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Dissertations / Theses on the topic 'Viral proteins'

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Published: 4 June 2021

Last updated: 30 July 2024

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1

Oliveira, Vivian Leite. "Impact of viral mmunomodulatory proteins." Doctoral thesis, Universidade Nova de Lisboa. Instituto de Tecnologia Química e Biológica, 2013. http://hdl.handle.net/10362/11946.

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Dissertation presented to obtain the Ph.D degree in Biology
Cerca de 50% do genoma dos vírus de DNA evoluiu direcionado para a manipulação de importantes funções celulares do hospedeiro. Estas estratégias são muito diversas e conferem ao vírus vantagens importantes sobre o sistema imunitário do hospedeiro. Esses genes são, por isso, potenciais fontes de informação para a geração de novos fármacos dirigidos à manipulação da resposta imunológica na saúde e na doença. Esta tese centra-se na análise da função de dois genes virais distintos, ambos com funções imunomoduladoras. O gene do Vírus da Peste Suína Africana codificado pela “open reading frame” I329L (ORF I329L), e o gene do vírus herpes-gama-68 de murino codificado pela “open reading frame” M2 (ORF M2). Ambos os vírus são conhecidos por codificar várias proteínas capazes de manipular componentes vitais da resposta antiviral. Neste trabalho nós demonstramos que tanto a ORF I329L quanto ORF M2 são capazes de manipular a imunidade inata ou adquirida.(...)

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2

Horridge, Jackie J. "RNA-protein interactions of the adenovirus proteins E1B 55K and E4 Orf6." Thesis, University of Warwick, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.322435.

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3

Lindström, Hannah Kim. "Molecular studies of the hepatitis C virus : the role of IRES activity for therapy response, and the impact of the non-structural protein NS4B on the viral proliferation /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-875-4/.

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4

Weinmaster, Geraldine Ann. "Structural and functional characterization of the Fujinami sarcoma virus transforming protein." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/25991.

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The phosphorylation of the Fujinami sarcoma virus transforming protein (FSV P140gag-fps) is complex, reversible and affects its tyrosine specific protein kinase activity and transforming function. The sites of phosphorylation within FSV P140gag-fps have been localized to various regions of the protein using partial proteolysis. The two major phosphotyrosine residues and a major phosphoserine residue are located in the C-terminal portion of the fps region, which contains the kinase active domain. A comparative tryptic phosphopeptide analysis of the gag-fps proteins of three FSV variants shows that the phosphotyrosine containing peptides have similar mobilities. To determine whether tyrosine phosphorylation affects protein function and to evaluate the substrate specificity of the protein kinase intrinsic to FSV P130gag-fps oligonucleotide-directed mutagenesis was used to change tyrosine-1073, the major site of P130gag-fps phosphorylation. Tyrosine-1073 was mutated to a phenylalanine and a glycine, amino acids that cannot be phosphorylated, and to the other commonly phosphorylated hydroxyamino acids, serine and threonine. Neither serine nor threonine were phosphorylated when substituted for tyrosine-1073 indicating a strict specificity for and oncogenic capacities. These data indicate that tyrosine phosphorylation stimulates the biochemical and biological activities of FSV P130gag-fps and suggest that tyrosine phosphorylation modulates protein function. Mutations within the putative ATP-binding site of P130gag-fps at lysine-950 destroy both its kinase and transforming activities, supporting the idea that the tyrosine kinase activity intrinsic to P130gag-fps is essential for its transforming function. The mutant protein was also shown to be phosphorylated at a second tyrosine site, which has been previously identified in wild-type P130gag-fps as a site exclusively phosphorylated in vivo. Phosphorylation of secondary tyrosine residues within a mutant protein devoid of intrinsic tyrosine protein kinase activity suggests that the FSV P130gag-fps may be a target for phosphorylation by cellular tyrosine specific protein kinases.
Science, Faculty of
Microbiology and Immunology, Department of
Graduate

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5

Helt, Anna-Marija. "Multiple biological activities of the human papillomavirus type 16 E7 oncoprotein contribute to the abrogation of human epithelial cell cycle control /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/11514.

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6

Kim, Irene. "Mechanisms of Membrane Disruption by Viral Entry Proteins." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10192.

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To enter and infect cells, viruses must overcome the barrier presented by the cell membrane. Enveloped viruses, which possess their own lipid bilayer, fuse their viral membrane with the cell membrane. Non-enveloped viruses, whose outer surface is composed of proteins, penetrate through the hydrophobic interior of the cell membrane. Viruses accomplish the processes by coupling conformational changes in viral "entry proteins" to membrane disruption. This dissertation investigates the membrane disruption mechanisms of rotavirus, a non-enveloped virus, and vesicular stomatitis virus (VSV), an enveloped virus. Rotavirus uses proteins of its outer capsid to penetrate the membrane and deliver a transcriptionally-active core particle into the cell cytoplasm. \(VP5^*\), an outer capsid protein, undergoes a foldback rearrangement that translocates three clustered hydrophobic loops by \(\sim 180^{\circ}\). This rearrangement resembles the foldback rearrangements of enveloped virus fusion proteins. In the first half of my dissertation, I show that the hydrophobicity of the \(VP5^*\) apex is required for membrane disruption during rotavirus cell entry by mutating hydrophobic residues within the loop to hydrophilic residues. One particular mutation diminishes liposome interaction by the protein, blocks membrane penetration by virus particles in cells, and reduces particle infectivity by 10,000-fold. VSV uses its fusion protein, G, to fuse at low pH. Unlike other viral fusion proteins, pH-induced conformational changes in G are reversible. In the second half of my dissertation, I measure the fusion kinetics of individual VSV particles using a single-particle fusion assay previously developed for influenza virus. I find that hemifusion by VSV consists of at least two steps, an initial step that is pH-dependent and reversible, and a second step that is pH-independent. At low pHs, the second step becomes the sole rate-limiting step. I also show that at pH 6.6, the VSV particle enters a stable intermediate state that binds tightly to membranes but does not precede to fusion. This dissertation uses a variety of experimental approaches to arrive at a more detailed understanding of how viruses use their entry proteins to either penetrate or fuse with the cell membrane.

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7

Biggs, Thelma Elizabeth. "The effects of viral proteins on macrophage function." Thesis, University of Southampton, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285659.

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8

Casey, John P. Jr. "Capsid catalysis : de novo enzymes on viral proteins." Thesis, Massachusetts Institute of Technology, 2015. http://hdl.handle.net/1721.1/99052.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2015.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 107-119).
Biocatalysis has grown rapidly in recent decades as a solution to the evolving demands of industrial chemical processes. Mounting environmental pressures and shifting supply chains underscore the need for novel chemical activities, while rapid biotechnological progress has greatly increased the utility of enzymatic methods. Enzymes, though capable of high catalytic efficiency and remarkable reaction selectivity, still suffer from relative instability, high costs of scaling, and functional inflexibility. Herein, M13 bacteriophage libraries are engineered as a biochemical platform for de novo semisynthetic enzymes, functionally modular and widely stable. Carbonic anhydrase-inspired hydrolytic activity via Zn²+ coördination is first demonstrated. The phage clone identified hydrolyzes a range of carboxylic esters, is active from 25°C to 80°C, and displays greater catalytic efficacy in DMSO than in water. Reduction-oxidation activity is subsequently developed via heme and copper cofactors. Heme-phage complexes oxidize multiple peroxidase substrates in a pH-dependent manner. The same phage clone also binds copper(II) and oxidizes a catechol derivative, di-tert-butylcatechol, using atmospheric oxygen as a terminal oxidant. This clone could be purified from control phage via Cu-NTA columns, enabling future library selections for phage that coördinate Cu²+ ions. The M13 semisynthetic enzyme platform complements biocatalysts with characteristics of heterogeneous catalysis, yielding high-surface area, thermostable biochemical structures readily adaptable to reactions in myriad solvents. As the viral structure ensures semisynthetic enzymes remain linked to the genetic sequences responsible for catalysis, future work could tailor the biocatalysts to high-demand synthetic processes by evolving new activities, utilizing high-throughput screening technology and harnessing M13's multifunctionality.
by John P. Casey, Jr.
Ph. D.

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9

Eid, Fatma Elzahraa Sobhy. "Predicting the Interactions of Viral and Human Proteins." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/77581.

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The world has proven unprepared for deadly viral outbreaks. Designing antiviral drugs and strategies requires a firm understanding of the interactions taken place between the proteins of the virus and human proteins. The current computational models for predicting these interactions consider only single viruses for which extensive prior knowledge is available. The two prediction frameworks in this dissertation, DeNovo and DeNovo-Human, make it possible for the first time to predict the interactions between any viral protein and human proteins. They further helped to answer critical questions about the Zika virus. DeNovo utilizes concepts from virology, bioinformatics, and machine learning to make predictions for novel viruses possible. It pools protein-protein interactions (PPIs) from different viruses sharing the same host. It further introduces taxonomic partitioning to make the reported performance reflect the situation of predicting for a novel virus. DeNovo avoids the expected low accuracy of such a prediction by introducing a negative sampling scheme that is based on sequence similarity. DeNovo achieved accuracy up to 81% and 86% when predicting for a new viral species and a new viral family, respectively. This result is comparable to the best achieved previously in single virus-host and intra-species PPI prediction cases. DeNovo predicts PPIs of a novel virus without requiring known PPIs for it, but with a limitation on the number of human proteins it can make predictions against. The second framework, DeNovo-Human, relaxes this limitation by forcing in-network prediction and random sampling while keeping the pooling technique of DeNovo. The accuracy and AUC are both promising ($>85%$, and $>91%$ respectively). DeNovo-Human facilitates predicting the virus-human PPI network. To demonstrate how the two frameworks can enrich our knowledge about virus behavior, I use them to answer interesting questions about the Zika virus. The research questions examine how the Zika virus enters human cells, fights the innate immune system, and causes microcephaly. The answers obtained are well supported by recently published Zika virus studies.
Ph. D.

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10

Hahn, Young Shin Lim Strauss James H. Strauss James H. "Functional analysis of viral nonstructural and structural proteins /." Diss., Pasadena, Calif. : California Institute of Technology, 1989. http://resolver.caltech.edu/CaltechETD:etd-06072007-075259.

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11

Nayak, Ramnath. "Characterization of the role of adenovirus-5 (Ad-5) gene products E2A, E4ORF6 and VA RNA on adeno-associated virus type 5 (AAV5) transcription, translation and replication." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/6005.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. "August 2007" Includes bibliographical references.

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12

Ainsworth, Julia. "Comparison of p53 and MAGI-3 regulation mediated by the E6 protein from high-risk human papillomavirus types 18 and 33." Thesis, McGill University, 2007. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=112368.

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The HPV E6-p53 interaction is well-understood, but not for all high-risk HPV types. In addition, HPV E6 p53-independent functions are gaining recognition for their importance in cellular transformation but require clarification. Thus, the aim of this study was two-fold: (1) to gain insight into the p53-E6 interaction for high-risk HPV-33 and, (2) to explore how high-risk HPV E6 proteins targets cellular MAGI-3 for degradation.
In vivo and in vitro results indicated that E6 from HPV types 18 and 33 interacted similarly with p53 although, variants of the HPV-33 E6 prototype demonstrated interesting disparities. Of note was HPV-33 E6 variant 2, which degraded p53 more efficiently than prototype HPV-33 E6 and HPV-18 E6. The E6 protein from HPV types 18 and 33 also potently degraded MAGI-3 via a different pathway than that used for p53. Specifically, proteasome inhibition did not interfere with MAGI-3 degradation and MAGI-3 was not ubiquitinated in the presence of the E6 protein.
Therefore, the results described herein enhance our understanding of high-risk HPV type 33 E6 and the E6-MAGI-3 interaction.

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13

Pearson, James L. "Analysis of transactivation of the capsid gene promoter of MVM by the NS1 protein." free to MU campus, to others for purchase, 1999. http://wwwlib.umi.com/cr/mo/fullcit?p9962554.

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14

Galloway, Summer E. "Functional characterization of conserved domains within the L protein component of the vesicular stomatitis virus RNA-dependent RNA polymerase implications for transcription and MRNA processing /." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2010r/galloway.pdf.

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15

Hobman, Tom Cunningham. "Molecular cell biology of Rubella virus structural proteins." Thesis, University of British Columbia, 1989. http://hdl.handle.net/2429/30614.

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Rubella virus (RV) is a small, enveloped, positive-stranded RNA virus in the family Togaviridae, and bears striking similarities to the prototype alphaviruses Semliki Forest virus (SFV) and Sindbis virus (SV) in terms of genome organization and structural protein expression strategy. However unlike alphaviruses, RV infection of cultured cells is characterized by relatively long latency periods, slow replication kinetics, limited cytopathology, and the ability to establish a persistent infection in virtually every cell line capable of supporting its growth. RV virions contain three structural proteins C, E2, and El which are derived by post-translational processing of a precursor polyprotein pllO (NF₂-C-E2-El-COOH). Processing and intracellular transport of RV structural proteins has been studied by jn vitro and jn vivo expression of RV cDNAs. It was found that targeting of El and E2 into the endoplasmic reticulum was mediated by two independently functioning signal peptides. Coincident with translocation into the ER, both proteins underwent addition of N-linked glycans and proteolytic processing. C protein did not appear to play a role in the processing of pllO. Expression of the RV structural proteins in COS cells revealed that E2 exited the ER, and was transported through the Golgi to the cell surface in an El-independent manner, although coexpression of El seemed to increase the rate of transport. Conversely, El was retained in a Golgi-like region and was not found on the plasma membrane in the absence of E2. Oligonucleotide-directed mutagenesis of El and E2 cDNAs showed that El andE2 both contain three N-linked glycans respectively. Lack of glycosylation did not appear to affect the intracellular localization of the RV glycoproteins in COS cells. A number of significant differences between RV and SFV/SV structural protein expression strategies were discovered, and their possible relationship to RV virion assembly are discussed.
Medicine, Faculty of
Medical Genetics, Department of
Graduate

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16

Ma, Hok-tsun, and 馬學俊. "RNA-Dependent RNA polymerase activity of the infectious bursal diseasevirus viral protein 1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30408192.

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17

Freeth, James Alexander. "The interactions of viral matrix proteins with lipid membranes." Thesis, Durham University, 2014. http://etheses.dur.ac.uk/10821/.

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This thesis describes the work undertaken to study the binding of lipid membranes by the viral matrix proteins hRSV-M and Influenza-A-M1. hRSV-M was recombinantly expressed and purified. It was the subjected to analysis by Langmuir-Blodgett trough experiments, Brewster angle microscopy, Confocal microscopy of giant unilamellar vesicles (GUVs), and binding studies with lipid nanodiscs. These studies showed hRSV-M having a preference for interacting with negatively charged lipids, namely phosphatidylserine, and for having different behaviours in Lo and Ld phases of membranes. During work on hRSV-M to improve its stability, it was discovered calcium stabilised the protein. This relationship was explored by ICPMS, differential scanning fluorimetry (DSF), circular dichroism (CD), mass spectrometry and microscale thermophoresis. This showed the hRSV-M is a calcium binding protein, containing two binding sites. Influenza-A-M1 was cloned into a plasmid vector and subsequently expressed and purified. The stability and structure of the protein was probed by DSF and CD measurements. The lipid interactions of this protein were then also explored by Langmuir-Blodgett trough isotherms and GUV binding under confocal microscopy. These showed that M1 is able to bind to phosphatidylserine containing membranes and causes vesicle budding from those membranes.

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18

Gao, William Ning Da. "Viral and cellular proteins involved in vaccinia virus egress." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/280280.

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Vaccinia virus (VACV) is a large double-stranded DNA virus with a cytoplasmic site of replication. It has a complex life cycle that produces two distinct infectious virion forms, Intracellular Mature Virions (IMVs) and Extracellular Enveloped Virions (EEVs). The host cell microtubule trafficking machinery is hijacked by the virus at three distinct positions of the viral life cycle. After virus entry, the virus cores are transported to pre-nuclear sites where they form viral factories that ultimately produce fully functional and infectious IMVs. A small proportion of IMVs are further transported to sites of wrapping, where they are enveloped by a host-derived double membrane to form Intracellular Enveloped Virions (IEVs). The IEVs are then transported to the cell periphery to facilitate efficient viral spread. The viral proteins A36, F12 and E2 together with the kinesin-1 microtubule motor protein are thought to be involved in IEV egress from the site of wrapping to the cell periphery, although the exact mechanism of movement is unclear. Until recently, A36 was the only known protein to interact with the kinesin-1 motor through kinesin light chain (KLC), but F12 has also been shown to interact with KLC through E2. The precise mechanism of how the IEV interacts with and activates the kinesin-1 motor protein is unclear, and this study explores the interactions of IEV proteins with KLCs in detail, mapping interactions between KLC and A36 or F12/E2. A36, F12 and E2 also show no sequence or predicted structural homology to any other known proteins, and structural studies were performed in an attempt solve their 3D structure. The CRISPR-Cas9 targeted genome editing tool was also utilised to knockout different KLC isoforms in multiple cell lines to assess their contribution to IEV egress as well as cellular trafficking. These studies will provide insight into the mechanisms behind the spatial and temporal control of kinesin motor activity in the cell.

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19

Berthold, François. "Grapevine fanleaf virus replication : viral proteins and host factors." Strasbourg, 2015. http://www.theses.fr/2015STRAJ086.

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20

Eifan, Saleh A. "Functional analysis of the orthobunyavirus nucleocapsid (N) protein." Thesis, St Andrews, 2008. http://hdl.handle.net/10023/542.

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21

He, Yupeng. "Modulation of the host cell signaling pathways and protein synthesis by hepatitis C virus nonstructural 5A protein /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/11491.

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22

Beyleveld, Mia. "Interaction of nonstructural protein NS3 of African horsesickness virus with viral and cellular proteins." Diss., Pretoria : [s.n.], 2007. http://upetd.up.ac.za/thesis/available/etd-12132007-115112.

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23

Ng, Ming-him, and 吳明謙. "Negative regulation of type-I interferon production by MIP-T3." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43572212.

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24

Lounsbach, Gillian Ruth. "Expression and epitopic analysis of the respiratory syncytial virus fusion protein in Escherichia coli." Thesis, University of Newcastle Upon Tyne, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.384807.

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25

Chan, Che-man. "Functional study of spike protein of a novel human coronavirus HKU1." Click to view the E-thesis via HKUTO, 2008. http://sunzi.lib.hku.hk/hkuto/record/B41896932.

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Ng, Ming-him. "Negative regulation of type-I interferon production by MIP-T3." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43572212.

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27

Jung, Cindy. "Quantitative analysis of lentivirus incorporation of heterologous viral and non-viral proteins for lung gene therapy." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/26648.

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Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2008.
Committee Chair: Joseph M. Le Doux; Committee Member: AndrÃ©s J. Garcia; Committee Member: Cheng Zhu; Committee Member: Nael McCarty; Committee Member: Richard Compans. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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28

Lundin, Marika. "Topology and membrane rearrangements of the hepatitis C virus protein NS4B /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-927-0/.

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29

Wark, Kim Louise. "Expression and processing of infectious bursal disease virus proteins." Thesis, University of Hertfordshire, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323651.

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30

Türe, Olcay. "Studies on the viral proteins of infectious bursal disease viruses /." The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487757723997915.

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31

Loredo, Varela Juan Luis. "Structural investigation of two viral proteins involved in DNA-packaging." Thesis, University of York, 2014. http://etheses.whiterose.ac.uk/7672/.

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Viral DNA-packaging motors are molecular machines that enable viruses to replicate by providing the means of storing the viral genome into empty procapsids. In double stranded DNA bacteriophages the molecular motor is comprised by three elements: the portal protein and the small and large terminases. The portal protein nucleates polymerisation of the capsid and scaffold proteins, initiating procapsid assembly, besides allowing passage of DNA. The small terminase recognises the viral genome and presents it to the large terminase which possesses both nuclease activity to cleave concatemeric DNA at the initiation of the packaging, and ATPase activity to drive translocation. Although currently several X-ray structures for the different components of the motor from different bacteriophages are available fundamental questions regarding the DNA recognition mechanism, stoichiometry and orientation of the motor components in vivo and the mechanism of ATP-driven DNA-translocation remain. This project focused on elucidating the X-ray crystal structures of (i) the major capsid protein, from Bacillus subtilis bacteriophage SPP1 and (ii) the small terminase protein from Thermus thermophilus bacteriophage G20C. Several constructs of the SPP1 capsid protein, including truncations at the N- and C-termini, single and double mutants and engineered proteins were generated in order to produce a protein suitable for crystallisation. Mutant uG13P;T104Y;A261W was the only construct that produced native and Se-Met crystals. The X-ray structure of the SPP1 capsid protein was determined at 3.0 Å resolution by single wavelength anomalous diffraction. The structure exhibited the HK97-fold consisting of the axial and peripheral domains and the extended E-loop. The X-ray structure of the small terminase from phage G20C was solved at 2.5 Å resolution by single wavelength anomalous diffraction. The structure consisted of circular nine-mers where the N- terminal domains of each subunit reside at the periphery of the assembly and the C-terminal oligomerisation domains form a central channel. The conserved structural features between small terminases suggest that the DNA-recognition mechanism might be conserved. DNA-binding experiments demonstrated that the G20C small terminase binds to viral and non-viral DNA with both the N- and C- terminal domains playing an important role. The structural information generated from these two elements of SPP1 and G20C bacteriophages provides insight into two different aspects of the assembly process: (i) how the capsid protein’s conformational plasticity may assist the assembly and (ii) DNA-recognition during virus particle construction. This information is critical for understanding similar processes in other viruses, in particular, in the evolutionarily related herpes viruses.

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Meissner, Christina Sylvia. "Influence of HCMV proteins pUL71 and pUL77 on viral maturation." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2011. http://dx.doi.org/10.18452/16414.

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Die Bildung infektiöser Viruspartikel des humanen Zytomegalievirus (HCMV) ist ein mehr-stufiger Prozess. Sie beginnt mit der Verpackung der DNA in die Kapside im Kern, gefolgt von weiterer Reifung während des Transports durch das Zytoplasma und der abschließenden Freisetzung aus der Zelle. Im Zuge dieser Arbeit wurden zwei Proteine, die Einfluss auf die ebengenannten Prozesse haben, analysiert. Der erste Teil der Arbeit befasst sich mit der funktionellen Charakterisierung des HCMV Pro-teins pUL77. Es ist bekannt, dass das homologe Protein pUL25 in alpha-Herpesvirinae essentiell für die DNA-Verpackung ist. Zunächst konnte das Protein als Kapsid-assoziiertes strukturelles Protein identifiziert werden. Es wurden Interaktionen von pUL77 mit DNA-Verpackungs- und Kapsidproteinen gezeigt. Weiterhin wurde die DNA-Bindungsfähigkeit von pUL77 in verschiedenen „in vitro“-Experimenten untersucht. Zusammengefasst weisen unsere Ergebnisse auf eine Funktion von HCMV pUL77 bei der DNA-Verpackung hin. Im zweiten Teil der Arbeit wurde das HCMV Protein pUL71 charakterisiert, das in allen Herpesviren konserviert vorkommt, dessen Funktion jedoch nicht charakterisiert ist. Zunächst wurde das Protein als strukturelles Tegumentprotein mit “earlylate“ Expressionskinetik klassifiziert. Weiterhin wurden die subzelluläre Lokalisation sowie virale und zelluläre Interaktionspartner untersucht. Die Ergebnisse weisen auf eine Funktion von HCMV pUL71 bei der Reifung und beim Transport der Virionen im Zytoplasma hin. „In silico“-Vorhersagen zeigten ein „Leuzin Zipper“-Motiv in pUL71, das als mögliche Oligomerisationsdomäne dienen könnte. Mutationen wurden in dieses Motiv eingebracht und die resultierenden Proteine auf ihre Oligomerisationsfähigkeit mit „in vitro“-Methoden und in rekombinanten Viren untersucht. Zusammenfassend konnten wir zeigen, dass das „Leuzin Zipper“-Motiv wichtig für die Funktion von pUL71 ist und diese mit einer unbeeinträchtigten Oligomerisation des Proteins zusammen hängt.
The morphogenesis of Human cytomegalovirus (HCMV) virions starts with the capsid assem-bly and DNA insertion in the nucleus followed by maturation during transport through the cytoplasm prior to release of virus progeny. In this study we are functionally characterising two proteins that are involved in those steps. The function of essential HCMV protein pUL77 is characterised in the first part of the study. HCMV pUL77 was shown to be a structural protein associated with capsids. Furthermore, our experiments demonstrated that HCMV pUL77 interacts with DNA packaging motor compo-nents and capsid proteins. The ability of HCMV pUL77 to bind double-stranded DNA was studied in “in vitro” assays designed for this study. The homologue α-Herpesvirinae protein pUL25 is described to be involved in processes connected with DNA packaging. Data ob-tained in this study demonstrates that HCMV pUL77 might serve a similar function. In the second part of the study HCMV pUL71, conserved throughout the Herpesvirus family but to date unclassified, was functionally characterised. HCMV pUL71 was defined a struc-tural tegument protein with early-late expression kinetics. We studied the sub-cellular local-isation and interactions of pUL71 with a subset of cellular and viral proteins. Thereby we could show that HCMV pUL71 function might be connected with processes of viral egress. By in silico analyses we identified a leucine zipper motif in pUL71 that might serve as a puta-tive oligomerisation domain. In order to investigate the function of the leucine zipper motif, we performed in vitro assays and investigated the alterations of the motif in the viral context. Taken together we can conclude that (i) an intact leucine zipper motif is crucial for the func-tion of pUL71 and (ii) this function is dependent upon undisturbed oligomerisation of the pro-tein.

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33

Hui, Daniel Jason. "The Mechanism of Protein Synthesis Inhibition by the P56 Family of Viral Stress Inducible Proteins." Connect to text online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1104848977.

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34

Haag, Lars. "The dynamic envelope of a fusion class II virus : molecular reorganizations during prefusion stages of Semliki forest virus /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-718-9/.

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35

Moës, Elien. "Theiler's murine encephalomyelitis protein 2C and its effect on membrane trafficking." Thesis, St Andrews, 2008. http://hdl.handle.net/10023/540.

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36

McGivern, David. "A functional analysis of the replication-associated proteins of maize streak virus." Thesis, University of East Anglia, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.249710.

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Yip, Chi-wai. "Characterization of cellular receptors of infectious bursal disease virus in chickens." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36759533.

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Tang, Weiliang. "Effects of conditional expression of hepatitis C virus proteins on non-transformed human hepatocyte line HH4 cells /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/6310.

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39

So, King-yan Leo, and 蘇敬仁. "Dynamics of the mammalian nuclear proteome during influenza viral infection using SILAC-based MS quantitative proteomics." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B47869860.

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Influenza has resided with the human race long before we have any written record of it. Its death toll is one of the highest among all other virus. In recent history, pandemic outbreaks of influenza have caused even more deaths. Therefore it is of great importance that we focus our resources on understanding its viral components and functions. In this study, chimeric mutagenesis was used to investigate the antigenic variance of antibodies I50C and I131B on H1N1 and H5N1 NP. It was revealed from previous study that antibodies I50C and I131B can detect H1N1 NP but not H5N1 NP. NP from influenza A strains A/Puerto Rico/8/1934 (PR8), A/Vietnam/3046/2004 (3046) and A/Indonesia/5/2005 (indo) were used to construct the NP chimeric mutants. Nucleotide sequence from the region spanning from bp 484-506 was chosen as template to design the primers for obtaining head and tail fragments which were components of the NP constructs. Results showed that antibodies I50C and I131B can only detect NP constructs with PR8 head fragments regardless of any tail fragments, and cannot detect NP constructs with 3046 or indo head fragments. Therefore the binding epitope on H1N1 NP tested by the antibodies I50C and I131B is deduced to be within bp 1-506. In order to understand the dynamics of host and viral nuclear proteome during the influenza A infection, the pulse SILAC (Stable Isotope Labeling of Amino acids on Cell lines) MS-proteomic approach was adopted. More and more research studies are MS-proteomic based as people recognize that proteins truly define the outcome of a cell, with fewer limitations by solely looking at the genome. The pulse SILAC technique involves incorporating “light” isotope-labeled amino acids such as arginine and lysine into cells’ proteins prior infection experiment. While the cells are under influenza infection, “heavy” isotope-labeled amino acids were used to label the cells 2 hour prior each harvesting time points. Since only proteins synthesized within the 2 hour windows are “heavy” isotope labeled, relative quantification of “heavy” isotope to “light” isotope by mass spectrometry (MS) can be calculated into heavy:light (H/L) ratios. Through this method we can know to what extents are the proteins affected and whether the effect is global or specific. Together with the temporal degree of the data, we can reveal the dynamics of host and viral nuclear proteome during the influenza A infection. MS results of the influenza viral proteins agree with the viral gene expression profile upon infections and corresponded well with time of viral protein expressions during influenza pathogenesis investigated by other research groups. A number of proteins were identified to increase in turnover rate at 8 hpi. This gives a partial view of up-regulated functions inside the nucleus during influenza A infection at that stage. The up-regulated proteins represent cellular functions that are related to: energy homeostasis, microtubule-dependent transport, DNA coiling regulation, transcription regulation, translation regulation and protein folding. The findings of this research present more information to understand influenza virus and provide a stepping stone for fellow influenza researchers.
published_or_final_version
Pathology
Master
Master of Philosophy

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Pong, Chi-him, and 龐智謙. "HIV-1 Tat induced immune responses and its effect on opportunistic infections." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/207196.

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Acquired immunodeficiency syndrome (AIDS) is a major problem in our current society. There are over 35 million of the population that are currently living with human immunodeficiency virus (HIV), and the number of HIV-infected patients are still rising every year in spite of our efforts to control it. Furthermore, within the AIDS affected population, opportunistic infection is a major cause of complications and is the number one cause of death. The HIV trans-activator (Tat) protein plays a major role in the AIDS pathogenesis. HIV-1 Tat is known to cause dysregulation of cytokines such as TNF-α, IL-6, and IL-10 in AIDS patients. In this study we recognized a proto-oncogene, c-Myc, could regulate the cytokine dysregulation caused by HIV-1 Tat in primary blood monocyte derived macrophages (PBMac). By knocking down the expression of c-Myc with gene specific small-interfering RNA (siRNA), we demonstrated that c-Myc may be critical for the expression of the pro-inflammatory cytokines TNF-α and IL-6. HIV-1 Tat was subsequently found to regulate the expression of c-Myc via the activation of dsRNA-activated protein kinase (PKR), ERK1/2 and p38 mitogen-activated protein kinase (MAPK). Furthermore, c-Myc regulation of the pro-inflammatory cytokines was demonstrated to have a role in AIDS related opportunistic infections. HIV-1 Tat was shown to increase the intracellular growth of Mycobacteria avium complex (MAC) within PBMac. This increase in MAC growth was in turn found to be regulated by TNF-α expression controlled by c-Myc. HIV-1 Tat was also demonstrated to induce the expression of RIG-I, a common pattern recognition receptor of double stranded RNA viruses, in PBMac. RIG-I is known to activate the viral immune responses such as the type-I interferon (IFN) and pro-inflammatory cytokine pathways. This induction of RIG-I by HIV-1 Tat was found to be regulated by c-Myc, as well as through other signalling kinases such as p38 MAPK and PKR. Tat induction of RIG-I ultimately led to the induction of IFN-α2 and IFN-β through the expression and nuclear translocation of the interferon regulatory factor-7 (IRF-7). This alteration in type-I IFN expression regulated by HIV-1 Tat and RIG-I was also found to play a role against AIDS related opportunistic infections. HIV-1 Tat is known to increase the infectivity of Kaposi’s sarcoma-related herpesvirus (KSHV), a common opportunistic viral infection. We were able to demonstrate that this increase in KSHV infectivity was regulated by RIG-I and type-I IFN induced by HIV-1 Tat. Lastly, this study also demonstrated how HIV-1 Tat was able to manipulate the expression of IL-8 induced by KSHV in PBMac. HIV-1 Tat was able to mediate the production of IL-8 induced by KSHV by altering the phosphorylation of the p38 MAPK and the signal transducer and activator of transcription-1 (STAT-1). Taken together, the results of this study showed how c-Myc and RIG-I may be able to play critical roles in HIV-1 Tat induced cytokine dysregulation. Furthermore, the importance of these pathways is further demonstrated in their roles in regulating the immune responses against opportunistic infections in AIDS patients.
published_or_final_version
Paediatrics and Adolescent Medicine
Doctoral
Doctor of Philosophy

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41

Donnelly, Michelle L. L. "A study of the 2A region of aphthoviruses." Thesis, University of St Andrews, 1997. http://hdl.handle.net/10023/13890.

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The proteins encoded by foot-and-mouth disease virus are expressed in the form of a polyprotein, which is processed by virus-encoded proteases to yield the mature viral proteins. The focus of this thesis is the 18 amino acid 2A region of foot-and-mouth disease virus (FMDV), which is (together with the first proline residue of 2B) capable of mediating a primary cleavage at its own carboxy-terminus, between the structural and replicative viral proteins. It was proposed that the 2A region performed this event via a novel proteolytic mechanism. Vectors encoding the FMDV 2A region, in frame, between two foreign gene sequences were constructed to allow the 2A region to be investigated in isolation from the rest of the virus proteins using in vitro translation systems. Detailed quantitative densitometric analyses of the translation products were carried out, which suggested non-stoichiometric expression of the two cleavage products. Single and multiple site-directed mutations were made to the 2A sequence and the activities of the resultant 2A regions determined to establish the identity of functional amino acid residues. The effect of the surrounding foreign protein sequence and the inclusion of progressively longer wild-type sequences prior to 2A was also examined. The carboxy-termini of cardiovirus 2A regions show significant sequence similarity to the FMDV 2A region and are known to mediate a similar primary cleavage. The cleavage activities of the carboxy-termini of cardiovirus 2A regions were compared to that of the FMDV 2A region and found to equally capable of mediating cleavage. The activity of FMDV 2A region was tested in prokaryotes and was found to be inactive. These studies indicated that the 2A cleavage was not a proteolytic cleavage, but more likely a translational effect. A new model for 2A-mediated activity is presented.

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42

Wu, Shang-Rung. "Activation of the spike proteins of alpha- and retroviruses." Stockholm, 2009. http://diss.kib.ki.se/2009/978-91-7409-736-8/.

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43

Estmer, Nilsson Camilla. "Viral Control of SR Protein Activity." Doctoral thesis, Uppsala : Acta Universatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5124-1/.

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44

Bardelli, Martino. "Strategies of viral multi-functional regulator proteins : adeno-associated virus Rep." Thesis, King's College London (University of London), 2016. https://kclpure.kcl.ac.uk/portal/en/theses/strategies-of-viral-multifunctional-regulator-proteins(6154fd50-eacd-4dbe-b456-bd08d2b13849).html.

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Adeno-associated virus (AAV) is a small non-pathogenic human DNA parvovirus. The AAV life cycle, which includes transcriptional regulation, DNA replication, assembly and site-specific integration, is orchestrated by AAV’s four Rep proteins. Structurally, these proteins share a AAA+ domain characteristic of the SF3 family of helicases, with the larger Rep68 and Rep78 additionally containing an N-terminal origin-binding domain (OBD) that specifically binds and nicks DNA. The combination of these domains is the basis for the remarkable multi-functionality displayed by Rep68 and Rep78. To date, structural studies of Rep68 and Rep78 have been limited by the tendency of these proteins to aggregate when purified. Here, we describe a fully functional Rep mutant that does not aggregate even at high concentrations and use this mutant to investigate the structural requirements for Rep functions. We demonstrate that one of the determinants regulating the oligomerisation of the Rep proteins lies in the linker connecting the helicase domain and OBD. We also identify a series of key residues at the interface between Rep monomers and show that mutating them has drastic effects both on the oligomerisation and functionality of the Rep proteins. Importantly, these oligomerisation-deficient mutants do not support the AAV life-cycle and fail to bind DNA efficiently, an important Rep function necessary for DNA nicking, transcriptional regulation, viral DNA replication and site-specific integration. Finally, understanding the molecular details of Rep and its functions will contribute to the development of new AAV-based vectors that exploit the Rep- mediated integration mechanism and potentially have a lower risk of insertional mutagenesis than retroviral vectors. In the last chapter, we describe an AAV vector for testing the safety and feasibility of AAV-mediated targeted gene addition in induced pluripotent stem (iPS) cells within the therapeutic context of SCID-X1, an immunodeficiency caused by mutations in the common gamma chain gene.

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45

Liang, Yuying. "Molecular characterization of rubella virus nonstructural proteins and viral RNA synthesis." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0020/NQ56576.pdf.

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46

Young, Natalie Jane. "Bovine Viral Diarrhoea Virus Subunit Vaccines : Contribution of Non-Structural Proteins." Thesis, Royal Veterinary College (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.498686.

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47

Murphy, Jane Clare. "The engineering of viral fusion proteins in the baculovirus expression system." Thesis, University of Southampton, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.240912.

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48

Shair, Kathy Ho Yen. "Electromelia virus-host interactions : the viral growth factor and Schlafen proteins." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619967.

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49

Gall, Jason G. D. "The role of adenovirus fiber and hexon proteins in virus-host interactions /." Access full-text from WCMC:, 1998. http://proquest.umi.com/pqdweb?did=1432807591&sid=9&Fmt=2&clientId=8424&RQT=309&VName=PQD.

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50

Ye, Chaoyang. "Transcription regulation of adeno-associated viruses." Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4709.

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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.
"May 2007" The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. Includes bibliographical references.

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