properties of viral capsids (protein assemblies forming shell containers) has become necessary as their perceived use as nano-materials for targeted drug delivery. In this thesis, a heterogeneous, spatially detailed model of the viral capsid is considered. This model takes into account the increased degrees of freedom between the capsomers (capsid sub-structures) and the interactions between them to better reflect their deformation properties. A spatially realistic finite element multi-domain decomposition of viral capsid shells is also generated from atomistic PDB (Protein Data Bank) information, and non-linear continuum elastic simulations are performed. These results are compared to homogeneous shell simulation re- sults to bring out the importance of non-homogenous material properties in determining the deformation of the capsid. Finally, multiscale methods in structural analysis are reviewed to study their potential application to the study of nanoindentation of viral capsids. / text

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Le virus de l’hépatite B (VHB) utilise la machinerie transcriptionnelle nucléaire pour sa réplication. Le génome viral est transporté de la périphérie cellulaire à l’enveloppe nucléaire. Généralement, ce transport intracytoplasmique rétrograde est facilité par le réseau de Mt via l’utilisation du complexe moteur de la dynéine. Nous avons montré que le transport des capsides du VHB dépend des Mt, ce qui permet l’adressage des capsides aux complexes du pore nucléaire (NPC) ; lequel est requis pour l’étape de libération du génome de la capside dans le noyau.Dans cette étude, nous avons utilisé des capsides provenant de virus récupérés dans du surnageant de HepG2.2.15, qui contiennent le génome mature partiellement double brin (capsides matures), et des capsides exprimées chez E.coli. Ces dernières sont utilisées telles quelles, capsides E.coli contenant de l’ARN, ou bien sont utilisées pour préparer des capsides vides. Après microinjection dans des ovocytes de Xenopus laevis, nous avons observé que les capsides vides et les capsides matures sont transloquées aux NPC avec une cinétique similaire. Les capsides contenant de l’ARN ne sont pas identifiées aux NPCs ce qui implique que le transport des deux autres types de capsides est actif. Cela a été confirmé par la pré-injection d’anticorps anti tubuline qui neutralisent le transport assuré par les Mt.L’attachement spécifique des capsides matures et vides aux Mt a été confirmé en utilisant des Mt polymérisés in vitro, nous avons montré que cette interaction nécessitait des protéines cytosoliques. En utilisant des expériences de coïmmunoprécipitation et de cosédimentation nous avons identifié une chaîne légère de la dynéine (DynLL1 membre de la famille Lc8) comme partenaire des capsides. Dans les expériences de microinjection, la comicroinjection d’un excès de DynLL1 avec les capsides inhibe leur transport vers les NPCs, indiquant que DynLL1 est impliquée dans le transport actif des capsides.DynLL2 qui n’interagit pas avec les capsides diffère de DynLL1 de seulement six acides aminés. Par mutagénèse dirigée de DynLL1, nous avons montré l’implication de deux acides aminés dans l’interaction directe avec les capsides. Ces deux acides aminés sont présents à la surface du dimère de DynLL1 et absents dans le sillon résultant de la dimérisation de DynLL1, sillon impliqué dans l’interaction avec la DynIC. Nous avons partiellement reconstitué le complexe DynIC, DynLL1 et capsides vides qui doit en partie refléter la situation in vivo. / Hepatitis B virus (HBV) needs the nuclear transcription machinery for replication. The virus thus depends on the transport of its genome from the cell periphery to the nuclear envelope. In general this retrograde intracytoplasmic trafficking is facilitated along Mt (MT) using motor protein complexes of the dynein family. As we showed earlier HBV capsid transport also depends upon intact MT in order to allow their arrival at the nuclear pores, which in turn is required for genome liberation from the capsid.In the analysis we used virus-derived HBV capsids obtained from the supernatant of HepG2.2.15, which contain the mature partially double-stranded DNA genome (mature capsids) and capsids expressed in E. coli. The latter were applied in two forms: as unspecific E. coli RNA- containing capsids and as empty capsids. Upon microinjection into Xenopus laevis oocytes we observed that mature and empty capsids were translocated to the nuclear pores with a similar kinetic. RNA-containing capsids failed to arrive at the pores implying that transport of the two other capsid types was active. Active translocation was confirmed by pre-injecting anti tubulin antibodies which interfere with MT-mediated translocation.In vitro reconstitution assays confirmed the specific attachment of mature and empty capsids to MTs and showed the need of further cytosolic proteins. Using pull-down and co-sedimentation experiments we identified one dynein light chain (DYNLL1, member of the Lc8 family) as interaction partner of the capsids. Injecting an excess of recombinant DYNLL1 with empty capsids into Xenopus laevis oocytes inhibited capsid transport to the nuclear pores indicating that DYNLL1 was only functional interaction partner implied in active transport.DNYLL2 did not interact with the capsids although differing from DYNLL1 by just six amino acids. Site directed mutagenesis of DYNLL1 revealed that two amino acids were critical for a direct interaction with the capsids. Both localized at the exterior of the DYNLL1 dimer and not in the groove of DYNLL1, which interacts with the dynein intermediate chain. Accordingly we could reconstitute a complex consisting of empty capsids, DYNLL1 and dynein intermediate chain as it should be in the in vivo situation.

Experiments show that MgSO4 salt has a non-monotonic effect as a function of MgSO4 concentration on the ejection of DNA from bacteriophage lambda. There is a concentration, N0, at which the minimum amount of DNA is ejected. At lower or higher concentrations, more DNA is ejected. We propose that this non-monotonic behavior is due to the overcharging of DNA at high concentration of Mg⁺² counterions. As the Mg⁺² concentration increases from zero, the net charge of ejected DNA changes its sign from negative to positive. N0 corresponds to the concentration at which DNA is neutral. Our theory fits experimental data well. The DNA-DNA electrostatic attraction is found to be -0.004 kBT/nucleotide. Simulations of DNA-DNA interaction of a hexagonal DNA bundle support our theory. They also show the non-monotonic DNA-DNA interaction and reentrant behavior of DNA condensation by divalent counterions. Three problems in understanding the capsid assembly for a retrovirus are studied: First, the way in which the viral membrane affects the structure of in vivo assembled HIV-1 capsid is studied. We show that conical and cylindrical capsids have similar energy at high surface tension of the viral membrane, which leads to the various shapes of HIV-1 capsids. Secondly, the problem of RNA genome packaging inside spherical viruses is studied using RNA condensation theory. For weak adsorption strength of capsid protein, most RNA genomes are located at the center of the capsid. For strong adsorption strength, RNA genomes peak near the capsid surface and the amount of RNA packaged is proportional to the capsid area instead its volume. Theory fits experimental data reasonably well. Thirdly, the condensation of RNA molecules by nucleocapsid (NC) protein is studied. The interaction between RNA molecules and NC proteins is important for the reverse transcription of viral RNA which relates to the viral infectivity. For strong adsorption strength of the NC protein, there is a screening effect by RNA molecules around a single NC protein.

No description available.

X-ray crystallography is one of the most powerful tools for the elucidation of the structure of biological macromolecules such as proteins and viruses. Crystallographic techniques are extensively used for investigations on protein structure, ligand-binding, mechanisms of enzyme catalyzed reactions, protein-protein interactions, role of metal ions in protein structure and function, structure of multi-enzyme complexes and viruses, protein dynamics and for a myriad other problems in structural biology. Crystallographic studies are essential for understanding the intricate details of the mechanism of action of enzymes at molecular level. Understanding the subtle differences between the pathogenic enzymes and host enzymes is necessary for the design of inhibitor molecules that specifically inhibit parasite enzymes. The current thesis deals with the application of biochemical and crystallographic techniques for understanding the structure and function of proteins from two pathogenic organisms – a plant virus Physalis Mottle Virus (PhMV), and a pathogenic bacterium, Salmonella typhimurium and also stress induced proteins from Oryza sativa. The thesis has been divided into seven chapters, with the first four chapters describing the work carried out on PhMV, while the rest of the chapters deal with the studies on stress response proteins from Oryza sativa and Salmonella typhimurium. The first part of the thesis deals with studies on viral capsids. Viruses are obligate parasites that have proteinaceous capsids enclosing the genetic material, which, in the case of small plant viruses, is invariably ss-RNA. X-ray diffraction studies on single crystals of viruses enable visualization of the structures of intact virus particles at near-atomic resolution. These studies provide detailed information regarding the coat protein folding, molecular interactions between protein subunits, flexibility of the N-and C-terminal segments and their probable importance in viral assembly, role of RNA in capsid assembly, nucleic acid (RNA)-protein interactions, the capsid structure and mechanism of assembly and disassembly. The present thesis deals with the capsid structure and analysis of the coat protein (CP) recombinant mutants of PhMV. Virus assembly, one of the important steps in the life cycle of a virus, involves specific interactions between the structural protein and cognate viral genome. This is a complex process that requires precise protein-protein and protein nucleic acid interactions. In fact, most of the biological functional units such as ribosomes and proteosomes also require highly co-ordinated macromolecular interactions for their functional expression. Viruses being simple in their architecture, serve as excellent model systems to understand mechanism of macromolecular assembly and provide necessary information for the development of antiviral therapeutics, especially in animal viruses. PhMV is a plant virus infecting several members of Solanaceae family. It belongs to the tymoviridae group of single stranded RNA viruses. Its genome is encapsidated in a shell comprising of 180 (architecture based on T = 3 icosahedral lattice) chemically identical coat protein (CP) subunits (~ 20,000Da) arranged with icosahedral symmetry. In an earlier phase of work, PhMV purified from infected plant leaves was crystallized in the space group R3 (a = 294.56 Å,  = 59.86). X-ray diffraction data to 3.8 Å resolution were recorded on films by screenless oscillation photography. Using this data of severely limited quality and poor completion (40%), the structure PhMV was determined by molecular replacement using the related turnip yellow mosaic virus (TYMV) structure as the phasing model. There was therefore a need to re-determine and improve the structure, which could be useful for understanding the earlier detailed studies on its biophysical properties. As a continuation of these studies, the present investigations were conceived with the goal of determining the natural top and bottom component capsid structures of PhMV. Investigations were also carried out to examine the possibility of enhancing the diffraction quality of PhMV crystals. The thesis begins with a review of the current literature on the available crystal structures of viruses and their implications for capsid assembly (chapter I). All experimental and computational methods used during the course of investigations are described in chapter II, as most of these are applicable to all the structure determinations and analyses. The experimental procedures described include cloning, overexpression, purification, crystallization and intensity data collection. Computational methods covered include details of various programs used during data processing, structure solution, refinement, model building, validation and analysis. Chapter III describes structural studies on top and bottom components of PhMV. Purified tymoviruses including PhMV are found to contain two classes of particles that sediment at different velocities through sucrose gradients and are called the top (sedimentation coefficient 54 Svedberg units(S)) and the bottom (115S) components. The top component particles are either devoid of RNA or contain only a small subgenomic RNA (5%) while the bottom component particles contain the full length genomic RNA. Only the bottom component is infectious. The top and bottom components were separately crystallized in P1 and R3 space groups, respectively. It is of interest to note that crystals of the bottom component obtained earlier belonged to R3 space group while recombinant capsids that lack of full length RNA as in natural top component crystallized in the P1 space group. A polyalanine model of the homologous TYMV was used as the phasing model to determine the structures of these particles by molecular replacement using the program AMoRe. The refinement of top and bottom component capsid structures were carried out using CNS version 1.1 and the polypeptide models were built into the final electron-density map using the interactive graphics program O. The quality of the map was sufficient for building the model and unambiguous positioning of the side chains. There is a significant difference in the radius of the top and bottom component capsids, the top component being 5 Å larger in radius. Thus, RNA makes the capsid more compact, even though RNA is not a pre-requisite for capsid assembly. Partially ordered RNA was observed in the bottom component. The refined models could form the basis for understanding the architecture, protein-protein interactions, protein-nucleic acid interactions, stability and assembly of PhMV. Chapter IV provides a detailed description of the mutations carried out on PhMV coat protein towards enhancing the diffraction quality of crystals. The gene coding for PhMV coat protein (PhMVCP) and several of its deletion and substitution mutants were originally cloned in pRSETC and pET-21 vectors by Mira Sastri and Uma Shankar in Prof. Savithri’s laboratory at the Department of Biochemistry. It was observed that the recombinant intact coat protein and several mutants lacking up to 30 amino acids from the N-terminal end could assemble into empty shells resembling the natural top component. None of these deletion mutants crystallized in forms that diffracted to high resolution. Based on the intersubunit contacts observed, three more site-specific mutants were designed. These three mutants were expressed in BL21 (DE3), purified and crystallized. Even these mutant crystals did not diffract to high resolution. The polypeptide fold of PhMV coat protein therefore was carefully examined for probable reasons. It was found that PhMV subunit has three major cavities. Three cavities are likely to increase the flexibility of protein subunits, which in turn may result in crystals of poor quality. Mutations V52W, S158Q and A160L were shown to fill up these cavities and with the view of obtaining better crystals. These site specific mutations were carried out the mutant proteins were purified. It was shown that the recombinant capsids are stable and possess T=3 architecture. Two mutants were crystallized and a data set for V52W extending to 6.0 Å resolution could be collected. Due to the limited resolution, further work was not pursued. It is plausible that the triple mutant will diffract to higher resolution. The second part of the thesis deals with stress response proteins from Oryza sativa and Salmonella typhimurium. It is known that viral infection and abiotic and biotic stresses induce a network of proteins in plants. Chapter V presents a review of the current literature on stress proteins, focusing mainly on Oryza sativa and S. typhimurium stress response proteins. Chapter VI describes the over expression of stress proteins SAP1 and SAP2 from rice. These stress related proteins confer tolerance to cold, dehydration and salt stress in rice. These proteins have been cloned in the expression vector pEt-28(a) and expressed in E. coli strain BL21 CodonPlus(DE3)RIL. The proteins were purified and crystallization trials were made. However, there were no hits. In an attempt to get crystals, nine deletion constructs of SAP1 were designed eliminating potentially disordered and unfolded regions based on a bioinformatics analysis. Crystallization trails are being carried out on three of the constructs. Structural studies on a universal stress protein from Salmonella typhimurium, which shares homology with the rice universal stress proteins, was initiated. Apart from this, several other stress related proteins of Salmonella typhimurium have also been selected for structural and functional studies. These include YdaA, YbdQ, Yic, Ynaf, Yec, Spy and Usb. All these were cloned and expressed in E. coli. Out of seven proteins, Ynaf, YdaA and YbdQ were found in the soluble fraction and were expressed in quantities suitable for structural studies. I could crystallize YdaA and Ynaf. X-ray diffraction data to resolutions of 3.6 Å and 2.3 Å were collected on crystals of YdaA and YnaF, respectively. A tentative structure of YnaF has been obtained. Further attempts to determine these structures are in progress. Biophysical, Biochemical functional characterization of YdaA and YnaF proteins are described. Structural studies on mannose-6-phosphate isomerase, an enzyme related to stress regulatory proteins from S. typhimurium are dealt with in Chapter VII. Mannose 6-phosphate isomerase (MPI) catalyzes the interconversion of mannose 6-phosphate and fructose 6-phosphate. The structure could be solved in its apo and holo forms (with two different metal atoms, Y3+ and Zn2+), and complexed with the cyclic form of the substrate fructose 6-phosphate (F6P) and Zn2+. Isomerization involves acid/base catalysis with proton transfer between C1 and C2 atoms of the substrate. Lys 132, His 131, His 99 and Asp 270 are close to the substrate and are likely to be the residues involved in proton transfer. Interactions observed at the active site suggest that the ring opening step is catalyzed by His 99 and Asp 270. An active site loop consisting of residues 130-133 undergoes conformational changes upon substrate binding. The metal ion is not close to the substrate atoms involved in proton transfer. Binding of the metal induces structural order in the loop consisting of residues 50-54. Hence, the metal atom does not appear to play a direct role in catalysis, but is probably important for maintaining the architecture of the active site. Based on these structures and earlier biochemical work, a probable isomerization mechanism has been proposed. The thesis concludes with a brief discussion on the future prospects of the work. The following manuscripts have been published or will be communicated for publication based on the results presented in the thesis:

No description available.

Le virus de l'herpès simplex de type 1 (VHS-1) est l'un des agents pathogènes humains les plus anciens et les plus efficaces. On estime que 3.7 milliards de personnes dans le monde vivent avec le VHS-1. Le virus persiste à l'état latent dans les neurones sensoriels, réapparaissant occasionnellement sous la forme d'une infection lytique qui endommage l'épithélium. Même si le VHS-1 provoque une maladie bénigne connue sous le nom de feu sauvage dans la majorité des cas, l'infection peut entraîner des conséquences catastrophiques telles que l'encéphalite et la kératite chez les personnes immunodéprimées les nouveau-nés. Compte tenu de la présence généralisée des infections à VHS-1, le virus représente une menace potentielle pour le système de santé. Le génome à ADN du VHS-1 est protégé par une cage protéique appelée capside. Bien que l'assemblage de la capside du VHS-1 et l'encapsidation du génome aient lieu à l'intérieur du noyau de l'hôte, les étapes finales de la maturation doivent être achevées dans le cytoplasme. Ainsi, pour la sortie du noyau, le virus a développé un mécanisme connu sous le nom d’enveloppement-déenveloppement-réenveloppement. La première étape de ce processus est principalement régulée par le complexe de sortie nucléaire (pUL31 et pUL34) et entraîne le bourgeonnement de la capside alors enveloppée dans l'espace périnucléaire. Par la suite, le déenveloppement de ces capsides périnucléaires et leur libération dans le cytoplasme seraient largement modulés par la kinase virale pUs3. Ce processus est sélectif, car les capsides remplies d'ADN (capsides C) sortent préférentiellement du noyau au détriment des intermédiaires viraux sans génome (capsides A et B). Cependant, nous ne savons pas pourquoi les capsides C sont favorisées lors de ce processus. En aval, le virus mûrit, recrute de nombreuses protéines puis acquiert une enveloppe à partir d'un compartiment cytoplasmique. Il sort ensuite de la cellule sous forme de virions enveloppés matures. Outre les facteurs viraux mentionnés et quelques protéines hôtes, l'implication de nombreuses autres protéines virales et cellulaires dans cette voie n'a pas été entièrement caractérisée. Pour élucider davantage ce processus de sélection de la capside C, nous avons profité de l'analyse MS/MS des capsides nucléaires du VHS-1 pour définir les facteurs hôtes et viraux spécifiques à chaque intermédiaire de capside nucléaire (Chapitre 2; Article 1). Nous avons trouvé deux protéines virales (pUL42 et pUL46) et sept facteurs de l'hôte (glycogène synthase, quatre protéines différentes liées à la kératine, fibronectine 1 et PCBP1) qui étaient spécifiques des capsides C matures. Fait intéressant, toutes ces protéines semblent posséder des fonctions qui ont le potentiel de médier la sortie nucléaire préférentielle des capsides C. Par conséquent, l'analyse fonctionnelle future de ces protéines pourrait nous fournir des informations inestimables sur la sortie nucléaire actuellement énigmatique des capsides du VHS-1. Les travaux en cours d'un collègue de laboratoire avec lequel je collabore impliquent PCBP1 en tant que modulateur de la sortie nucléaire (mémoire de Mackenzie Thornbury). Nous nous sommes ensuite concentrés sur un ensemble de données protéomiques déjà existantes des virions extracellulaires matures, qui a identifié jusqu'à 49 protéines hôtes incorporées dans le virus, y compris une hélicase à ARN humaine appelée DDX3X qui s'est avérée être un modulateur actif de la propagation virale (Chapitre 2; Article 2). Nous avons remarqué que cette protéine se déplace vers le noyau tard lors de l'infection, coïncidant avec la majeure partie de la sortie nucléaire virale. Par conséquent, nous avons émis l'hypothèse que DDX3X serait impliqué dans la sortie nucléaire virale. Nous avons découvert que, tardivement au cours de l'infection, pUL31 interagit avec DDX3X au niveau du noyau. Nous avons également constaté que DDX3X stimule de grandes agrégations de capsides virales matures dans la périphérie nucléaire. Fait intéressant, la redirection de DDX3X vers le bord nucléaire dépend de la présence de la machinerie de sortie nucléaire virale (pUL31, pUL34 et pUs3) et de capsides matures. Enfin, nos données ont montré qu'en l'absence de DDX3X, les capsides C s'accumulent entre les deux membranes nucléaires, probablement à la suite d'une incorporation inefficace de pUs3 au site de sortie. Ces résultats ont élucidé une nouvelle fonction de DDX3X et pourraient ouvrir de nouvelles voies passionnantes de recherche pour développement d’antiviraux en ciblant cette hélicase à ARN cellulaire. / Herpes simplex virus type 1 (HSV-1) is one of the oldest and most successful human pathogens. It is estimated that 3.7 billion people worldwide are living with HSV-1. The virus latently persists in sensory neurons, occasionally recurring as a lytic infection which damages the connected epithelium. Even though HSV-1 causes a mild disease known as the cold sore in majority of cases, the infection can have catastrophic consequences such as encephalitis and keratitis in immunocompromised individuals, newborns and, more rarely, in immune competent adults. Considering the widespread presence of HSV-1 infections, the virus poses a potential threat to the healthcare system. The DNA genome of HSV-1 is protected by a protein cage called a capsid. Although HSV-1 capsid assembly and genome packaging take place inside the host nucleus, the final steps of maturation must be completed inside the cytoplasm. Since the large diameter of these viral capsids (~125 nm) far exceeds the 30 nm cut-off of the nuclear pore complex, the virus has evolved a mechanism known as envelopment-deenvelopmentreenvelopment. The first step of this complex process is mainly regulated by the components of the nuclear egress complex (pUL31 and pUL34) and results in the budding of enveloped capsid into the perinuclear space. Subsequently, deenvelopment of these perinuclear capsids and their release into the cytoplasm is thought to be largely modulated by the viral kinase pUs3. This process is selective as DNA-filled capsids (C-capsids) preferentially exit the nucleus compared to genome-free viral intermediates (A- and Bcapsids). However, it is unclear how C-capsids are preferentially selected for the nuclear egress. Further downstream, the virus matures and recruit numerous proteins onto the viral capsids and acquire an envelope from a cytoplasmic compartment. It then exits the cell as mature enveloped virions. Apart from the mentioned viral factors and a handful of host proteins, implication of many other viral and cellular proteins in this pathway have not been fully characterized. To further resolve this process of C-capsid selection, we took advantage of MS/MS analysis of HSV-1 nuclear capsids to define host and viral factors specific to each nuclear capsid intermediate (Chapter 2; Article 1). We found two viral proteins (pUL42 and pUL46) and seven host factors (glycogen synthase, four different keratin-related proteins, fibronectin 1, and PCBP1) that were specific to mature C-capsids. Interestingly, all these proteins seem to possess functions that have the potential to mediate the preferential nuclear exit of C-capsids. Therefore, future functional analysis of these proteins might provide us with invaluable insights into the currently enigmatic nuclear egress of HSV-1 capsids. Ongoing work by a lab colleague with which I collaborate implicates PCBP1 as a modulator of nuclear egress (memoir of Mackenzie Thornbury). We then focused on an existing proteomics data set of mature extracellular virions, which revealed 49 virus-incorporated host proteins, including a human RNA helicase called DDX3X that we found to be an active modulator of viral propagation (Chapter 2; Article 2). We observed that DDX3X relocates to the nuclear rim late during infection, coinciding with the bulk of viral nuclear egress, and leading us to hypothesize that DDX3X is involved in the process. We discovered that, late during the infection, pUL31 interacts with DDX3X at the nuclear rim. We also found that DDX3X stimulates large aggregations of mature viral capsids in the nuclear periphery. Unexpectedly, redirection of DDX3X to the nuclear rim was dependent on the presence of the viral nuclear egress machinery (pUL31, pUL34 and pUs3) and mature capsids. Lastly, our data showed that in the absence of DDX3X, C-capsids accumulate in the perinuclear space, likely as the result of inefficient incorporation of pUs3 to the site of egress. These results have elucidated a novel function for DDX3X and may open new and exciting paths to produce antivirals by targeting this cellular RNA helicase.