African monkey species are natural hosts of simian hemorrhagic fever virus (SHFV) and develop persistent, asymptomatic infections. SHFV was previously shown to also cause a rapid onset fatal hemorrhagic fever disease in macaques. Infection of macaques with a new isolate of SHFV from persistently infected baboon sera, that showed high nucleotide identity with the lab strain LVR, resulted in viremia, pro-inflammatory cytokine and tissue factor production, and symptoms of coagulation defects. Primary macrophages and myeloid dendritic cell cultures from disease-susceptible macaques efficiently replicated SHFV and produced pro-inflammatory cytokines, including IL-6 and TNF-α, as well as tissue factor. Cells from disease resistant baboons produced low virus yields and the immunomodulatory cytokine IL-10. IL-10 treatment of macaque cells decreased IL-6 levels but had no effect on TNF-α levels, tissue factor or virus production suggesting that IL-10 plays a role in modulating immunopathology in disease-resistant baboons but not in regulating the efficiency of virus replication. SHFV is a member of the family Arteriviridae. The SHFV genome encodes 8 minor structural proteins. Other arteriviruses encode 4 minor structural proteins. Amino acid sequence comparisons suggest that the four additional SHFV minor structural proteins resulted from gene duplication. A full-length infectious clone of SHFV was constructed and produced virus with replication kinetics comparable to the parental virus. Mutant infectious clones, each with the start codon of one of the minor structural proteins substituted, were analyzed. All eight SHFV proteins were required for infectious virus production. The SHFV nonstructural polyprotein is processed into the mature replicase proteins by several viral proteases including papain-like cysteine proteases (PLPs). Only one or two PLP domains are present in other arteriviruses but SHFV has three PLP domains. Analysis of in vitro proteolytic processing of C- and N-terminally tagged polyproteins indicated that the PLP in each of the three SHFV nsp1 proteins is active. However, the nsp1α protease is more similar to a cysteine protease than a PLP. Analysis of the subcellular localization of the three SHFV nsp1 proteins indicated they have divergent functions.

African monkey species are natural hosts of simian hemorrhagic fever virus (SHFV) and develop persistent, asymptomatic infections. SHFV was previously shown to also cause a rapid onset fatal hemorrhagic fever disease in macaques. Infection of macaques with a new isolate of SHFV from persistently infected baboon sera, that showed high nucleotide identity with the lab strain LVR, resulted in viremia, pro-inflammatory cytokine and tissue factor production, and symptoms of coagulation defects. Primary macrophages and myeloid dendritic cell cultures from disease-susceptible macaques efficiently replicated SHFV and produced pro-inflammatory cytokines, including IL-6 and TNF-α, as well as tissue factor. Cells from disease resistant baboons produced low virus yields and the immunomodulatory cytokine IL-10. IL-10 treatment of macaque cells decreased IL-6 levels but had no effect on TNF-α levels, tissue factor or virus production suggesting that IL-10 plays a role in modulating immunopathology in disease-resistant baboons but not in regulating the efficiency of virus replication. SHFV is a member of the family Arteriviridae. The SHFV genome encodes 8 minor structural proteins. Other arteriviruses encode 4 minor structural proteins. Amino acid sequence comparisons suggest that the four additional SHFV minor structural proteins resulted from gene duplication. A full-length infectious clone of SHFV was constructed and produced virus with replication kinetics comparable to the parental virus. Mutant infectious clones, each with the start codon of one of the minor structural proteins substituted, were analyzed. All eight SHFV proteins were required for infectious virus production. The SHFV nonstructural polyprotein is processed into the mature replicase proteins by several viral proteases including papain-like cysteine proteases (PLPs). Only one or two PLP domains are present in other arteriviruses but SHFV has three PLP domains. Analysis of in vitro proteolytic processing of C- and N-terminally tagged polyproteins indicated that the PLP in each of the three SHFV nsp1 proteins is active. However, the nsp1α protease is more similar to a cysteine protease than a PLP. Analysis of the subcellular localization of the three SHFV nsp1 proteins indicated they have divergent functions.

Introdução: A epilepsia do lobo temporal mesial (ELTM) é a forma mais comum de epilepsia na população adulta, tendo a esclerose hipocampal como principal substrato neuropatológico. Uma elevada proporção dos pacientes com ELTM apresentam história familiar positiva para a epilepsia, sugerindo a participação de fatores genéticos nesta síndrome. O citoesqueleto neuronal é essencial para os processos fisiológicos das células nervosas e crises epilépticas parecem afetar esta estrutura. O citoesqueleto neuronal possui importantes componentes regulatórios, dentre eles as proteínas associadas aos microtúbulos do tipo 2 (MAP2) e tau. Objetivos: Avaliar a densidade neuronal (células imunomarcadas com NeuN), neobrotamento das fibras musgosas (por histoquímica de neo-Timm) e a expressão imunohistoquímica das proteínas MAP2 e tau no hipocampo de casos cirúrgicos de ELTM (subtipos familiar e esporádico) e controles. As mesmas análises foram conduzidas no modelo animal de lítiopilocarpina. Métodos: Casos ELTM (n=38) foram divididos em ELTM familiar (n=20) e ETLM esporádica (n=18). Hipocampos controles (n=10) foram provenientes de necrópsias de sujeitos sem histórico de problemas neurológicos. No modelo animal de lítio-pilocarpina, animais submetidos ao status epilepticus (SE) foram sacrificados nos seguintes tempos pós-SE: 1, 7, 15 e 60 dias e classificados como grupos SE1, SE7, SE15 e SE60. Animais controle foram injetados com salina. Resultados: O grupo ELTM apresentou menor densidade neuronal que o controle nas regiões da camada granular, hilo, CA4, CA3, CA1 e prosubículo. O grupo ELTM mostrou maior valor de cinza da histoquímica de neo-Timm na camada granular, molecular interna e molecular externa e maior espessura do neobrotamento axonal na camada molecular interna em relação ao grupo controle. O grupo ELTM esporádica teve maior valor de cinza da histoquímica de neo-Timm e tendência à maior espessura do neobrotamento que o grupo ELTM familiar na camada molecular interna. O grupo ELTM apresentou menor expressão de MAP2 que o grupo controle no hilo, CA4, CA3, CA1 e prosubículo e maior expressão que o controle na camada granular, CA2 e parasubículo. O grupo ELTM esporádica teve maior expressão de MAP2 que o grupo ELTM familiar em CA1 e córtex entorrinal. O grupo ELTM apresentou maior expressão de tau que o grupo controle nas regiões da camada granular, hilo, CA3, CA2 e córtex entorrinal. O grupo ELTM esporádica demonstrou menor imunorreatividade para tau que o grupo ELTM familiar no córtex entorrinal. No modelo de lítio-pilocarpina, os grupos submetidos ao SE apresentaram menor densidade neuronal e maior neobrotamento que o grupo salina. Quanto à expressão de MAP2, os grupos SE60 e SE15 apresentaram maiores valores de expressão que os demais grupos em todas as regiões analisadas. A expressão de tau em CA3 não foi diferente entre os grupos animais analisados. Conclusão: Nossos resultados existem perda neuronal, reorganização sináptica das fibras musgosas e alterações na expressão de proteínas MAP2 e tau no hipocampo de pacientes com ELTM. Dentre os casos ELTM, encontramos diferenças no neobrotamento de fibras musgosas e na expressão de MAP2 e tau entre os grupos ELTM familiar e esporádica, indicando que estes grupos se apresentam de forma distinta em relação à epilepsia. Encontramos resultados II semelhantes em relação à densidade neuronal e o neobrotamento de fibras musgosas entre pacientes com ELTM e no modelo experimental. Porém, em relação à expressão das proteínas MAP2 e tau, encontramos algumas diferenças entre humanos e animais com ELTM. Nossos resultados sugerem que apesar do modelo de epilepsia induzida por lítio-pilocarpina ser relevante para o estudo da ELTM humana e mimetizar importantes aspectos neuropatológicos, a correspondência quanto à expressão de algumas proteínas estruturais não é completa. Estudos adicionais de expressão de proteínas do citoesqueleto em outros modelos animais de ELTM serão de grande importância para o melhor entendimento do processo epileptogênco. / Introduction: Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy in adults and has hippocampal sclerosis as the main pathological substrate. A high proportion of patients with MTLE have positive familial history for epilepsy, suggesting the involvement of genetic factors in this syndrome. Seizures may affect the neuronal cytoskeleton, an structure that is essential in the physiological processes of nerve cells. Components of the neuronal cytoskeleton include microtubule-associated protein type 2 (MAP2) and tau. Objectives: Our aim was to evaluate neuronal density, mossy fiber sprouting and immunohistochemical expression of MAP2 and tau in the hippocampus of surgical cases of MTLE (familial and sporadic subtypes) and controls. The same analysis were conducted in the MTLE lithiumpilocarpine animal model.Methods: MTLE cases (n = 38) were divided into familial MTLE (n = 20) and sporadic MTLE (n = 18). Control hippocampi (n = 10) were obtained from autopsies of subjects without history of epilepsy. In the lithium-pilocarpine animal model, male Wistar rats were submitted to status epilepticus (SE) and were killed at the following post-SE days: 1, 7, 15 and 60, and were further classified SE1, SE7, SE15 and SE60. Control animals were injected with saline. Results: MTLE showed decreased neuronal density than controls in the granular layer, hilus, CA4, CA3, CA1 and prosubiculum. MTLE group showed increased neo-Timm gray value in the granular layer, inner and outer molecular layer, as well as increased mossy fiber length of mossy fiber in the inner molecular layer when compared to controls. Sporadic MTLE specimens exhibited increased inner molecular layer gray value than familial MTLE. MTLE hihppocampi showed decreased MAP2 expression in the hilus, CA4, CA3, CA1 and prosubiculum. In the granular layer, CA2 and parasubiculum, MAP2 expression was higher in MTLE specimens than in controls. CA1 and entorhinal cortex from sporadic MTLE hippocampi showed increased MAP2 expression than familial MTLE. Tau expression was increased in the granular layer, hilus, CA3, CA2 and entorhinal cortex of MTLE specimens. Sporadic MTLE exhibited lower tau immunoreactivity in the entorhinal cortex than familial MTLE. In the lithiumpilocarpine animal model, rats submitted to SE presented lower values of neuronal density and mossy fiber sprouting than controls. SE15 and SE60 showed increased MAP2 expression in all hippocampal subfields. Tau expression in CA3 was not different among the groups. Conclusion: Our results indicate that besides neuronal loss and axonal sprouting, MTLE specimens also exhibit dendritic abnormalities related to MAP2 expression. Increased tau immunoreactivity in epileptogenic hippocampi indicates possible abnormal expression related to mossy fiber sprouting in chronic MTLE. We found differential sprouting, MAP2 and tau expression between sporadic and familial MTLE. It is possible that different genetic background might result in somehow distinct neuropathological substrates between the two MTLE subtypes, although their clinical manifestation is quite similar. While neuronal loss and axonal sprouting profiles in human MTLE and chronic phase of the lithium-pilocarpine animal model are comparable, we could not find corresponding results regarding MAP2 and tau expression. IV Several studies have shown that chemo-convulsant as pilocarpine and kainic acid result in widespread brain epileptic discharges, which are different from the more focal hippocampal discharges seen in human MTLE. Despite its limitations, the lithium-pilocarpine model stands as an important and widely used animal model of epilepsy. Besides that, other animal models in which ictal discharges and lesions are more limited to the hippocampal formation might better mimic what we see in human MTLE.

Polioviruses, Coxsackieviruses, and Echoviruses belonging to the Picornaviridae family of positive-stranded, non-enveloped viruses, are highly infectious and associated with a range of illnesses in children from minor febrile illness to severe, potentially fatal conditions (eg, aseptic meningitis, encephalitis, paralysis and myocarditis). The viruses encodes 11 viral proteins along with the transient set of intermediates unique to viral propagation. 3A, one of the non-structural proteins, plays a crucial role in viral replication by anchoring the replication complex to the membrane vesicle and by recruiting essential cellular factors to the site of replication. It is an 89 amino-acid longprotein, and consists of a soluble N-terminal region and a hydrophobicC-terminal region. The soluble region contains two amphipathic alphahelices that form a hairpin, which are flanked by unstructured regions.Since, Enteroviruses have limited coding capacity,viral protein interactions with cellular proteins and lipids are essentialin viral replication, translation, polyprotein processing andpathogenesis. Understanding these interactions is essential inunderstanding the molecular mechanisms associated pathogenesis, andidentifying drug targets. Our studies are aimed at identifying hostfactors interacting with 3A protein and their functional significance invirus replication.We have identified thepotential 3A-interacting cellular candidate proteins using pull-down followed by liquid chromatography associated mass spectrometry. Gene ontology analysis revealed asignificant enrichment in cellular pathways, functions, and proteindomains in comparison with the control. Further studies were focused on Sec12 (guanine nucleotideexchange factor), ACBD3 (acyl-CoA binding domain containing 3) andPhosphatidylinositol 4-kinase beta (PI4KIIIß) interactions with the 3Aprotein, and their significance in viral replication. Sec12 (GEF) initiates the COPII vesicle-mediated ER-to-Golgi membrane trafficking by recruiting and activating the small GTP binding protein Sar1A to the membrane, which further recruits Sec23/24, cargo and Sec13/31 coat proteins to form functional COPII vesicles.We demonstrated that Sec12 and 3A interact directly in the ER through their C-terminal hydrophobic regions in oligomerization independent manner, leading toreduced the level of recruitment of individual COPII components such as Sar1A, Sec24A, and Sec31A to the membranes, thereby inhibiting virus replication. But in infected cells, other viral proteins such as 2B and 2BC likely stabilize the membrane-recruited Sar1A to support the viral replication. The viral proteins, ACBD3, PI4KIIIß interacted and co-localized with the Echovirus 3A protein.Knockdown of Sec12 or PI4KIIIß and expression of 3A or DN-Sar1A inhibited Echovirus replication, unlike proteins which support the COPII vesicle mediated ER-to-Golgi trafficking.Our results collectively indicate Sec12 is a crucial component in the anterograde membrane trafficking and is a novel host factor in Echovirus replication.

Introdução: A epilepsia do lobo temporal mesial (ELTM) é a forma mais comum de epilepsia na população adulta, tendo a esclerose hipocampal como principal substrato neuropatológico. Uma elevada proporção dos pacientes com ELTM apresentam história familiar positiva para a epilepsia, sugerindo a participação de fatores genéticos nesta síndrome. O citoesqueleto neuronal é essencial para os processos fisiológicos das células nervosas e crises epilépticas parecem afetar esta estrutura. O citoesqueleto neuronal possui importantes componentes regulatórios, dentre eles as proteínas associadas aos microtúbulos do tipo 2 (MAP2) e tau. Objetivos: Avaliar a densidade neuronal (células imunomarcadas com NeuN), neobrotamento das fibras musgosas (por histoquímica de neo-Timm) e a expressão imunohistoquímica das proteínas MAP2 e tau no hipocampo de casos cirúrgicos de ELTM (subtipos familiar e esporádico) e controles. As mesmas análises foram conduzidas no modelo animal de lítiopilocarpina. Métodos: Casos ELTM (n=38) foram divididos em ELTM familiar (n=20) e ETLM esporádica (n=18). Hipocampos controles (n=10) foram provenientes de necrópsias de sujeitos sem histórico de problemas neurológicos. No modelo animal de lítio-pilocarpina, animais submetidos ao status epilepticus (SE) foram sacrificados nos seguintes tempos pós-SE: 1, 7, 15 e 60 dias e classificados como grupos SE1, SE7, SE15 e SE60. Animais controle foram injetados com salina. Resultados: O grupo ELTM apresentou menor densidade neuronal que o controle nas regiões da camada granular, hilo, CA4, CA3, CA1 e prosubículo. O grupo ELTM mostrou maior valor de cinza da histoquímica de neo-Timm na camada granular, molecular interna e molecular externa e maior espessura do neobrotamento axonal na camada molecular interna em relação ao grupo controle. O grupo ELTM esporádica teve maior valor de cinza da histoquímica de neo-Timm e tendência à maior espessura do neobrotamento que o grupo ELTM familiar na camada molecular interna. O grupo ELTM apresentou menor expressão de MAP2 que o grupo controle no hilo, CA4, CA3, CA1 e prosubículo e maior expressão que o controle na camada granular, CA2 e parasubículo. O grupo ELTM esporádica teve maior expressão de MAP2 que o grupo ELTM familiar em CA1 e córtex entorrinal. O grupo ELTM apresentou maior expressão de tau que o grupo controle nas regiões da camada granular, hilo, CA3, CA2 e córtex entorrinal. O grupo ELTM esporádica demonstrou menor imunorreatividade para tau que o grupo ELTM familiar no córtex entorrinal. No modelo de lítio-pilocarpina, os grupos submetidos ao SE apresentaram menor densidade neuronal e maior neobrotamento que o grupo salina. Quanto à expressão de MAP2, os grupos SE60 e SE15 apresentaram maiores valores de expressão que os demais grupos em todas as regiões analisadas. A expressão de tau em CA3 não foi diferente entre os grupos animais analisados. Conclusão: Nossos resultados existem perda neuronal, reorganização sináptica das fibras musgosas e alterações na expressão de proteínas MAP2 e tau no hipocampo de pacientes com ELTM. Dentre os casos ELTM, encontramos diferenças no neobrotamento de fibras musgosas e na expressão de MAP2 e tau entre os grupos ELTM familiar e esporádica, indicando que estes grupos se apresentam de forma distinta em relação à epilepsia. Encontramos resultados II semelhantes em relação à densidade neuronal e o neobrotamento de fibras musgosas entre pacientes com ELTM e no modelo experimental. Porém, em relação à expressão das proteínas MAP2 e tau, encontramos algumas diferenças entre humanos e animais com ELTM. Nossos resultados sugerem que apesar do modelo de epilepsia induzida por lítio-pilocarpina ser relevante para o estudo da ELTM humana e mimetizar importantes aspectos neuropatológicos, a correspondência quanto à expressão de algumas proteínas estruturais não é completa. Estudos adicionais de expressão de proteínas do citoesqueleto em outros modelos animais de ELTM serão de grande importância para o melhor entendimento do processo epileptogênco. / Introduction: Mesial temporal lobe epilepsy (MTLE) is the most common form of epilepsy in adults and has hippocampal sclerosis as the main pathological substrate. A high proportion of patients with MTLE have positive familial history for epilepsy, suggesting the involvement of genetic factors in this syndrome. Seizures may affect the neuronal cytoskeleton, an structure that is essential in the physiological processes of nerve cells. Components of the neuronal cytoskeleton include microtubule-associated protein type 2 (MAP2) and tau. Objectives: Our aim was to evaluate neuronal density, mossy fiber sprouting and immunohistochemical expression of MAP2 and tau in the hippocampus of surgical cases of MTLE (familial and sporadic subtypes) and controls. The same analysis were conducted in the MTLE lithiumpilocarpine animal model.Methods: MTLE cases (n = 38) were divided into familial MTLE (n = 20) and sporadic MTLE (n = 18). Control hippocampi (n = 10) were obtained from autopsies of subjects without history of epilepsy. In the lithium-pilocarpine animal model, male Wistar rats were submitted to status epilepticus (SE) and were killed at the following post-SE days: 1, 7, 15 and 60, and were further classified SE1, SE7, SE15 and SE60. Control animals were injected with saline. Results: MTLE showed decreased neuronal density than controls in the granular layer, hilus, CA4, CA3, CA1 and prosubiculum. MTLE group showed increased neo-Timm gray value in the granular layer, inner and outer molecular layer, as well as increased mossy fiber length of mossy fiber in the inner molecular layer when compared to controls. Sporadic MTLE specimens exhibited increased inner molecular layer gray value than familial MTLE. MTLE hihppocampi showed decreased MAP2 expression in the hilus, CA4, CA3, CA1 and prosubiculum. In the granular layer, CA2 and parasubiculum, MAP2 expression was higher in MTLE specimens than in controls. CA1 and entorhinal cortex from sporadic MTLE hippocampi showed increased MAP2 expression than familial MTLE. Tau expression was increased in the granular layer, hilus, CA3, CA2 and entorhinal cortex of MTLE specimens. Sporadic MTLE exhibited lower tau immunoreactivity in the entorhinal cortex than familial MTLE. In the lithiumpilocarpine animal model, rats submitted to SE presented lower values of neuronal density and mossy fiber sprouting than controls. SE15 and SE60 showed increased MAP2 expression in all hippocampal subfields. Tau expression in CA3 was not different among the groups. Conclusion: Our results indicate that besides neuronal loss and axonal sprouting, MTLE specimens also exhibit dendritic abnormalities related to MAP2 expression. Increased tau immunoreactivity in epileptogenic hippocampi indicates possible abnormal expression related to mossy fiber sprouting in chronic MTLE. We found differential sprouting, MAP2 and tau expression between sporadic and familial MTLE. It is possible that different genetic background might result in somehow distinct neuropathological substrates between the two MTLE subtypes, although their clinical manifestation is quite similar. While neuronal loss and axonal sprouting profiles in human MTLE and chronic phase of the lithium-pilocarpine animal model are comparable, we could not find corresponding results regarding MAP2 and tau expression. IV Several studies have shown that chemo-convulsant as pilocarpine and kainic acid result in widespread brain epileptic discharges, which are different from the more focal hippocampal discharges seen in human MTLE. Despite its limitations, the lithium-pilocarpine model stands as an important and widely used animal model of epilepsy. Besides that, other animal models in which ictal discharges and lesions are more limited to the hippocampal formation might better mimic what we see in human MTLE.

The final step of paramyxovirus infection requires the assembly of viral structural components at the plasma membrane of infected cells followed by budding of virions. While the matrix (M) protein of some paramyxoviruses has been suggested to play a central role in the assembly and release of virus particles, the specific viral and host protein requirements are still unclear. Using Newcastle disease virus (NDV) as a prototype paramyxovirus, we explored the role of each of the NDV structural proteins in virion assembly and release. For these studies, we established a virus-like particle (VLP) system for NDV. The key viral proteins required for particle formation and the specific viral protein-protein interactions required for assembly and release of particles were explored in chapter 2. First we found that co-expression of all four proteins resulted in the release of VLPs with densities and efficiencies of release (1.18 to 1.16 g/cm3and 83.8%±1.1, respectively) similar to that of authentic virions. Expression of M protein alone, but not NP, F-K115Q or HN proteins individually, resulted in efficient VLP release. No combination of proteins in the absence of M protein resulted in particle release. Expression of any combination of proteins that included M protein yielded VLPs, although with different densities and efficiencies of release. To address the roles of NP, F and HN proteins in VLP assembly, the interactions of proteins in VLPs formed with different combinations of viral proteins were characterized by co-immunoprecipitation. The co-localization of M protein with cell surface F and HN proteins in cells expressing all combinations of viral proteins was characterized. Taken together, the results show that M protein is necessary and sufficient for NDV budding. Furthermore, they suggest that M protein – HN protein and M protein - NP interactions are responsible for incorporation of HN protein and NP proteins into VLPs and that F protein is incorporated indirectly due to interactions with NP and HN protein. Since the vacuolar protein sorting (VPS) system is involved in the release of several enveloped RNA viruses, chapter 3 describes studies which explored the role of the VPS system on NDV particle release. First, we characterized the effects of three dominant negative mutant proteins of the VPS pathway on particle release. Expression of dominant negative mutants of CHMP3, Vps4 and AIP1 proteins inhibited M protein particle release as well as release of complete VLPs. Mutation of a YANL sequence in the NDV M protein to AANA inhibited particle release while replacement of this sequence with either of the classical late domain motifs, PTAP or YPDL, completely restored particle release. The host protein AIP1, which binds YXXL late domain sequences, is incorporated into M protein particles. These results suggest that an intact VPS pathway is necessary for NDV VLP release and that the YANL sequence is an NDV M protein L domain. The sequence and structure of the Newcastle disease virus (NDV) fusion (F) protein are consistent with its classification as a type 1 glycoprotein. We have previously reported, however, that F protein can be detected in at least two topological forms with respect to membranes in both a cell-free protein synthesizing system containing membranes as well as infected COS-7 cells (J. Virol. 2004 77:1951). One form is the classical type 1 glycoprotein while the other is a polytopic form in which approximately 200 amino acids of the amino terminal end as well as the cytoplasmic domain (CT) are translocated across membranes. Furthermore, we detected CT sequences on surfaces of F protein expressing cells and antibodies specific for these sequences inhibited red blood cell fusion to HN and F protein expressing cells suggesting a role for surface expressed CT sequences in cell-cell fusion. In chapter 4, we extended these findings and found that the alternate form of the F protein can also be detected in infected and transfected avian cells, the natural host cells of NDV. Furthermore, the alternate form of F protein was also found in virions released from both infected COS-7 cells and avian cells by Western analysis. Mass spectrometry confirmed its presence in virions released from avian cells. Two different polyclonal antibodies raised against sequences of the CT domain of the F protein slowed plaque formation in both avian and COS-7 cells. Antibody specific for the CT domain also inhibited single cycle infections as detected by immunofluorescence of viral proteins in infected cells. The potential roles of this alternate form of the NDV F protein in infection are discussed. Virus-like particles (VLPs) generated from different viruses have been shown to have potential as good vaccines. Chapter 5 explored the potential of NDV VLPs as a vaccine for NDV or as a vaccine vector for human pathogens. Significant quantities of NDV VLPs can be produced from tissue culture cells. These VLPs are as pure as virions prepared in eggs. In addition, some rules for incorporation of viral proteins into VLPs were also explored. We found that the cytoplasmic domain of the fusion (F) protein is necessary for its incorporation into VLPs. We found that an HN protein with an HA tag at its carboxyl terminus was incorporated into VLPs. We also found that the HN and F proteins of NDV, strain B1, can be incorporated into VLPs with M and NP of strain AV. The demonstration of specific domains required for protein incorporation into particles is important in using NDV VLPs as a vaccine vector for important human pathogens. In conclusion, this dissertation presents results that show that the M protein plays a central role in NDV assembly and release, a finding that is consistent with findings with other paramyxoviruses. More importantly, this work extends the current knowledge of paramyxovirus assembly and release by providing the first direct evidence of interactions between paramyxovirus proteins. These interactions between viral proteins provide a rational basis for incorporation of viral proteins into particles. This work also provides a clearer understanding of the role of the host vacuolar protein sorting machinery in NDV budding. A clear understanding of virus assembly and budding process contributes to the design of strategies for therapeutic intervention and in the development of safer, more economical and effective vaccines.

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In the present thesis, two positive sense single-stranded RNA viruses have been used as models to understand the structure and function of viral-encoded proteins. One of them, Pepper Vein Banding Virus (PVBV; genus Potyvirus; family Potyviridae) is a flexuous, rod-shaped virus that encodes for a polyprotein of size ~340 kDa. The polyprotein undergoes proteolytic processing by viral-encoded proteases, of which Nuclear Inclusion-a Protease (NIa-Pro) is the major protease. It is a serine-like cysteine protease which cleaves between a Q/A or Q/S, present in the context of the heptapeptide recognition sequence. The temporal regulation of intermediates and mature proteins released by NIa-Pro cleavage is crucial for a successful infection. In the present study, histidine-tagged NIa-Pro, Viral Protein genome-linked (VPg), and the cleavage site mutant (E191A) VPg-Pro were over-expressed in E. coli and purified. The protease activity of NIa-Pro was monitored using an HPLC-based protease assay developed using a peptide substrate. NIa-Pro protease activity was found to get modulated upon interaction with VPg and upon undergoing phosphorylation. Both these events have been found to involve the face of NIa-Pro which contains the solvent-exposed Trp143. Mutational studies and molecular dynamics analyses provide evidence that this residue is buried upon interaction of NIa-Pro with VPg, and any perturbation of its orientation influences the active site Cys151 via an extensive interaction network. This interaction was found to enhance the velocity of NIa-Pro protease activity, especially if the two domains were present in trans (VPg+Pro). In addition, the main-chain –NH2 group of Trp143 was found to be hydrogen-bonded to the side chain –OH group of Ser129, the residue which was identified to undergo phosphorylation by host plant kinases. Interestingly, when the two domains were present in cis (E191A VPg-Pro), no phosphorylation was observed. Mutations of Ser129 (to phosphorylation-mimic Asp or phosphorylation-deficient Ala residues) which affected this H-bond were found to disturb Trp143 and Cys151 orientation, which drastically reduced the protease activity of NIa-Pro. Within the polyprotein, VPg is present at the N-terminus of NIa-Pro and the cleavage site between them is suboptimal (E/A). In the present study, VPg-Pro was shown to be covalently linked to the genomic RNA present in the virions. Interestingly, during purification, VPg could only be purified from the soluble when it was expressed at the N-terminus of NIa-Pro. A series of bioinformatics and biophysical analysis of VPg showed that PVBV VPg, like other potyviral VPgs, exists as a molten-globule. Moreover, while VPg was shown to harbour the Walker motifs, it was found to exhibit an ATPase activity only when it was present with the NIa-Pro (especially in cis). Lys47 and Asp88:Glu89 were found crucial for optimal activity. Over all the results demonstrated that there is a reciprocal modulation of structure and function of the VPg and NIa-Pro domains. These results can explain the possible significance of an impeded cleavage rate between the two domains of VPg-Pro during PVBV infection. The precursor, VPg-Pro, could offer the advantage of evading the inhibitory phosphorylation of NIa-Pro by the host, as well as drive certain viral processes by virtue of its ATPase activity. And subsequent cleavage of the domains and their trans interaction could offer a higher turnover rate which might assist sufficient CP production required for viral morphogenesis. Another virus, Tobacco Streak Virus (TSV) that belongs to the Ilarvirus genus of the Bromoviridae family is a spherical virus which forms pleiomorphic icosahedral virus particles. It has a tripartite genome and each RNA is encapsidated individually. In the present thesis, TSV was used as a model to understand the properties of its structural protein-the coat protein (CP), with the aim of deciphering TSV assembly process. Thus, the CP gene from TSV RNA 3 was cloned and over-expressed in E. coli. The coat protein thus expressed formed virus-like particles (VLPs), which could be disassembled into dimers using high CaCl2 concentrations. Reassembly of VLPs was possible from dimers even in the absence of any nucleic acid. Mutational analysis of the N-terminal disordered domain showed that 26 amino acid residues from the amino-terminus could be crucial for capsid heterogeneity while, zinc-binding domain was essential for assembly. Overall, the present study shows that the flexible W-C loop of PVBV NIa-Pro, the disordered N-terminal region of PVBV VPg and the disordered N-terminal region of TSV CP harbour residues crucial for regulation of protein function. Such regulatory elements would ultimately allow viruses to maintain a smaller protein number, and thus a smaller genome size.

Rotavirus is one of the leading etiological agents of gastroenteritis in young of many species including humans worldwide and is responsible for about 600,000 infant deaths per annum. Rotavirus belongs to the Reoviridae family, and its genome is composed of 11 double-stranded RNA segments that encode six structural proteins and six nonstructural proteins. Rotavirus replication is fully cytoplasmic and occurs within highly specialized regions called viroplasms. NSP2 and NSP5 have been shown to be essential for viroplasm formation and, when co-expressed in uninfected cells, to form viroplasm¬like structures. A recent study suggest a key role for NSP5 in architectural assembly of viroplasms and in recruitment of viroplasmic proteins, containing four structural (VP1, VP2, VP3 and VP6) and two nonstructural (NSP2 and NSP5) proteins. NSP5, the translation product of gene segment 11 has a predicted molecular eight of 21 kDa. NSP5 has been reported to exist in multiple isoforms ranging in size from 28-and 32-35 kDa from a 26-kDa precursor has been attributed to O-glycosylation and hyperphosphorylation. To study different properties of the protein, recombinant NSP5 containing an N-terminal hisidine tag was expressed in bacteria and purified by affinity chromatography. A significant observation was the similarity in phosphorylation property of the bacterially expressed and that expressed in mammalian cells. While the untagged recombinant protein failed to undergo phosphorylation in vitro, addition of His tag or deletions at the N-terminus promoted phosphorylation of the protein in vitro, which is very similar to the reported properties exhibited by the corresponding proteins expressed in mammalian cells. Phosphorylation of NSP5 in vitro is independent of the cell type from which the extract is derived suggesting that the kinases that phosphorylate NSP5 are distributed in all cell types. Among the C-terminal deletion mutants studied, NH-∆C5 and NH-∆C10 were phosphorylated better than full-length NSP5, but NH-∆C25 and NH¬∆C35 showed substantial reduction in the level of phosphorylation compared to full-length NSP5. These results indicate that the C-terminal 30 residues spanning the predicted α-helical domain of NSP5 are critical for its phosphorylation in vitro which is in correspondence with previous findings that C-terminal 21 amino acids of NSP5 direct its insolubility, hyperphosphorylation, and VLS formation. The results revealed that though the tagged full-length and some of the mutants could be phosphorylated in vitro, they are not suitable substrates for hyperphosphorylation unlike the similar proteins expressed in mammalian cells or infected cells. Analysis by western blot and mass spectrometry revealed that the bacterially expressed NH-NSP5 is indeed phosphorylated. It appears that prior phosphorylation in bacteria renders the protein conformationally not amendable for hyperphosphorylation by cellular kinases in vitro. Mutation of the highly conserved proline marginally enhanced its phosphorylation in vitro but the stability of protein is affected. Notably, mutation of S67A, identified as a critical residue for the putative caesin kinase-I and-II pathways of NSP5 phosphorylation, affected neither the phosphorylation nor the ATPase activity of NSP5. These results suggest that bacterially expressed NSP5 by itself has undectable auto-kinase activity and it is hypophosphorylated. Purified recombinant NSP5 has been reported to possess an Mg¬ 2+-dependent ATP-specific triphosphatase activity. The results indicated that deletion of either C-terminal 48 amino acids or N-terminal 33 residues severely affected the ATPase activity of recombinant NSP5, underlying the importance of both N-and C-terminal domains for NSP5 ATP hydrolysis function. NSP5 expressed in rotavirus infected cells exists as inter-molecular disulfide-linked dimeric forms and it appears that the 46 kDa isoforms, that are phosphorylated, corresponds to dimer as revealed by western blotting. Analytical gel filtration analysis of NH-NSP5, NH-ΔN43 and NH-ΔN33-ΔC25 showed most of the proteins in void volume, but an additional peak corresponding to the mass of dimeric species further supports that NSP5 is basically a dimer that undergoes oligomerization. Analysis by sucrose-gradient fractionation revealed that NH-NSP5 and NH-ΔN43 proteins were mainly distributed in the lower fraction of the gradient suggesting the existence of high molecular weight complexes or higher oligomers. The multimeric nature of NSP5 and its mutants was further confirmed by dynamic light scattering which suggests that high molecular weight complexes are of homogenous species. The correlation curves showed a low polydispersity distribution and a globular nature of recombinant NH-NSP5 proteins. The present results clearly demonstrate that dimer is the basic structural unit of NSP5 which undergoes oligomerization to form a complex consisting of about 20-21 dimers. The nonstructural protein 5 is hyperphosphorylated in infected cells and cellular kinases have been implicated to be involved in its phosphorylation. NSP5 contains multiple consensus sites for phosphorylation by several kinases, but the cellular kinases that specifically phosphorylate NSP5 in infected cells are yet to be identified. Previous studies from our laboratory using signaling pathway inhibitors revealed that recombinant NH¬NSP5 and its deletion mutants can be phosphorylated in vitro by purified cellular kinases and by mammalian cell extracts. These studies also showed the involvement of PI3K-Akt and MAPK signaling pathways in NSP5 phosphorylation and a negative role for GSK3β in the phosphorylation of bacterially expressed recombinant NSP5 in vitro. In the present work, using phospho-specific anti-Ser9 GSK3β antibody, we observed that GSK3β is inactivated in a rotavirus infected MA104 cells in a strain-independent manner. GSK3β¬specific small interfering RNA (siRNA-GSK3β) reduced GSK3β levels leading to increased level of synthesis of the structural rotavirus protein VP6 and NSP5 hyperphosphorylation compared to control siRNA. The pharmacological kinase inhibitors (LY294002, Genistein, PD98059, and Rapamycin) studies at the concentrations tested did not significantly affect rotavirus infection as seen from the number foci, while U0126 severely affected rotavirus replication. The results clearly demonstrated the importance of the MEK1/2 signaling pathway in the successful replication of rotavirus and NSP5 hyperphosphorylation in rotavirus-infected cells. In contrast inhibition of GSK3β activity by LiCl, increased in general, the number of foci by greater than 2-fold for all viral strains studied. These results suggest that MEK1/2 pathway majorly contributes to GSK3β inactivation in rotavirus infected cells. Thus, our results reveal that rotavirus activates both the PI3K/Akt and FAK/ERK1/2 MAPK pathways and appears to utilize them as a strategy to activate mTOR, and inhibit GSK3β through phosphorylation on serine 9, the negative regulator of rotavirus NSP5 phosphorylation, and thus facilitate translational competence of rotaviral mRNAs during virus replication cycle. It was shown previously in the laboratory by co-immunoprecipitation assay that Hsp70 interacts with rotaviral proteins VP1 and VP4 in rotavirus-infected mammalian cells. In this study, the interactions between Hsp70 with VP1 and VP4 were further evaluated in vitro by GST-pull down assay. It was observed that the N-terminal ATPase and C-terminal peptide-binding domain of Hsp70 is necessary for its direct interaction with VP1 and VP4. The presence of Hsp70 in purified double-and triple-layered virus particles further supported the observed interactions of rotaviral proteins VP1 and VP4 with Hsp70. However, the specific interaction observed between Hsp70 and rotaviral capsid proteins, VP1 and VP4 in viral particles suggests that Hsp70 has an important role during rotavirus assembly which requires further investigation.

My thesis is divided into five chapters, starting with a general introduction in first chapter and sample preparation and protein-NMR assignment techniques in second chapter. The remaining three chapters focus on three different areas/projects that I have worked on. Chapter 1: Introduction to nanomaterials and all the experimental techniques This chapter reviews different kinds of nanomaterials and their application utilized for protein-nanomaterial interaction in our study, along with the introduction to different spectroscopy and microscopy techniques used for the interaction studies. Starting with introduction of nanomaterials and all the experimental techniques, which constitute the arsenal for structural studies of the protein-nanomaterial interaction, different steps enroute to structural and dynamic interaction are outlined in detail. Chapter 2: Preparation and Characterization of Proteins used for nanomaterial interaction studies Proteins are generally of three kinds- globular (structured), intrinsically disordered and membrane bound. These proteins have different functions in living organisms and play a major role to maintain metabolism and other important factors. To probe protein-nanomaterial interactions, we have chosen different protein/peptides. This chapter describes the protocol/procedure used for purifying the proteins. For studying a globular protein, ubiquitin was chosen. Nanomaterial-IDP interaction was investigated using the intrinsically disordered central linker domain of human insulin like growth factor binding protein-2 (L-hIGFBP2). The hydrophobic membrane interacting part of the prion protein was chosen as a representative membrane protein. The characterization of the proteins by NMR spectroscopy is also described. Chapter 3: A nanomaterial based novel macromolecular crowding agent Carbon quantum dots (CQD) are nanomaterials with size less than 10 nm, first obtained in 2004 during purification of single-walled carbon-nanotubes. Since then CQDs have been used in a wide range of applications due to their low cost of preparation and favorable properties such as chemical inertness, biocompatibility, non-toxicity and solubility in aqueous medium. One of the applications of CQDs has been their use for imaging and tracking proteins inside cells, based on their intrinsic fluorescence. Further, quantum dots exhibit concentration dependent aggregation while retaining their solubility. Fluorescent carbon quantum dots (CQD) induce macromolecular crowding making them suitable for probing the structure, function and dynamics of both hydrophilic and hydrophobic peptides/ proteins under near in-cell conditions. We have prepared hydrophilic and hydrophobic quantum dots to see the crowding effect. After characterization of CQD, we tested the property of proteins with CQD and found that CQD behaves as a macromolecular crowding agent by mimicking near in-cell conditions. In our study, we have chosen a globular protein, an intrinsically disordered protein (IDP) and one hydrophobic membrane peptide. We have also compared the crowding property of CQD with ficoll which is widely used commercial crowding agent. The overall study tells that the CQD acts like crowding agent and can be used for the study of macromolecular crowding effect. This makes them suitable for structural and functional studies of proteins in near in-cell conditions. Chapter 4: Ubiquitin-Graphene oxide interactions Described here is the interaction of human ubiquitin with GO using NMR spectroscopy and other techniques such as Fluorescence spectroscopy, isothermal titration calorimetry (ITC), UV-Visible spectroscopy, dynamic light scattering (DLS), zeta potential measurements and transmission electron microscopy (TEM). The globular protein ubiquitin interacts with GO and undergoes a dynamic and reversible association-dissociation in a fast exchange regimen as revealed by NMR spectroscopy. The conformation of the protein is not affected and the primary interaction is seen to be electrostatic in nature due to the polar functional groups present on the protein and GO sheet surface. For the first time we have shown that the interaction between ubiquitin and GO is dynamic in nature with fast and reversible adsorption/desorption of protein from the surface of GO. This insight will help in understanding the mechanistic aspects of interaction of GO with cellular proteins and will help in designing appropriate functionalized graphene oxide for its biological application. Chapter 5: Section A: Interaction of an intrinsically disordered protein (L-HIGFBP2) with graphene oxide The interaction between intrinsically disordered linker domain of human insulin-like growth factor binding protein-2 (L-hIGFBP2) with GO was studied using NMR spectroscopy and other techniques such as isothermal titration calorimetry (ITC), dynamic light scattering (DLS), zeta-potential measurements. The study revealed that the disordered protein L-hIGFBP2 interacts with GO through electrostatic interaction and undergoes a dynamic and reversible association-dissociation in a fast exchange regime. The conformation of the protein is not affected. Section B: Stability of an Intrinsically disordered protein through weak interaction with Silver nanoparticles Using NMR spectroscopy and other techniques we probed the mechanism of L-hIGFBP2–AgNP interactions which render the IDP stable. The study reveals a mechanism which involves a relatively fast and reversible association–dissociation of L-hIGFBP2 (dynamic exchange) from the surface of AgNP. The AgNP–L-hIGFBP2 complex remains stable for more than a month. The techniques employed in addition to NMR include UV-Visible spectroscopy, dynamic light scattering (DLS), zeta potential measurements and transmission electron microscopy (TEM) to probe the protein-AgNP interaction here in this section.