Academic literature on the topic 'Viruses; X-ray crystallography'
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Journal articles on the topic "Viruses; X-ray crystallography"
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Stewart, P. L., S. D. Fuller, and R. M. Burnett. "Bridging the resolution gap between x-ray crystallography and electron microscopy." Proceedings, annual meeting, Electron Microscopy Society of America 52 (1994): 92–93. http://dx.doi.org/10.1017/s0424820100168190.
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While x-ray crystallography provides atomic resolution structures of proteins and small viruses, electron microscopy can provide complementary structural information on larger assemblies. A significant computational challenge is faced in bridging the resolution gap between the two techniques. X-ray crystallographic data is collected in the range of 2-10 Å, while image reconstructions from electron micrographs are at a resolution of 25-35 Å. A further problem is that density derived from cryo-electron micrographs is distorted by the contrast transfer function of the microscope, whichaccentuates certain resolution bands.A novel combination of electron microscopy and x-ray crystallography has revealed the various structural components forming the capsid of human type 2 adenovirus. An image reconstruction of the intact virus (Fig. 1), derived from cryo-electron micrographs, was deconvolved with an approximate contrast transfer function to mitigate microscope distortions (Fig. 2). A model capsid was calculated from 240 copies of the crystallographic structure of the major capsid protein and filtered to the correct resolution (Fig. 3).
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Blakeley, Matthew. "Macromolecular crystallography using neutrons." Biochemist 36, no. 3 (June 1, 2014): 40–42. http://dx.doi.org/10.1042/bio03603040.
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When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.
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Kojić-Prodić, Biserka. "A century of X-ray crystallography and 2014 international year of X-ray crystallography." Macedonian Journal of Chemistry and Chemical Engineering 34, no. 1 (June 2, 2015): 19. http://dx.doi.org/10.20450/mjcce.2015.663.
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The 100<sup>th</sup> anniversary of the Nobel prize awarded to Max von Laue in 1914 for his discovery of diffraction of X-rays on a crystal marked the beginning of a new branch of science - X-ray crystallography. The experimental evidence of von Laue's discovery was given by physicists W. Friedrich and P. Knipping in 1912. In the same year W. L. Bragg described the analogy between X-rays and visible light and formulated the Bragg's law, a fundamental relation, that connected the wave nature of X-rays and fine structure of a crystal at atomic level. In 1913 the first simple diffractometer was constructed and structure determination started by the Braggs, father and son. In 1915 their discoveries were awarded by Nobel prize in physics. Since then, X-ray diffraction has been basic method for determination of three-dimensional structures of synthetic and natural compounds. The three-dimensional structure of molecule defines its physical, chemical, and biological properties. All over the past century significance of X-ray crystallography has been recognized by about forty Nobel prizes. The examples of X-ray structure analysis, of simple crystals of rock salt, diamond and graphite, and then of complex biomolecules such as B12-vitamin, penicillin, haemoglobin/myoglobin, DNA, and biomolecular complexes such as viruses, chromatin, ribozyme, and other molecular machines, have illustrated the development of the method. Among these big discoveries double helix DNA structure is epochal one of 20<sup>th</sup> century. These discoveries together with many others within X-ray crystallography completely changed our views and helped to be developed different new fields of science such as molecular genetics, biophysics, structural molecular biology, material science, and many others. During the last decade, an implementation of free electron X-ray lasers, a new experimental tool, has opened up femtosecond dynamic crystallography. This highly advanced methodology enables to solve the structures and dynamics of the most complex biological assemblies involved in a cell metabolism. The advancements of science and technology over 20<sup>th</sup> and 21<sup>st</sup>centuries are of great influence on our views in almost all human activities. The importance of X-ray crystallography for science and technology advocates for its high impact on a wide area of research and declares it as highly interdisciplinary science. Briefly saying, crystallography defines the shape of our modern world.<p>The essay is far from being complete and it is concentrated on single crystal diffraction. The wide area of X-ray crystallography hardly can be reviewed in a single article. However, it highlights the most striking examples illustrating some of the milestones over past century.</p><p> </p>
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Humphrey, Charles D., Betty H. Robertson, and B. Khanna. "Hepatitis A Virus Aggregation in Suspensions of Purified Virus." Proceedings, annual meeting, Electron Microscopy Society of America 48, no. 1 (August 12, 1990): 280–81. http://dx.doi.org/10.1017/s042482010018015x.
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Virus capsid structure as determined by x-ray crystallography or by elec imaging of virus particles in thefrozen hydrated state has received con interest during the past decade. Specific functional proteins were localized recently on the Rotavirus capsid by using cryo-electron microscopy, indicating the potential for morphological studies that rel directly to capsid protein function.Most cryo-electron microscopy studies have involved investigation of vir were 40 nm or greater in diameter. Smaller viruses may provide a greate practical difficulty in their preparation and imaging.Highly purified virus for study by x-ray crystallographic studies or ele microscopic evaluation of frozen hydrated particles requires stringent c particle aggregation. Preparations for x-ray crystallography should agg an orderly manner to form arrays and ordered crystals of sufficient size Preparations for cryo-electron microscopy are more desirable when the pa numerous but not over-lapping (Fig. 1). We have experienced uncontrolla aggregation including considerable over-lapping of hepatitis A virus (HA particles when purified preparations were stored in phosphate or tris buffers (Fig. 2).
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Verdaguer, Nuria, Diego Ferrero, and Mathur R. N. Murthy. "Viruses and viral proteins." IUCrJ 1, no. 6 (October 14, 2014): 492–504. http://dx.doi.org/10.1107/s205225251402003x.
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For more than 30 years X-ray crystallography has been by far the most powerful approach for determining the structures of viruses and viral proteins at atomic resolution. The information provided by these structures, which covers many important aspects of the viral life cycle such as cell-receptor recognition, viral entry, nucleic acid transfer and genome replication, has extensively enriched our vision of the virus world. Many of the structures available correspond to potential targets for antiviral drugs against important human pathogens. This article provides an overview of the current knowledge of different structural aspects of the above-mentioned processes.
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Harrison, Stephen. "Virus crystallography from its beginnings until 1978." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C932. http://dx.doi.org/10.1107/s2053273314090676.
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Viruses, first crystallized in the 1930's, were for many years the only exemplars of large macromolecular assemblies accessible to x-ray crystallography. The talk will outline the most interesting biological questions these structures posed, review some of the early technical challenges, and describe some of the specific history that led to the first published virus crystal structure in 1978.
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Burkhardt, Anja, Martin Warmer, Nicolas Stuebe, Jan Roever, Bernd Reime, Saravanan Panneerselvam, Tim Pakendorf, Jan Meyer, Pontus Fischer, and Alke Meents. "X-ray Crystallography at Beamline P11 at PETRA III." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1725. http://dx.doi.org/10.1107/s2053273314082746.
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The bio-imaging and diffraction beamline P11 at PETRA III is dedicated to structure determination of periodic (crystalline) and aperiodic biological samples. The beamline features two experimental endstations: an X-ray microscope and a crystallography experiment. Basis of design was to provide an extremely stable and flexible setup ideally suited for micro and nano beam applications. The X-ray optics consist of a HHL double crystal monochromator, followed by two horizontal deflecting and one vertical deflecting X-ray mirrors. All mirrors are dynamically bendable and used to generate an intermediate focus at 65.5 m from the source with a size of 37 × 221 µm2FWHM (v × h). All experiments are installed on an 8 m long granite support which provides a very stable setup for micro beam experiments. The crystallography endstation is located at the end of the granite at 72.9 m from the source. The experiment is equipped with a high precision single axis goniostat with a combined sphere of confusion of less than 100 nm. X-ray energies are tunable between 5.5 and 30 keV. A second focusing bendable KB mirror system can be used for further demagnification of the secondary source. In this way the beam size can be freely adjusted between 4 × 9 µm2and 300 × 300 µm2FWHM (v × h) with 1013ph/s at 12 keV. Smaller beam sizes down to 1 × 1 µm2with more than 2 × 1011ph/s in the focus can be realized by slitting down the secondary source at the cost of flux. The crystallography endstation is equipped with a Pilatus 6M-F detector which allows fast data collection with up to 25 Hz. Due to the very small beam divergence of the X-ray beam P11 is ideally suited to measure large unit cell systems, such as viruses or large molecular complexes. In addition, the beamline is capable of high-throughput crystallography and fast crystal screening. Crystals can be mounted in less than 10 s using an automatic sample changer. The large sample dewar provides space for 368 crystals.
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Tang, Liang, and John E. Johnson. "Structural Biology of Viruses by the Combination of Electron Cryomicroscopy and X-ray Crystallography†." Biochemistry 41, no. 39 (October 2002): 11517–24. http://dx.doi.org/10.1021/bi020170j.
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Mizianty, Marcin J., Xiao Fan, Jing Yan, Eric Chalmers, Christopher Woloschuk, Andrzej Joachimiak, and Lukasz Kurgan. "Covering complete proteomes with X-ray structures: a current snapshot." Acta Crystallographica Section D Biological Crystallography 70, no. 11 (October 23, 2014): 2781–93. http://dx.doi.org/10.1107/s1399004714019427.
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Structural genomics programs have developed and applied structure-determination pipelines to a wide range of protein targets, facilitating the visualization of macromolecular interactions and the understanding of their molecular and biochemical functions. The fundamental question of whether three-dimensional structures of all proteins and all functional annotations can be determined using X-ray crystallography is investigated. A first-of-its-kind large-scale analysis of crystallization propensity for all proteins encoded in 1953 fully sequenced genomes was performed. It is shown that current X-ray crystallographic knowhow combined with homology modeling can provide structures for 25% of modeling families (protein clusters for which structural models can be obtained through homology modeling), with at least one structural model produced for each Gene Ontology functional annotation. The coverage varies between superkingdoms, with 19% for eukaryotes, 35% for bacteria and 49% for archaea, and with those of viruses following the coverage values of their hosts. It is shown that the crystallization propensities of proteomes from the taxonomic superkingdoms are distinct. The use of knowledge-based target selection is shown to substantially increase the ability to produce X-ray structures. It is demonstrated that the human proteome has one of the highest attainable coverage values among eukaryotes, and GPCR membrane proteins suitable for X-ray structure determination were determined.
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Rossmann, Michael G. "Structure of viruses: a short history." Quarterly Reviews of Biophysics 46, no. 2 (May 2013): 133–80. http://dx.doi.org/10.1017/s0033583513000012.
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AbstractThis review is a partially personal account of the discovery of virus structure and its implication for virus function. Although I have endeavored to cover all aspects of structural virology and to acknowledge relevant individuals, I know that I have favored taking examples from my own experience in telling this story. I am anxious to apologize to all those who I might have unintentionally offended by omitting their work.The first knowledge of virus structure was a result of Stanley's studies of tobacco mosaic virus (TMV) and the subsequent X-ray fiber diffraction analysis by Bernal and Fankuchen in the 1930s. At about the same time it became apparent that crystals of small RNA plant and animal viruses could diffract X-rays, demonstrating that viruses must have distinct and unique structures. More advances were made in the 1950s with the realization by Watson and Crick that viruses might have icosahedral symmetry. With the improvement of experimental and computational techniques in the 1970s, it became possible to determine the three-dimensional, near-atomic resolution structures of some small icosahedral plant and animal RNA viruses. It was a great surprise that the protecting capsids of the first virus structures to be determined had the same architecture. The capsid proteins of these viruses all had a ‘jelly-roll’ fold and, furthermore, the organization of the capsid protein in the virus were similar, suggesting a common ancestral virus from which many of today's viruses have evolved. By this time a more detailed structure of TMV had also been established, but both the architecture and capsid protein fold were quite different to that of the icosahedral viruses. The small icosahedral RNA virus structures were also informative of how and where cellular receptors, anti-viral compounds, and neutralizing antibodies bound to these viruses. However, larger lipid membrane enveloped viruses did not form sufficiently ordered crystals to obtain good X-ray diffraction. Starting in the 1990s, these enveloped viruses were studied by combining cryo-electron microscopy of the whole virus with X-ray crystallography of their protein components. These structures gave information on virus assembly, virus neutralization by antibodies, and virus fusion with and entry into the host cell. The same techniques were also employed in the study of complex bacteriophages that were too large to crystallize. Nevertheless, there still remained many pleomorphic, highly pathogenic viruses that lacked the icosahedral symmetry and homogeneity that had made the earlier structural investigations possible. Currently some of these viruses are starting to be studied by combining X-ray crystallography with cryo-electron tomography.
Dissertations / Theses on the topic "Viruses; X-ray crystallography"
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Tate, John Graham. "Structural studies on bovine enterovirus." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318546.
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Hengrung, Narin. "Structure of the RNA-dependent RNA polymerase from influenza C virus." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:694e16a6-f94e-4375-a1f9-7e250aea7343.
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The influenza virus causes a disease that kills approximately 500,000 people worldwide each year. Influenza is a negative-sense RNA virus that encodes its own RNA-dependent RNA polymerase. This protein (FluPol) carries out both genome replication and viral transcription. Therefore, like the L-proteins of non-segmented negative-sense RNA (nsRNA) viruses, FluPol also contains mRNA capping and polyadenylation functionality. In FluPol, capping is achieved by snatching cap structures from cellular mRNAs, so requiring cap-binding and endonuclease activities. This makes FluPol a substantial machine. It is a heterotrimeric complex, composed of PB1, PB2 and PA/P3 subunits, with a total molecular weight of 255 kDa. PB1 houses the polymerase active site, whereas PB2 and PA contain, respectively, cap-binding and endonuclease domains. Currently, we only have high resolution structural information for isolated fragments of FluPol. This severely hampers our understanding of influenza replication and consequently inhibits the development of therapies against the virus. In this DPhil project, I have determined a preliminary structure for the heterotrimeric FluPol of influenza C/Johannesburg/1/66, solved by x-ray crystallography to 3.6 Å. Overall, FluPol has an elongated structure with a conspicuous deep groove. PB1 displays the canonical right-hand-like polymerase fold. It sits at the centre of the particle, sandwiched between the two domains of P3, and with PB2 stacked against one side of this dimer. In the structure, the polymerase and endonuclease catalytic sites are both ~40 Å away from the cap-binding pocket. This pocket also faces a tunnel leading to the polymerase core. This suggests a mechanism for how capped cellular mRNAs are cleaved and then fed into the polymerase active site to prime transcription. The structure also hints at a unique trajectory for template RNA, in which the RNA exits at an angle ~180° from which it came in. This provides an explanation for how the polymerases of influenza, and other nsRNA viruses, can copy templates that are packaged into ribonucleoprotein complexes. My work reveals the first molecular structure of any polymerase from an nsRNA virus. It uncovers the arrangement of functional domains within FluPol, illuminating the mechanisms of this and related viral polymerases. This work will help focus future experiments into FluPol biology, and should hopefully spur the development of novel antiviral drugs.
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Rodrigues, Catarina. "Etudes structurales et biophysiques de proteines du virion d' ATV, un bicaudavirus infectant des crenarchees du genre acidianus." Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4087.
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Les virus sont les entités biologiques les plus abondantes dans les océans (∼1031 particules). Ils colonisent tous les écosystèmes de la planète y compris les environnements extrêmement acides, chauds et salins, environnements où les archées sont les organismes dominants. Les virus infectant les Crenarchées hyperthermophiles présentent des morphologies exceptionnelles et aussi une très faible proportion de gènes possédant des homologues avec de fonction connue. Parmi ces virus, le virus ATV (Acidianus two-Tailed virus), infecte les archées hyperthermophiles du genre Acidianus. ATV a la propriété unique de présenter un important développement structural complètement indépendante de son hôte, à l'extérieur de celui-Ci. Les virions d'ATV développent de longues queues à chaque extrêmité de sa capside, mais seulement à des températures proches de celles de l'habitat de son hôte, 85°C. Le sujet de ma thèse a porté sur l'étude structurale de protéines du virion d'ATV. J'ai résolu la structure cristalline de la protéine ATV-273, qui possède un nouveau fold α/β. J'ai aussi déterminé la forme de l'enveloppe de cette protéine par SAXS. J'ai montré qu'il est possible de placer deux dimères d'ATV-273, observés dans la structure cristalline, dans cette enveloppe. Ce résultat est aussi en accord avec l'état d'oligomérisation en solution déterminé par chromatographie d'exclusion stérique couplée à la diffusion de la lumière. La fonction de cette protéine reste cependant inconnueViruses are the most abundant biological entity in the oceans (∼1031 particles) and remarkably, viruses populate every ecosystem on the planet including the extreme acidic, thermal, and saline environments where archaeal organisms dominate. The viruses infecting hyperthermophilic Crenarchaea revealed exceptional morphologies and also a very low proportion of genes with recognizable functions and homologues. Among these viruses we find ATV (Acidianus two-Tailed virus). ATV is a virus infecting hyperthermophilic archaea of the genus Acidianus, which has the unique property of undergoing a major morphological development outside and independently of the host cell. Virions develop long tails at each pointed end of the initial lemon-Shaped particle, at temperatures close to those of the host natural habitat, 85 °C. The subject of my thesis has focused on the virion proteins of ATV. I have solved the crystal structure of ATV-273 that revealed a new α/β fold. I have also obtained a SAXS envelope where it is possible to fit two crystal dimers, in agreement with the oligomerization state in solution as determined by size-Exclusion chromatography coupled to multi angle light scattering. The function of this protein, however, could be not determined. Moreover, a negative staining electron microscopy model was obtained for the AAA+ ATPase ATV-618, which belongs to the MoxR familiy and presents sequence high similarity with the AAA-ATase RavA from Escherichia coli K12. I have shown that this thermostable AAA-ATPase enzyme assumes a hexameric ring organisation in the presence of ATP
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Menon, Smita Kesavankutty. "X-ray crystallographic studies of the proteins from sulfolobus spindle-shaped viruses (SSVs)." Thesis, Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/menon/MenonS0809.pdf.
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Viruses populate virtually every ecosystem on the planet. Fuselloviridae are ubiquitous crenarchaeal viruses found in high-temperature acidic hot springs around the world. However, compared to eukaryotic and bacterial viruses, our knowledge of viruses infecting the archaea is limited. Fuselloviral genomes show little similarity to other organisms, generally precluding functional predictions. However, structural studies can reveal distant evolutionary relationships and provide functional insights that are not apparent from the primary amino acid sequence alone. Several such structural studies have already contributed to our understanding of the Sulfolobus Spindle-shaped viruses (Fuselloviridae). Here we report the structure of two proteins, SSV1 F112 and SSVRH D212. Biochemical, proteomic and structural studies of F112 reveal a monomeric intracellular protein that adopts a winged helix DNA binding fold. Continuing these efforts, a second structure was also determined where the overall fold and conservation of active site residues place D212 within the PD-(D/E)XK nuclease superfamily. Notably, the structure of F112 contains an intrachain disulfide bond, prompting analysis of cysteine usage in this and other hyperthermophilic viral genomes. The analysis supports a general abundance of disulfide bonds in the intracellular proteins of hyperthermophilic viruses and the evolutionary implications of such distribution are discussed. Here we review and describe our progress towards understanding these viruses at a molecular level.
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Larson, Eric Thomas. "X-Ray Crystallographic Studies of Sulfolobus Turetted Icosahedral Virus (STIV): A Hyperthermophilic Virus from Yellowstone National Park." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/larson/LarsonE1206.pdf.
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Sulfolobus turreted icosahedral virus (STIV) was isolated from acidic hot springs of Yellowstone National Park and was the first hyperthermophilic virus described with icosahedral capsid architecture. Structural analysis of the STIV particle and its major capsid protein suggests that it belongs to a lineage of viruses that predates the division of the three domains of life. Functional predictions of the viral proteins are hindered because they lack similarity to sequences of known function. Protein structure, however, may suggest functional relationships that are not apparent from the sequence. Thus, we have initiated crystallographic studies of STIV and expect to gain functional insight into its proteins while illuminating the viral life cycle. These studies may also provide genetic, biochemical, and evolutionary insight into its thermoacidophilic host and the requirements for life in these harsh environments. The first three proteins studied in structural detail are A197, B116, and F93. As anticipated, these structures suggest possible functions. The structure of A197 reveals a glycosyltransferase GT-A fold. Within the context of the GT-A fold, are the canonical DXD motif and a putative catalytic base, hallmarks of this family of enzymes, strongly suggesting glycosyltransferase activity for A197. B116 is a unique structure that lacks significant homology to known protein structures. However, sequence similarity to proteins from other hyperthermophilic viruses reveals conserved surface features suggesting interaction with a host macromolecule, likely DNA. The F93 structure reveals a winged-helix fold common among DNA-binding proteins, in particular, the MarR-like family of transcriptional regulators. The most likely role for F93 is thus regulation of viral transcription. Interestingly, B116 contains an intramolecular disulfide bond while F93 contains an intermolecular disulfide bond. The presence of these disulfide bonds was not anticipated because these proteins are expected to be localized within the host cell. This prompted analysis of the cysteine distribution in the STIV genome, which suggests that disulfide bonds are common in intracellular (cytoplasmic) proteins encoded by STIV. This work is in accordance with accumulating evidence that disulfide bonds are common stabilizing elements in the intracellular proteins of thermophilic organisms in general, and extends the observation to genomes of hyperthermophilic viruses.
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Voss, James. "Chikungunya envelope glycoprotein structure at neutral PH determined by X-ray crystallography." Paris 7, 2011. http://www.theses.fr/2011PA077021.
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Le virus de Chikungunya (CHIKV) est un alphavirus émergent, transmis par les moustiques, qui a provoqué des épidémies de maladies débilitantes chez homme pendant les dernières cinq années. L'invasion de CHIKV dans les cellules sensibles est médiée par deux glycoprotéines virales, E1 et E2, qui portent respectivement les boucles de fusion à la membrane et les déterminants antigéniques principaux, et forment une couche protéinique icosaédrique à la surface du virion. La glycoprotéine E2, provenant du clivage par la furine du précurseur p62 (en E3 et E2), est responsable de la liaison au récepteur, tandis que E1 est impliqué dans la fusion membranaire. Dans le cadre d'un effort multidisciplinaire pour comprendre la biologie de CHIKV, nous avons déterminé les structures cristallines de l'hétérodimère précurseur immature (p62-E1; 2. 17 A de résolution) et du complexe mature (E3-E2-E1; 2. 6 A de résolution). Les structures atomiques nous ont permis de faire la synthèse d'une multitude de données génétiques, biochimiques, immunologiques et de microscopie électronique accumulées pendant plusieurs années sur les arbovirus en général. Cette analyse donne une image détaillée de l'architecture fonctionnelle de la couche de surface (25 MDa) des alphavirus. Les structures des complexes matures et immatures de CHIKV a aussi permis de décrire les causes et les mécanismes du changement de conformation des protéines d'enveloppe du virion lors du passage de celui-ci dans l'endosome à pH acide et précédant la fusion membranaireChikungunya is an emerging mosquito-bome alphavirus that has caused widespread outbreaks of debilitating human disease in the past five years. CHIKV invasion of susceptible cells is mediated by two viral glycoproteins, E1 and E2, which carry the main antigenic determinants and form an icosahedral shell at the virion surface. Glycoprotein E2, derived from furin cleavage of the p62 precursor to E3 and E2 is responsible for receptor binding and is the major viral antigen. The E1 protein is responsible for inducing the fusion of viral and cellular membranes in the target cell endosome which is required for release of the viral nucleocapsid into the cytoplasm to initiale infection of a cell. While the structure of E1 has been determined, the structure of E2"has remained elusive over the years. This thesis reports the atomic structures of the mature (E3/E2/E1) and immature (P62/E1) envelope glycoprotein complexes from Chikungunya virus determined by X-ray crystallography using a recombinant protein construct. This construct contained the covalently linked ectodomains of p62 and E1. Diffracting crystals of the purified complexes were obtained at neutral pH when the linker joining the ectodomains was cleaved. The glycoprotein structures were fit into reconstructions of the alphavirus virion obtained from cryo-electron microscopy (cryoEM). This analysis resulted in an inferred atomic model of the entire 25MDa surface of the highly conserved alphavirus virion and allowed for the synthesis of a wealth of genetic, biochemical, immunological and electron microscopy data accumulated over the years on alphaviruses in general
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Persson, Magnus. "Structural Studies of Bacteriophage PRR1 and HIV-1 protease." Doctoral thesis, Uppsala universitet, Strukturell molekylärbiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-135159.
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Viruses are a diverse genera of organisms adapted to thrive in many different hosts from prokaryotic to eukaryotic. We present here the structure of bacteriophage PRR1 virus-like particle (VLP), belonging to Leviviridae family. Our structure reveals calcium ions in the VLP. Metal ions are rare in the VLP among the Leviviridae and the calcium ions were found to affect VLP stability. Gene expression in Leviviridae is controlled by a specific interaction between the viral coat protein that assembles to create the VLP, and the genomic RNA. This interaction has been thoroughly studied for the levivirus MS2 but other structural data are scarce. We have solved the structure of PRR1 VLP in complex with its RNA operator stem-loop. Binding of the stem-loop in PRR1 shows similarities to MS2 but also a different arrangement of the nucleotides, in the area of the loop that we could interpret, compared to MS2. The structures of PRR1 increase our knowledge about translational control in Leviviridae and add new information about particle stability within this family. The other virus we investigated is the more infamous human pathogen, the HIV. Because of the high mutation rate of HIV new drugs are needed on a continuous basis. We describe here the structure of two new protease inhibitors bound to the HIV-1 protease and compare them with two previously published inhibitors. Due to an extended P1´site the new compounds are able to exploit a new interaction to Phe53 in the protease structure.Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 724
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Baeza, Gabriela. "X-ray Crystallographic Structure of theMurine Norovirus protease at 1.66 Å Resolutionand Functional Studies of the β-ribbon." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-70426.
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In humans, noroviruses (NVs) cause acute epidemic and viral gastroenteritis. NVs do not only infect humans; viruseshave also been found in pigs, cows, sheep, mice and dogs. The focus in this project has been on the murine norovirus(MNV). MNV is a member of the viral family Caliciviridae and it consists of a single-stranded, positive sense RNAgenome. The genome includes three open reading frames (ORFs), ORF1 encodes for a polyprotein that consists of theprecursor to the 6-7 non-structural (NS) proteins. The polyprotein is cleaved by the NS6 protease. The NS6 isresponsible for all the cleaving in ORF1 and that makes it an attractive target for antiviral drugs. The NS6 proteinstructure has been determined at 1.66 Å resolution using X-ray diffraction techniques. Surprisingly, the electrondensity map revealed density for a peptide bound in the active site. The peptide had a length of 7 residues andoriginated from the C-terminus of another chain in an adjacent asymmetric unit. The active site triad was composed ofthe conserved residues; histidine 30, aspargine 54 and cysteine 139, however in the structure the cysteine 139 ismutated to an alanine to inactivate the protease. Activity assays were performed to probe the importance of the residuein position 109 in the β-ribbon located close to the active site. The three full-length constructs with the mutations;I109A, I109S and I109T were found to have less activity than the full-length wt (1-183). A truncated protease, lacking9 residues in the C-terminus, also had less activity. This indicates that the terminal residues are also important foractivity.
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Velloso, Lucas Malard. "Structural insights into glycoprotein transport and viral escape /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7349-780-0/.
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Folio, Christelle. "Études fonctionnelle et structurale de deux protéines rétrovirales d’intérêt thérapeutique : la protéine Tax du virus HTLV et la protéine de capside du FIV." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1245/document.
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Les rétrovirus sont un enjeu de santé publique, aussi bien humaine qu'animale. La compréhension des déterminants structuraux sous-jacents à la fonction de leurs protéines constitue une étape essentielle dans le développement de stratégies antirétrovirales efficaces.Ce manuscrit porte sur l'étude des bases structurales des mécanismes moléculaires impliqués dans les fonctions clés des rétrovirus que sont i) la régulation de l'expression des protéines de rétrovirus complexes et ii) l'assemblage des particules virales, à travers l'étude de deux protéines rétrovirales d'intérêt thérapeutique : la protéine Tax du virus T-lymphotrope humain (HTLV) et la protéine de capside du virus de l'immunodéficience féline (FIV). L'étude structurale de ces deux protéines d'intérêt et la compréhension des mécanismes moléculaires nécessaires à leurs fonctions permettraient d'ouvrir la voie à la conception de nouvelles stratégies antirétrovirales.Malgré de nombreux tests d'expression et de purification, l'étude structurale de la protéine Tax du HTLV n'a pu être réalisée, en raison de son insolubité. Cependant, ce travail doctoral a permis de résoudre, pour la première fois, la structure cristallographique de la protéine de capside entière du FIV. Bien que cette dernière adopte un repliement similaire aux autres capsides rétrovirales dont la structure est connue, elle présente également des spécificités structurales dont les conséquences fonctionnelles seront discutéesRetroviruses are a major concern of public health in humans but also in animals. A better understanding of the structural determinants underlying the functions of retroviral proteins is a crucial step for the development of efficient antiretroviral therapies.This manuscript studies the structural basis of the molecular mechanisms implicated in key functions of retroviruses such as, i) the regulation of complex retroviruses protein expression and ii) the assembly of viral particles, through the study of two retroviral proteins of therapeutic interest: the human T-lymphotropic virus (HTLV) Tax protein and the feline immunodeficiency virus (FIV) capsid protein. The functional and structural studies of these two proteins and the understanding of the molecular mechanisms required for their functions will pave the way to the conception of new antiretroviral therapeutic strategies.Despite several expression and purification assays, no structural studies could be performed for the HLTV Tax protein. However, this study allowed the resolution of the first structure for the full-length FIV capsid protein by X-ray crystallography. Although the FIV capsid protein displays a standard a-helical topology like other retroviral CAs, it also harbors original features whose functional consequences will be discussed
Books on the topic "Viruses; X-ray crystallography"
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Macromolecular crystallography with synchrotron radiation. Cambridge [England]: Cambridge University Press, 1992.
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Helliwell, John R. Macromolecular crystallography with synchrotron radiation. Cambridge: Cambridge University Press, 2004.
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Helliwell, John R. Macromolecular Crystallography with Synchrotron Radiation. Cambridge University Press, 2005.
Find full textBook chapters on the topic "Viruses; X-ray crystallography"
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Verdaguer, Nuria, Damià Garriga, and Ignacio Fita. "X-Ray Crystallography of Viruses." In Subcellular Biochemistry, 117–44. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-6552-8_4.
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Wharton, S. A., A. J. Hay, R. J. Sugrue, J. J. Skehel, W. I. Weis, and D. C. Wiley. "Membrane Fusion by Influenza Viruses and the Mechanism of Action of Amantadine." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 1–12. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50006-9.
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Acharya, Ravi, Elizabeth Fry, Derek Logan, David I. Stuart, Graham Fox, Dave Rowlands, and Fred Brown. "Structure of Foot-and-Mouth Disease Virus." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 161–71. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50017-3.
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Stammers, D. K., K. L. Powell, B. A. Larder, G. Darby, D. J. M. Purifoy, M. Tisdale, D. M. Lowe, et al. "Structural Studies on Human Immunodeficiency Virus Reverse Transcriptase." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 309–19. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50028-8.
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Laver, W. Graeme, Gillian M. Air, Ming Luo, A. Portner, S. D. Thompson, and Robert G. Webster. "Crystal Structures of Influenza Virus Neuraminidase Complexed with Monoclonal Antibody Fab Fragments." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 49–60. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50010-0.
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Arnold, Edward, and Gail Ferstandig Arnold. "Virus Structure and the AIDS Problem: Strategies for Antiviral Design Based on Structure." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 283–95. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50026-4.
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Hughes, Stephen H., Andrea L. Ferris, and Amnon Hizi. "Analysis of the Reverse Transcriptase of Human Immunodeficiency Virus Expressed in Escherichia coli." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 297–307. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50027-6.
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Darke, Paul L., Chih-Tai Leu, Jill C. Heimbach, Irving S. Sigal, James P. Springer, Manuel A. Navia, Paula M. D. Fitzgerald, and Brian M. McKeever. "Human Immunodeficiency Virus (Type 1) Protease: Enzymology and Three-Dimensional Structure of a New AIDS Drug Target." In Use of X-Ray Crystallography in the Design of Antiviral Agents, 321–34. Elsevier, 1990. http://dx.doi.org/10.1016/b978-0-12-438745-4.50029-x.
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Lorber, B., and R. Giegé. "Biochemical Aspects and Handling of Macromolecular Solutions and Crystals." In Crystallization of Nucleic Acids and Proteins. Oxford University Press, 1999. http://dx.doi.org/10.1093/oso/9780199636792.003.0006.
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The quality and quantity of the macromolecular samples are important prerequisites for successful crystallizations. Proteins and nucleic acids extracted from living cells or synthesized in vitro differ from small molecules by additional properties intrinsic to their chemical nature and their larger size. They are frequently difficult to prepare at a high degree of purity and homogeneity. Besides traces of impurities, harsh treatments may decrease their stability and activity through different kinds of alterations. Consequently, the quality of biomacromolecules depends on the way they are prepared and handled. As a general rule purity and homogeneity are regarded as conditions sine qua non. Accordingly, purification, stabilization, storage, and handling of macromolecules are essential steps prior to crystallization attempts. Other difficulties in crystal growth may come from the source of the biological material. It is advisable to have at disposal a few milligrams of material when starting first crystallization trials although structures were solved with submilligram quantities of protein (1). Once crystals suitable for X-ray analysis can be produced, additional material is often needed to improve their quality and size and to prepare heavy-atom derivatives. It is thus essential that isolation procedures are able to supply enough fresh material of reproducible quality. Similar situations are encountered with multi-macromolecular assemblies (e.g. viruses, nucleosomes, ribosomal particles, or their subunits). This chapter discusses biochemical methods used to prepare and characterize macromolecules intended for crystallization assays. Practical aspects concerning manipulation and qualitative analyses of soluble proteins will be emphasized. The cases of nucleic acids and membrane proteins are described in more detail in Chapters 8 and 9. Peculiar aspects of molecular biology that are important for crystallogenesis are presented in Chapter 3. They include the design of engineered macromolecules with new physical properties or modified to simplify purification or crystallographic analysis. Finally, methods for identification of macromolecular content of crystals and measurements of their density are presented as well. Many biological functions are sustained by classes of proteins and nucleic acids universally present in living organisms so that the source of macromolecules may seem unimportant. In fact, better crystallization conditions or better diffracting crystals are frequently found by switching from one organism to another.
Conference papers on the topic "Viruses; X-ray crystallography"
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Johnson, J. E., and Z. Chen. "Virus crystallography using synchrotron X-ray radiation." In X-ray and inner-shell processes. AIP, 1990. http://dx.doi.org/10.1063/1.39824.
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Lo, V. L., and R. P. Millane. "Ab initio Determination of Virus Electron Density in X-ray Crystallography." In Signal Recovery and Synthesis. Washington, D.C.: OSA, 2009. http://dx.doi.org/10.1364/srs.2009.stub2.
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