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1
Hoy, Julie Anne. "Structural characterization of ligand binding in hexacoordinate hemoglobins." [Ames, Iowa : Iowa State University], 2006.
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Pang, Bo, and 龐博. "Structural characterization of H1N1 nucleoprotein-nucleozin binding sites." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/205641.
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Although influenza is usually acute self-limiting respiratory infection, influenza viruses are among the most common pathogens that threaten the health of humans and animals worldwide. Various anti-viral therapeutic agents are currently used for treatment and prophylaxis of influenza virus, but the problem is that the targets of these drugs are easily mutated and result in resistance. Therefore, medications that have broad spectrum coverage are urgently needed to combat with the disease. Since nucleoprotein (NP), which is encoded by influenza virus genome, is regarded as a druggable target due to its conserved sequence and important functions during influenza virus life cycle, numerous studies are focused on this protein in attempts to develop broad-spectrum anti-influenza therapeutics. Recently, Kao et al. found that the addition of a novel small molecule nucleozin could lead to large aggregates of NP, which in turn caused cessation of virus replication. Give that the interaction between NP and nucleozin is still not unveiled, it is crucial to identify the binding sites using X-ray crystallography.
The full length influenza A/WSN/33 (H1N1) NP gene was cloned into pET28 vector, with His-tag in its C-terminus and overexpressed in E.coli strain Rosetta 2. Cell culture was purified by HisTrap HP and Superdex-200 16/60 gel filtration columns. Crystals were grown using the vapour diffusion method and the NP-nucleozin complex was prepared by soaking native crystal in solution containing 0.25 mM nucleozin for 2h. Crystals of the complex can diffract to 3.0 Å at the Shanghai Synchrotron Radiation Facility. The structure of NP was determined by molecular replacement and it belongs to space group C121 with two NP trimers per asymmetric unit. After further refinement, two nucleozin molecules were found in each asymmetric unit, and each of them could bind with two NP molecules at the same time. The ligand binding pockets were formed by the combination of Y289/N309 pocket from one NP molecule, and R382 pocket from another NP molecule. Therefore, the function of nucleozin is to bridge two NP molecules and lead to NP aggregation, which are in agreement with functional studies on nucleozin. Furthermore, computational models of the NP-nucleozin binding are provided to reveal the mechanism of nucleozin induced aggregation. In addition, recent work on interaction between NP and another novel molecule named compound A has also been briefly described and compared with NP-nucleozin complex at the end of this thesis. Collectively, this study presents a new paradigm for better understanding of how NP and nucleozin interact with each other and hence result in NP aggregates, which is envisaged to accelerate the development of anti-influenza therapeutic agents.published_or_final_version
Physiology
Doctoral
Doctor of Philosophy
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Butan, Carmen Crina. "Structural characterization of the RNA binding domain of BTV non-structural protein 2." Thesis, Birkbeck (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414198.
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Santelli, Eugenio. "The binding of MEF2A to DNA : biochemical and structural characterization /." [S.l.] : [s.n.], 2000. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13752.
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Gilbert, Sunny Deshea. "Biochemical and structural characterization of ligand binding by the purine riboswitch." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3256472.
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Desjardins, Geneviève. "Structural characterization of DNA binding and autoinhibition by the Ets1 transcription factor." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/52606.
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Ets1 belongs to the ETS transcription factor family and plays key roles in regulating eukaryotic gene expression. The affinity of the Ets1 for its cognate DNA sites is autoinhibited by an intrinsically disordered serine-rich region (SRR) and an appended helical inhibitory module (IM). Through transient interactions, the SRR both sterically blocks the ETS domain and allosterically stabilizes the IM to modulate DNA-binding affinity. Calmodulin-dependent kinase II phosphorylation of five serines within the SRR progressively reinforces autoinhibition in response to calcium signaling.
Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine/tyrosine (ϕ) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-ϕ-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces
autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively-charged DNA recognition interface and an adjacent
region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression.
We also investigated by NMR spectroscopy the interaction of Ets1 with specific and nonspecific oligonucleotides. Upon binding DNA, helices HI-1 and HI-2 of the IM unfold. Thus, autoinibition does not impart DNA-binding specificity. Using amide chemical shift perturbation mapping, we also show that Ets1 binds both specific and non-specific oligonucleotides through its canonical ETS domain interface. However, the non-specific complex is formed by weak and
dynamic electrostatic interactions, whereas the specific complex involves well-ordered hydrogen bonds and salt bridges. In support of this conclusion, five lysine sidechains are protected from rapid hydrogen exchange upon binding of specific DNA, whereas only one is stabilized in the non-specific complex. Overall, these data are consistent with Ets1 rapidly finding specific DNA sites within the genome via facilitated diffusion (sliding and hopping) within a vast background of non-specific sequences.Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Brooksbank, Robert Alan. "Expression, purification and structural characterization of the DNA-binding domain of BZLF1." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321537.
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Oke, Muse. "Functional and structural characterization of the transferrin binding protein A from Neisseria meningitidis." Thesis, Birkbeck (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413693.
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Juntunen, K. (Kari). "Functional and structural characterization of nuclear vitamin D receptor and its ligand binding domain." Doctoral thesis, University of Oulu, 2002. http://urn.fi/urn:isbn:9514268784.
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Abstract
The hormonally active form of vitamin D, 1,25(OH)2D3, is involved in many biological functions throughout the body, such as regulation of calcium and phosphate homeostasis, bone remodeling and controlling cell proliferation and differentiation. Vitamin D receptor (VDR), a member of the nuclear hormone receptor (NHR) super family, mediates those genomic actions of 1,25 (OH)2D3 by actively repressing or activating its target genes. In the present study recombinant human nuclear VDR and its ligand binding domain (LBD) were expressed in Spodoptera frugiperda (Sf9)
insect cells and in E.coli. Recombinant proteins were purified and their biochemical and biophysical properties were characterized.
Recombinant VDR was shown to bind to the vitamin D response element (VDRE) of osteopontin and osteocalcin genes as a homodimer or as a heterodimer with the retinoid X receptor (RXR)-αΔAB.
Full-length VDR and its LBD were demonstrated to bind natural ligand 1,25 (OH)2D3 with high affinity. The binding affinities of several vitamin D analogs were also determined. Ligand binding induced conformational change within the receptor was studied using several methods such as partial proteolytic digestion, small angle neutron scattering (SANS), native gel electrophoresis and circular dichroism (CD) spectroscopy. Results indicate that ligand binding induces conformational change within VDR and different 1,25(OH)2D3 analogs might induce a somewhat different conformation within the receptor. This is seen as an unequal capacity of analogs to stabilize receptor against proteases or heat and as differences in the promotion of receptor homodimerization.
Compared to other nuclear hormone receptors, VDR presents a large insertion region at the N-terminal part of the LBD between helices H1 and H3, encoded by an additional exon. In the present study this additional exon was deleted and the properties of mutated LBD were compared to the wild type LBD.
Biochemical analyses indicated that the mutant protein exhibits the same ligand binding, dimerization with RXR and transactivation properties as the wild-type VDR, suggesting that the insertion region does not affect these main functions. Furthermore, solution studies by small angle X-ray scattering indicated that the insertion region in the VDR locates on the surface of molecule and it is not structurally well ordered.
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Sharif, Azar. "Structural characterization of the polycomb repressor complex 1 binding partner ubiquitin specific protease 11." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/39355.
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Ubiquitin Specific Protease 11 (USP11), USP4 and USP15 are highly conserved and are characterised by an N-terminal 'domain present in ubiquitin specific proteases' (DUSP) and 'ubiquitin-like' (UBL) domains. This DUSP-UBL (DU) domain is thought to be involved in substrate recognition. It was shown that USP11 co-purifies with human Polycomb Repressive Complex type 1 (PRC1) and regulates the stability of the E3 ligase component of PRC1 (Maertens et al, 2010). PRC1 repress transcription from the INK4a tumour suppressor locus. Hence knockdown of USP11 in primary human fibroblasts causes de-repression of INK4a, followed by a senescence-like proliferative arrest. In this project we aimed to map the interaction between USP11 and PRC1 components (BMI1, RING2, MEL18 and CBX8). We used two methods to investigate their interactions; yeast two-hybrid and in vitro pull down. Unexpectedly, we could not confirm a direct interaction between USP11 and any PRC1 component. We hypothesize that the lack of post-translation modifications, the presence of fusion tags and/or the need of a multi-subunit PRC1 complex might be needed to observe a high affinity interaction. We also aimed to map the interaction between three PRC1 components; RING2, BMI1 and RYBP, with the ultimate aim of solving the X-ray structure of the complex. The main obstacle in this project was to express, extract and purify these proteins at high levels in bacterial culture. Preliminary data suggests that RYBP and BMI1 do not interact directly. Here we report the 3.6 Å resolution X-ray structure of the human USP11 DU. The sequence linking the DUSP and UBL domains, the DU finger, could not be assigned in the electron density map due to low resolution. Comparison with the related USP4 DU crystal structure reveals that the structures are mostly conserved.
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Taubert, Alexander. "Characterization of DNA binding of the two zinc finger domains of transcription factor zBED6." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-396233.
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The zinc finger protein, zBED6, is a transcriptional regulator of IGF2 along with hundreds of other genes relating to development and growth. Studies on the growth of commercially bred pigs discovered a single nucleotide substitution in the third intron of IGF2 which disrupts the binding of zBED6 and is responsible for the three-fold upregulation of IGF2 in skeletal muscle. The mutation is linked to decreased subcutaneous fat deposition, larger organ size, and increased skeletal muscle mass. Three different constructs of the zBED6 protein made by Björklund 2018 were expressed and purified to characterize their binding affinity, where one contained both zinc finger domains and two of the constructs contained only one zinc finger domain each. Electrophoretic mobility shift assay protocol was optimized to determine the apparent Kd (= 210 ± 31nM) for the full-length construct C13 and to determine which zinc finger domain was sensitive to the mutation in the IGF2 gene. The first zinc finger domain seems to be more specific in its binding target. Preliminary microscale thermophoresis results were highly variable, needing further optimization of the protocol in order to obtain a full binding curve. The next steps involve site directed mutagenesis of residues binding DNA to determine which interactions are the most significant and possibly crystallization studies as well.
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Ghosh, Madhumita. "Structural and biochemical characterization of proteins involved in cancer." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974284823.
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Shanker, Sreejesh. "Structural and biochemical characterization of cell cycle regulatory proteins and their inhibitors." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=974284882.
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Kumar, Sandeep. "Biochemical, Mechanistic, and Structural Characterization of DNA Polymerase X from African Swine Fever Virus." The Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=osu1211380265.
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Bohl, Casey Edward. "Structural characterization of androgen receptor interactions with nonsteroidal ligands." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1116362600.
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Bortoluzzi, Alessio. "Structural characterization of Mycobacterium tuberculosis RNA polymerase binding protein A (RbpA) and its interactions with sigma factors." Thesis, University of Leicester, 2013. http://hdl.handle.net/2381/28401.
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The RNA polymerase binding protein A (RbpA) is a 13 kDa protein, encoded by the gene Rv2050, that was shown to be essential for the growth and survival of the important human pathogen Mycobacterium tuberculosis. Although is not clear yet why RbpA is essential in M. tuberculosis, significant progress has been made in the characterization of the protein. For instance, it was shown that RbpA binds to the β-subunit of the RNA polymerase (RNAP) and activates transcription. Interestingly, it was reported that RbpA can enhance the transcription activity of the RNAP containing the primary σ-subunit σ[superscript A] but does not have any detectable effect if the RNAP is associated with the alternative σ-subunit σ[superscript F]. Moreover, it was also shown that RbpA might influence the response of M. tuberculosis to the current frontline anti-tuberculosis drug rifampicin. The research project described in this thesis contributes to the ongoing efforts to characterize RbpA by providing the structure of the protein and identifying the principle σ-subunit σ[superscript A], and the principle-like σ-subunit σ[superscript B], as interaction partners. The solution structure of RbpA reveals the presence of a central structured region and highly dynamic N- and C- termini. Both termini are involved in the formation of a tight complex with the σ-subunit but only the C-terminal region appears to be essential for this interaction. The finding that RbpA also binds to the RNAP σ-subunit suggests new possibilities for the mechanism of action used by RbpA to activate transcription. Furthermore, preliminary data obtained using a ΔRv2050 conditional mutant strain of M. tuberculosis suggest that the interaction with the σ-subunit is essential for the functionality of RbpA.
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Collins, Courtney E. "Characterization of SPOC/NCoR Binding: A Thermodynamic and Structural Analysis of Corepressors in the Notch Signaling Pathway." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1510926401526291.
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WEGRECKI, MARCIN. "Structural, biophysical and functional characterization of Nop7-Erb1-Ytm1 complex and its implications in eukaryotic ribosome biogenesis." Doctoral thesis, Universitat Politècnica de València, 2015. http://hdl.handle.net/10251/55941.
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[EN] Ribosome biogenesis is one of the most important and energy-consuming processes in the cell. However, the vast majority of the events and factors that are involved in the synthesis of ribosomal subunits are not well understood. Ribosome maturation comprises multiple steps of rRNA processing that require sequential association and dissociation of numerous assembly factors. These proteins establish a complex network of interactions that are essential for the pathway to continue. Extensive studies in Saccharomyces cerevisiae allowed to identify some of the genetic and functional correlations between the pre-ribosomal factors that could be organized into interdependent clusters or sub-complexes. A heterotrimer formed by Nop7, Erb1 and Ytm1 (PeBoW complex in mammals) is crucial for the proper formation of the 60S subunit. Depletion of any of the three proteins is inviable and certain truncations result in aberrant processing of 27SA2 rRNA thus impairing cell proliferation. Nop7 and Erb1 have been shown to bind RNA and are recruited to the pre60S before Ytm1. It is also known that the trimer has to be removed from the nascent particle in order to promote its normal maturation. Despite its relevance in the cell, the exact role of PeBoW is not clear and the interactions within the complex have been poorly characterized.
In this study we carry out an extensive biochemical and structural analysis of Nop7-Erb1-Ytm1 trimer from S. cerevisiae and from a thermophilic fungus Chaetomium thermophilum. We have been able to reconstitute a stable complex in vitro that was then used in crystallographic trials. We have solved the structure of the C-terminal domain of Erb1 from yeast that folds into a seven-bladed ß-propeller. We prove that this part of the protein binds RNA in vitro, a property that might be important for its function. Moreover, in spite of previous reports suggesting that the ß-propeller domain of Erb1 would not be essential for ribosome biogenesis, we could solve the crystal structure of Ytm1 bound to the carboxy-terminal portion of Erb1 from C. thermophilum. That finding led us to redefine the macromolecular interactions that hold the complex together. First, we have verified that the N-terminal region of Nop7 interacts with Erb1. Furthermore, we have shown that a good affinity binding takes place in vitro between WD40 domain of Ytm1 and the ß-propeller of Erb1. Upon careful analysis of the interface involved in dimer formation we have designed a mutant of Erb1 that exhibits weaker association with Ytm1. We confirm our structural and biophysical data using S. cerevisiae. We prove that a point mutation that decreases the affinity between propellers of Erb1 and Ytm1 negatively affects growth in yeast because it interferes with 60S production. We show that a very conserved interface of protein-protein interaction could be targeted in order to hinder cell proliferation.[ES] El ensamblaje de ribosomas es uno de los procesos más importantes y costosos energéticamente en una célula eucariota. A pesar de ello, se sabe relativamente poco acerca de la gran mayoría de los eventos y factores implicados en la síntesis de las subunidades ribosomales. La maduración de ribosomas comprende numerosos pasos de procesamiento del rRNA que requieren la asociación y disociación de más de doscientos factores de ensamblaje. Esas proteínas establecen una compleja red de interacciones que son esenciales para que el proceso pueda llevarse a cabo. Los estudios realizados en Saccharomyces cerevisiae han permitido la identificación de algunas correlaciones genéticas y funcionales entre los factores prerribosomales. Es el caso del heterotrímero formado por Nop7, Erb1 e Ytm1 (complejo PeBoW en mamíferos), que es imprescindible para la correcta formación de la subunidad 60S. La ausencia de cualquiera de las tres proteínas es inviable y también se conocen ciertas variantes truncadas que alteran el procesamiento del rRNA 27SA2 y de este modo afectan la proliferación celular. Se ha demostrado que Nop7 y Erb1 se asocian al rRNA y que su reclutamiento al pre60S ocurre antes de la unión a Ytm1. Además se sabe que el trímero tiene que separarse de la partícula prerribosomal emergente con el fin de favorecer su maduración. A pesar de su gran relevancia en la célula, no está claro el papel exacto del complejo PeBoW y tampoco se dispone de conocimientos suficientes acerca de las interacciones intermoleculares que lo mantienen. Durante el desarrollo de este proyecto se ha llevado a cabo un exhaustivo análisis bioquímico y estructural del trímero Nop7-Erb1-Ytm1 procedente de S. cerevisiae y del hongo termofílico Chaetomium thermophilum. En este trabajo hemos sido capaces de reconstituir el complejo estable in vitro que posteriormente se ha utilizado en los ensayos de cristalización, con los que hemos podido resolver la estructura del dominio carboxi-terminal de Erb1 de levadura, cuyo plegamiento corresponde a una hélice enrollada (ß-propeller) de siete hojas. Gracias a la información estructural, hemos demostrado que esa parte de la proteína es capaz de unir RNA in vitro, lo que puede ser una propiedad importante para su función. Además, a pesar de los estudios anteriores que sugerían que la hélice enrollada de Erb1 no era esencial en la biogénesis del ribosoma, hemos resuelto la estructura cristalina de la proteína Ytm1 unida al dominio C-terminal de Erb1 de C. thermophilum. Ese descubrimiento nos ha permitido redefinir las interacciones macromoleculares que mantienen el complejo. Inicialmente hemos confirmado que el extremo amino-terminal de Nop7 interacciona con Erb1. A continuación, hemos demostrado que el dominio WD40 de Ytm1 se une al ß-propeller de Erb1 con una buena afinidad. Después de un detallado análisis de la superficie involucrada en la formación del dímero, hemos sido capaces de diseñar una variante mutada de Erb1 que se asocia más débilmente con Ytm1. Los hallazgos estructurales y biofísicos se han confirmado in vivo usando S. cerevisiae donde hemos demostrado que una mutación puntual que disminuye la afinidad de unión entre los dominios C-terminales de Erb1 e Ytm1 manifiesta un efecto negativo sobre el crecimiento de levadura porque interfiere con la síntesis de 60S. Nuestros resultados establecen un buen ejemplo de una superficie conservada involucrada en interacciones proteína-proteína, que podría considerarse una buena diana para inhibir la proliferación celular eucariota.
[CAT] L'ensamblatge de ribosomes és un dels processos més importants i energèticament costosos en una cèl·lula eucariota. Tot i això, es coneix relativament poc de la majoria dels factors implicats en la síntesi de les subunitats ribosomals. La maduració de ribosomes compren moltes etapes de processament del rRNA que requereix l'associació i dissociació de més de dos-cents factors d'ensamblatge. Aquestes proteïnes estableixen una complexa xarxa de interaccions que són essencials perquè el procés es pugi dur a terme. Els estudis realitzats en Saccharomyces cerevisiae han permès la identificació de algunes correlacions genètiques i funcionals entre els factors pre-ribosomals. Aquest és el cas del heterotrímer comprés per Nop7, Erb1 i Ytm1 (complex PeBoW en mamífers), que és imprescindible per a la correcta formació de la subunitat 60S. L'absència de qualsevol de les tres proteïnes és inviable i també és coneixen certes variants truncades que alteren el processament del rRNA 27SA3 i que d'aquesta manera afecten a la proliferació cel·lular. S'ha demostrat que Nop7 i Erb1 s'associen al rRNA i que el seu reclutament al pre60S té lloc abans de l'unió a Ytm1. A més a més, es sap que el trímer ha de separar-se de la partícula pre-ribosomal emergent per tal que es produeixi la seua maduració. Malgrat la seua rellevància en la cèl·lula, no s'ha aclarit el paper exacte del complex PeBoW i tampoc n'hi ha coneixements suficients de les interaccions intermoleculars que el mantenen. Durant el desenvolupament d'aquest projecte s'ha dut a terme un exhaustiu anàlisi bioquímic i estructural del trímer Nop7-Erb1-Ytm1 de S. cerevisiae i del fong termofílic Chaetomium thermophilum. En aquest treball hem estat capaços de reconstituir el complex estable in vitro que posteriorment s'ha utilitzat en el assajos de cristal·lització, amb els que hem pogut resoldre l'estructura del domini carboxi-terminal de Erb1 de llevat i que té un plegament corresponent a una hèlix enrotllada (ß-propeller) de set fulles. Gràcies a la informació estructural, hem pogut demostrar que aquesta part de la proteïna té la capacitat d'unir RNA in vitro, el que pot ser una propietat important per a la seua funció. A més a més, malgrat que els estudis anteriors suggerien que la hèlix enrotllada de Erb1 no era essencial en la biogènesis del ribosoma, hem pogut resoldre la estructura cristal·lina de la proteïna Ytm1 unida al domini C-terminal de Erb1 de C. thermophilum. Aquest descobriment ens ha permès redefinir les interaccions macromoleculars que mantenen el complex. Inicialment, hem confirmat que l'extrem amino-terminal de Nop7 interacciona amb Erb1. A continuació, hem demostrat que el domini WD40 de Ytm1 s'uneix al ß-propeller de Erb1 amb bona afinitat. Després d'un anàlisi detallat de la superfície involucrada en la formació del dímer, hem estat capaços de dissenyar una variant mutada de Erb1 que s'associa més dèbilment amb Ytm1. Les dades estructurals i biofísiques s'han confirmat in vivo utilitzant S. cerevisiae on hem demostrat que una mutació puntual que disminueix l'afinitat d'unió entre els dominis C-terminals de Erb1 i Ytm1 manifesta un efecte negatiu en el creixement del llevat perquè interfereix amb la síntesi del 60S. Els nostres resultats estableixen un bon exemple de una superfície conservada involucrada en interaccions proteïna-proteïna, que es podria considerar una bona diana per a inhibir la proliferació cel·lular eucariota.
Wegrecki, M. (2015). Structural, biophysical and functional characterization of Nop7-Erb1-Ytm1 complex and its implications in eukaryotic ribosome biogenesis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/55941
TESIS
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Blissing, Annica. "Thiopurine S-methyltransferase - characterization of variants and ligand binding." Licentiate thesis, Linköpings universitet, Kemi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-136558.
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Thiopurine S-methyltransferase (TPMT) belongs to the Class I S-adenosylmethionine-dependent methyltransferase (SAM-MT) super family of structurally related proteins. Common to the members of this large protein family is the catalysis of methylation reactions using S-adenosylmethionine (SAM) as a methyl group donor, although SAM-MTs act on a wide range of different substrates and carry out numerous biologically important functions. While the natural function of TPMT is unknown, this enzyme is involved in the metabolism of thiopurines, a class of pharmaceutical substances administered in treatment of immune-related disorders. Specifically, methylation by TPMT inactivates thiopurines and their metabolic intermediates, which reduces the efficacy of clinical treatment and increases the risk of adverse side effects. To further complicate matters, TPMT is a polymorphic enzyme with over 40 naturally occurring variants known to date, most of which exhibit lowered methylation activity towards thiopurines. Consequently, there are individual variations in TPMTmediated thiopurine inactivation, and the administered dose has to be adjusted prior to clinical treatment to avoid harmful side effects. Although the clinical relevance of TPMT is well established, few studies have investigated the molecular causes of the reduced methylation activity of variant proteins. In this thesis, the results of biophysical characterization of two variant proteins, TPMT*6 (Y180F) and TPMT*8 (R215H), are presented. While the properties of TPMT*8 were indistinguishable from those of the wild-type protein, TPMT*6 was found to be somewhat destabilized. Interestingly, the TPMT*6 amino acid substitution did not affect the functionality or folding pattern of the variant protein. Therefore, the decreased in vivo functionality reported for TPMT*6 is probably caused by increased proteolytic degradation in response to the reduced stability of this protein variant, rather than loss of function. Also presented herein are novel methodological approaches for studies of TPMT and its variants. Firstly, the advantages of using 8-anilinonaphthalene-1-sulfonic acid (ANS) to probe TPMT tertiary structure and active site integrity are presented. ANS binds exclusively to the native state of TPMT with high affinity (KD ~ 0.2 μm) and a 1:1 ratio. The stability of TPMT was dramatically increased by binding of ANS, which was shown to co-localize with the structurally similar adenine moiety of the cofactor SAM. Secondly, an enzyme activity assay based on isothermal titration calorimetry (ITC) is presented. Using this approach, the kinetics of 6-MP and 6-TG methylation by TPMT has been characterized.
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Valiveti, Aswani Kumar. "Structural characterization of metal and DNA binding to DREAM protein, a calcium sensing transcriptional repressor in pain modulation." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/3975.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2006.Thesis research directed by: Molecular and Cell Biology. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Manoharan, Malini. "Genomic, structural and functional characterization of odorant binding proteins in olfaction of mosquitoes involved in infectious disease transmission." Phd thesis, Université de la Réunion, 2011. http://tel.archives-ouvertes.fr/tel-00979587.
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The role of odorant binding proteins in the olfaction of mosquitoes, the primary mechanism of human host recognition, has been an important focus of biological research in the field of infectious disease transmission by these insects. This thesis provides an in depth knowledge of these proteins in three mosquito species Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus. A large scale analysis on these genomes has been carried out towards the identification of the odorant binding proteins in the mosquito genomes. Identification of many new OBP members, in particular in the Aedes aegypti and Culex quinquefasciatus species, and an extensive phylogenetic analysis presenting a novel classification of the OBP subfamilies of these mosquito species has been proposed. This results further demonstrates the extraordinary multiplicity and diversity of the OBP gene repertoire in these three mosquito genomes and highlights the striking sequence features that are nevertheless highly conserved across all mosquito OBPs. Owing to the availability of homologous structures from mosquitoes or related species, the 3D structure modelling of all the Classic OBPs from the three genomes (representing in total 137 structures) has been performed. This was completed by large scale docking studies on these structures by screening a large set of compounds that are known to be mosquito attractants or repellents. These provide many exciting new insights into the structural and functional aspects towards understanding the efficacy of some repellents and of some attractants from human emanations. Through molecular dynamics simulation, the structural changes observed in an OBP bounded to an odorant when pH conditions are modified were characterized and the probable mechanism of ligand binding and release is presented. This work provides the first insights to many of the long awaited questions on the genomic, structural and functional characterization of mosquito OBPs and can be viewed as a reliable starting point for further experimental research focussed on these aspects.
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Grimm, Nicole Elena. "Characterization of the Schizosaccharomyces pombe protection of telomeres 1 (Pot1) DNA-binding domains by biochemical and structural techniques." Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1460859.
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Okamoto, Patricia Michiyo. "Nitrate reductase of Neurospora crassa : characterization of its gene, nit-3, and structural studies of its heme-binding domain /." The Ohio State University, 1992. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487776801320659.
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Hébert-Losier, Andréa 1983. "Structural and functional characterization of a novel endogenous steroid, estradienolone (ED), in human pregnancy." Thesis, McGill University, 2008. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=116111.
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Our lab has previously reported the identification of a novel endogenous 19-nor steroid, estradienolone (ED), in pregnant women that strongly bound to sex hormone binding globulin. Estrogen-receptor related receptors (ERRs), which have no known natural ligands, are a family of orphan receptors consisting of 3 isoforms: ERRalpha, ERRbeta and ERRgamma. The ERRs have been shown to actively modulate estrogenic responses, to play an essential role in pregnancy, and are implicated in breast cancer prognosis. My results show that ED acts as an antagonist of the ERRalpha confirming preliminary results obtained by our group. Studies of cellular responses demonstrate that ED has strong anti-mitogenic properties. ED inhibited the growth of both estrogen receptor (ER)-positive (MCF-7) and ER-negative (MDA-MB-231) breast cancer cells in a dose-dependent manner but did not have any effects on the proliferation of the non-cancerous immortalized epithelial breast MCF-10A cells. The finding that ED inhibits proliferation of both ER negative and ER positive breast cancer cells, and regulate ERR transcriptional activity may have important ramifications in breast cancer therapy.
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Jakob, Leonhard [Verfasser], and Gunter [Akademischer Betreuer] Meister. "Structural and functional characterization of the RNA-binding proteins Loquacious and Brain tumor from Drosophila melanogaster / Leonhard Jakob ; Betreuer: Gunter Meister." Regensburg : Universitätsbibliothek Regensburg, 2017. http://d-nb.info/1129956628/34.
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Nickolaus, Chen [Verfasser], and Wolfgang E. [Akademischer Betreuer] Trommer. "The Molten Globule State of Maltose-Binding Protein: Structural Characterization by Electron Paramagnetic Resonance Spectroscopy / Chen Nickolaus ; Betreuer: Wolfgang E. Trommer." Kaiserslautern : Technische Universität Kaiserslautern, 2017. http://d-nb.info/1123572135/34.
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Sturm, Noé. "Characterization of natural product biological imprints for computer-aided drug design applications." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAF059/document.
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La comparaison de site peut-elle vérifier l’hypothèse: «Les origines biosynthétiques des produits naturels leurs confèrent des activités biologiques»? Pour répondre à cette question, nous avons développé un outil modélisant les propriétés accessibles au solvant des sites de liaison. La méthode a montré des aspects intéressants, mais elle souffre d’une sensibilité aux coordonnées atomiques. Cependant, des méthodes existantes nous ont permis de prouver que l’hypothèse est valide pour la famille des flavonoïdes. Afin d’étendre l’étude, nous avons développé un procédé automatique capable de rechercher des structures d’enzymes de biosynthèse de produits naturels disposant de sites actifs capables de lier une molécule de petite taille. Nous avons trouvé les structures de 117 enzymes.Les structures nous ont permis de caractériser divers modes de liaison substrat-enzyme, nous indiquant l’empreinte biologique des produits naturels ne correspond pas toujours au modèle « clé- serrure »Can computational binding site similarity tools verify the hypothesis: “Biosynthetic moldings give potent biological activities to natural products”? To answer this question, we designed a tool modeling binding site properties according to solvent exposure. The method showed interesting characteristics but suffers from sensitivity to atomic coordinates. However, existing methods have delivered evidence that the hypothesis was valid for the flavonoid chemical class. In order to extend the study, we designed an automated pipeline capable of searching natural products biosynthetic enzyme structures embedding ligandable catalytic sites. We collected structures of 117 biosynthetic enzymes. Finally, according to structural investigations of biosynthetic enzymes, we characterized diverse substrate-enzyme binding-modes, suggesting that natural product biological imprints usually do not agree with the “key-lock” model
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Sitar, Tomasz. "Structural basis for the inhibition of insulin-like growth factors by insulin-like growth factor-binding proteins and structural and biochemical characterization of formins - the actin nucleating factors." kostenfrei, 2007. http://mediatum2.ub.tum.de/doc/652583/652583.pdf.
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Fleming, Christopher Daniel Redinbo Matthew Robert. "Structural insights into xenobiotic and organophosphate binding by human carboxylesterase 1 and efforts made towards the characterization of the androgen receptor modulator MAGE-11." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1228.
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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.Title from electronic title page (viewed Mar. 26, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics." Discipline: Biochemistry and Biophysics; Department/School: Medicine.
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Lange, Anja. "Structural characterization of the interaction of the Stam2's ubiquitin binding domains with ubiquitin chains by NMR : Cooperativity or not, that is the question !" Thesis, Lyon 1, 2010. http://www.theses.fr/2010LYO10308.
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Résumé en anglais uniquementFrom the discovery of ubiquitin and its function as signal for proteasomal degradation over 20 years ago to this days, it became evident that ubiquitin is a universal signal in eukaryotic cells. Ubiquitin in its different forms is involved in many versatile cellular processes. Knowing that the ubiquitin signal is differently translated, depending on its occurrences as mono-ubiquitin or poly-ubiquitin, raises the question: how do cells distinguish between the different occurrences of ubiquitin and translate it into the proper response? Proteins interacting with ubiquitin contain so called ubiquitin binding domains (UBDs), whereas the affinities to ubiquitin vary from a few _M to mM. So far only three (K63, K48 and linear chains) out of the eight possible chain-linkages can be produced in sufficient amounts to characterize their interaction with UBDs. K48- and K63- linked ubiquitin chains regulate different cellular events and need to be recognized by different proteins. Thus, it is of prime importance to characterize the binding of different UBDs to these two kinds of ubiquitin chains, as it can give important clues related to the general mechanism of chain discrimination by ubiquitin adapter proteins. Some isolated UBDs exhibit a preference for one chain linkage type over the other, whereas others do not discriminate between mono-ubiquitin or K63- and K48-linked chains. Interestingly, many ubiquitin adapter proteins harbor more than one UBD. STAM2 is a ubiquitin adapter protein, that is involved in endosomal receptor sorting and supposed to preferentially bind mono-ubiquitin and K63- over K48-linked ubiquitin. STAM2 contains two UBDs (a VHS and UIM domain) that were shown to bind to ubiquitin . The current manuscript shows that STAM2’s SH3 domain binds ubiquitin as well. To understand the function of the sequential arrangement of three UBDs in one protein, first binding of the individual VHS and UIM domains to monoubiquitin as well as K48- and K63-linked di-ubiquitin was investigated. This work shows, that the VHS domain displays a different mode of binding for K63- and K48-linked diubiquitin. In spite of the fact, that the apparent Kd for both chains is the same, only one VHS domain can bind to K48-linked di-ubiquitin chains (with a preference for the distal domain), whereas K63-linked di-ubiquitin can accommodate two VHS domains at a time. Since no conclusion can be drawn with respect to the apparent Kds, the different binding modes might gain more impact in consideration of the ensemble of three UBDs. Results presented in this manuscript, based on a construct containing the VHS and UIM domain, show that binding to K63- but not K48-linked di-ubiquitin is cooperative
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Wang, Qianmin Verfasser], and Elena [Akademischer Betreuer] [Conti. "Structural and Biochemical Characterization of Cell Shaping Proteins : 1. Microtubule Binding Protein p150glued and 2. Intraflagellar Transport Protein 172 / Qianmin Wang ; Betreuer: Elena Conti." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2017. http://d-nb.info/1148276807/34.
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Tavares, Macedo Joana [Verfasser], and Bärbel [Akademischer Betreuer] Blaum. "Production and glycan binding characterization of human properdin and structural elucidation of c-Jun N-terminal kinase 3 inhibitors / Joana Tavares Macedo ; Betreuer: Bärbel Blaum." Tübingen : Universitätsbibliothek Tübingen, 2019. http://d-nb.info/1201644925/34.
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Rechlin, Chris [Verfasser], and Gerhard [Akademischer Betreuer] Klebe. "Insights into Protein-Ligand Molecular Recognition: Thermodynamic, Kinetic and Structural Characterization of Inhibitor Binding to Aldose Reductase and Carbonic Anhydrase II / Chris Rechlin ; Betreuer: Gerhard Klebe." Marburg : Philipps-Universität Marburg, 2016. http://d-nb.info/1119318017/34.
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Port, Sarah A. [Verfasser], Ralph H. [Akademischer Betreuer] Kehlenbach, Achim [Akademischer Betreuer] Dickmanns, and Heinz [Akademischer Betreuer] Neumann. "Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-binding Sites Involved in Nucleocytoplasmic Transport / Sarah A. Port. Gutachter: Achim Dickmanns ; Heinz Neumann. Betreuer: Ralph H. Kehlenbach." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://d-nb.info/1076398685/34.
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Gallego, Alonso Pablo. "Structural studies on protein-protein interactions: Analysis of the regulation of the DYNLL/LC8 binding to Nek9 and characterization of the enzymes composing the arginine deiminase pathway in mycoplasma penetrans." Doctoral thesis, Universitat Autònoma de Barcelona, 2014. http://hdl.handle.net/10803/285569.
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Las interacciones proteína-proteína (PPIs, por sus siglas en inglés) son contactos físicos intencionados que se dan entre dos o más proteínas. Estas interacciones forman la red de interacciones de proteínas y forman el núcleo del sistema interatómica de toda célula viva. Fallos en este sistema producidos por PPIs aberrantes están relacionados con fallos en la transducción de señales. Agregación proteica y una pérdida de regulación celular. De hecho, las PPIs anormales forman parte de las bases de enfermedades como el Alzheimer y el cáncer. La importancia del sistema interatómico hace que sea necesario investigar las PPIs, sus funciones y propiedades estructurales, en diferentes modelos.
En este trabajo la cristalografía de rayos X es entre otras técnicas la principal para estudiar las PPIs. La investigación de PPIs se ha llevado a cabo a través de dos modelos experimentales diferentes: En el primero, hemos analizado el rol de la fosforilación en un péptido derivado de la Kinsasa mitótica Nek9 en la unión con LC8, una proteína asociada a Nek9; En el segundo modelo, hemos resuelto las estructuras de los tres enzimas que forman la vía de la arginina deiminasa en Mycoplasma penetrans.
La proteína Nek9/Nercc1 de la familia de proteínas Kinasa NIMA juega un papel esencial en el control del huso mitótico. DYNLL/LC8 fue descrita con un complemento del complejo de la dyneina, sin embargo, actualmente se le conocen múltiples proteínas asociadas y de ha propuesto que LC8 tiene un rol general como núcleo de dimerización que dirige varias proteínas. Los últimos trabajos indican que la unión de LC9 con Nek9 está regulada por autofosforilación. En este trabajo proponemos un nuevo mecanismo regulatorio defosforilación que interfiere en la unión de LC8 con sus proteínas asociadas.
El metabolismo de la arginina para producir ATP es considerado esencial para microorganismos como Mycoplasma penetrans en condiciones anaeróbicas. Además, esta vía ha sido asociada en los mecanismos de patogenicidad y virulencia en ciertos organismos, por ejemplo, protegiendo del estrés acídico en la infección. En este trabajo presentamos las estructuras de la vía de la arginina deiminasa de M.penetrans: arginina deiminasa (ADI), ornitina carbamoyltransferasa (OTC) and carbamato kinasa (CK). Las estructuras de M.penetrans ADI y CK revelan los cambios estructurales que se dan durante el mecanismo de reacción. En el caso de enzima OCT de M.penetrans comparamos su estructura cuaternaria con otros organismos, incluyendo termófilos, revelando la formación de esta estructura cuaternaria común organizada por unas interfaces con una baja homología de secuencia.
Los resultados presentados en esta tesis enfatizan la importante contribución de la cristalografía de rayos X para estudiar las propiedades de las PPIs. La regulación de de las PPIs, sus diferencias estructurales y funcionales dependientes de su asociación, modificaciones posttraducionales y la adaptación a ambiental a través de la evolución son algunas de las propiedades y factores de dependencia de las PPIs estudiadas en este trabajo de tesis.Protein-Protein Interactions (PPIs) are intentional physical contacts established between two or more proteins. These interactions form the large protein interaction network and are the core of the entire interatomic system of any living cell. Flaws in the interaction network by aberrant PPIs involve signal transduction fails, protein aggregation and a completely loss of cell's regulation. Indeed, missense PPIs are the basis of multiple diseases, such as Alzheimer's disease and cancer. The significance of the interatomic system makes worth to studying PPIs, their functions and structural properties, in different models. In the present work X-ray crystallography is the main technique used, in addition to other methods to study Protein-Protein interactions. The study of protein-protein interactions is performed through two different experimental models: In the first model, we analyzed the role of phosphorylation in the interaction of a peptide derived from the mitotic kinase Nek9 with its binding partner LC8; In the second model, we decipher the structures of the three enzymes composing the arginine deiminase pathway in Mycoplasma penetrans. The NIMA family protein kinase Nek9/Nercc1 plays a main role in the control of the mitotic spindle. DYNLL/LC8 was originally described as a component of the dynein complex, but the recent discovery of multiple interaction partners for LC8 has proposed that it has a general role as a dimerization hub that organizes different protein partners. Recent experiments suggested that LC8 binding to Nek9 was regulated by Nek9 autophosphorylation. The present work sheds light into a novel phosphorylation regulatory mechanism that interferes with LC8 protein-protein complex formation. The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M.penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). M.penetrans ADI and CK structures disclose the structural conformation shifts upon the reaction mechanism of these proteins. In the case of M.penetrans OCT its dodecameric quaternary structure is compared with other organisms (including some thermophiles), revealing the formation common quaternary structure arranged interfaces with a low sequence homology. The results collected in this thesis emphasize the important contribution of X-ray crystallography for studding PPIs properties. PPIs regulation, structural and functional differences depending on their association, posttranslational modifications and the environment adaptation thought evolution are some of the PPI properties and dependence factors studied in this thesis work.
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Kowalska, Kaja [Verfasser], Tad A. [Akademischer Betreuer] Holak, Bernd [Akademischer Betreuer] Reif, and Robert [Akademischer Betreuer] Huber. "Biochemical and biophysical characterization of CD44 and its binding partner, hyaluronic acid and structural investigations of the ubiquitin-like protein 5 / Kaja Kowalska. Gutachter: Bernd Reif ; Robert Huber. Betreuer: Tad A. Holak." München : Universitätsbibliothek der TU München, 2012. http://d-nb.info/1031513604/34.
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Batista, Adelina Braga. "CaracterizaÃÃo estrutural da Mo-CBP3, uma albumina 2S de sementes de Moringa oleifera lamarck e seu modo de aÃÃo contra fungos fitopatogÃnicos." Universidade Federal do CearÃ, 2013. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=10389.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel SuperiorMo-CBP3 à uma proteÃna ligante à quitina, purificada de sementes de Moringa oleifera, com amplo espectro de aÃÃo contra fungos fitopatogÃnicos. No presente trabalho, novas propriedades estruturais da Mo-CBP3 sÃo descritas, revelando correlaÃÃo entre sua estabilidade estrutural e atividade antifÃngica. Em adiÃÃo, para melhor compreensÃo dos mecanismos pelos quais essa proteÃna exerce aÃÃo antifÃngica, sua habilidade de induzir a produÃÃo endÃgena de espÃcies reativas de oxigÃnio e de causar alteraÃÃes morfolÃgicas e ultraestruturais foi analisada, usando Fusarium solani como modelo. F. solani à uma espÃcie de fÃcil manuseio e desenvolvimento rÃpido, ideal para ensaios in vitro, e de relevÃncia, por se tratar de um fungo que ataca culturas economicamente importantes. Com foco na utilizaÃÃo segura da Mo-CBP3 como agente quÃmico contra fungos, seus efeitos citotÃxicos sobre cÃlulas eucariÃticas tambÃm foram investigados. Mo-CBP3 à uma proteÃna ligante à quitina de 18,0 kDa, de acordo com PAGE-SDS. Todavia, anÃlise por espectrometria de massas revelou que essa proteÃna consiste de mÃltiplas isoformas com massas moleculares variando entre 12,2 e 12,3 kDa. Mo-CBP3 à composta por duas cadeias polipeptÃdicas de 5,0 e 9,0 kDa, denominadas de cadeia A e cadeia B, respectivamente. A cadeia B contÃm a sequÃncia NH2-terminal representada por CPAIQRCCQQLRNIQPPCRCCQ, enquanto que a cadeia A tem o resÃduo NH2-terminal bloqueado. cDNA codificador da cadeia B foi obtido com iniciadores sintetizados a partir de sua sequÃncia NH2-terminal. AnÃlises in silico das sequÃncias de nucleotÃdeos e de aminoÃcidos deduzida confirmaram a presenÃa de isoformas e massa molecular da Mo-CBP3 e identificaram sÃtios potenciais de O-glicosilaÃÃo e fosforilaÃÃo. AlÃm disso, similaridades entre Mo-CBP3 e outras proteÃnas de M. oleifera, bem como com albuminas 2S, foram detectadas. A estrutura secundaria da Mo-CBP3 à composta por 30,3% α-hÃlices, 16,3% folhas β, 22,3% voltas e 30,4% estruturas ao acaso. Na espectroscopia de fluorescÃncia, excitaÃÃes de uma soluÃÃo da Mo-CBP3 a 280 nm e 295 nm produziram emissÃo mÃxima a 303 e 309 nm, respectivamente. A estrutura da Mo-CBP3 à altamente estÃvel, se apresentando indiferente Ãs mudanÃas de temperatura e pH. Mo-CBP3 (0,05-0,1 mg/mL) se mostrou capaz de inibir a germinaÃÃo de conÃdios de vÃrios fungos fitopatogÃnicos, incluindo F. solani, F. oxysporum, Colletotrichum musae e C. gloeosporioides. Similarmente, Mo-CBP3 (0,05 mg/mL) foi capaz de inibir o crescimento micelial de F. solani e apresentou tanto efeito fungistÃtico como fungicida, dependendo da concentraÃÃo usada. LigaÃÃo da Mo-CBP3 à superfÃcie de cÃlulas fÃngicas ocorre, pelo menos em parte, via interaÃÃo eletrostÃtica, jà que NaCl 0,15 M aboliu seu efeito inibitÃrio. Mo-CBP3 induziu a produÃÃo de espÃcies reativas de oxigÃnio e causou perda de assimetria e deformaÃÃes em cÃlulas de F. solani. DesorganizaÃÃo do sistema de endomembranas, condensaÃÃo do citosol e aumento de vacuolizaÃÃo tambÃm foram observados. Mo-CBP3 nÃo mostrou atividade hemolÃtica e nem foi capaz de alterar a viabilidade das cÃlulas MCF-7 e Caco-2, sugerindo que essa proteÃna nÃo à tÃxica para cÃlulas humanas. Com base na alta estabilidade e no amplo espectro de aÃÃo contra fungos fitopatogÃnicos em baixas concentraÃÃes e, tambÃm, na ausÃncia de citotoxicidade para cÃlulas humanas testadas, Mo-CBP3 tem grande potencial para desenvolvimento de novas drogas antifÃngicas ou na produÃÃo de plantas transgÃnicas mais resistentes a fungos.
Mo-CBP3 is a chitin-binding protein purified from Moringa oleifera seeds that displays broad inhibitory activity against phytopathogenic fungi. In this work, we report new structural features of Mo-CBP3 that reveal a correlation between its structural stability and antifungal activity. In addition, to gain better insights into the mechanisms by which this protein acts as an antifungal agent, its ability to induce the endogenous production of reactive oxygen species and to trigger morphologic and ultrastructural alterations were analysed using Fusarium solani as a model. F. solani is an easy-to-handle and fast-developing species, making it ideal for in vitro assays, and it holds relevance as a phytopathogenic fungus that attacks economically important crop plants. To fully explore the biosafety of Mo-CBP3 as a chemical agent against fungi, its cytotoxic effects on eukaryotic cells were also investigated. Mo-CBP3 is a chitin-binding protein of 18.0 kDa, according to SDS-PAGE. However, by mass spectrometry analysis, it was observed that this protein consists of multiple isoforms with molecular masses ranging between 12.2 and 12.3 kDa. Mo-CBP3 is composed by two polypeptide chains of 5.0 and 9.0 kDa, named A and B chain, respectively. The B chain contains the following NH2-terminal sequence CPAIQRCCQQLRNIQPPCRCCQ while the A chain has a blocked NH2-terminal residue. cDNA encoding the B chain was obtained with primers of its NH2-terminal sequence. In silico analyses of nucleotide and deduced amino acid sequences confirmed the presence of isoforms and molecular mass of Mo-CBP3 and identified potential sites of O-glicosylation and phosphorilation. Moreover, similarities between Mo-CBP3 and other M. oleifera proteins as well as 2S albumins were detected. The secondary structure of Mo-CBP3 showed 30.3% α-helices, 16.3% β-sheets, 22.3% turns and 30.4% unordered forms. In the fluorescence spectroscopy, excitation of Mo-CBP3 solution at 280 nm and 295 nm gave emission maxima at 303 and 309 nm, respectively. The Mo-CBP3 structure is highly stable and retains its antifungal activity regardless of temperature and pH. Mo-CBP3 (0.05-0.1 mg/mL) was able to inhibit the conidia germination of several phytopathogenic fungi, including F. solani, F. oxysporum, Colletotrichum musae and C. gloeosporioides. Similarly, Mo-CBP3 was inhibitory to the mycelial mass development of F. solani at 0.05 mg/mL and has both fungistatic and fungicidal effects, depending on the concentration used. Binding of Mo-CBP3 to the fungal cell surface is achieved, at least in part, via electrostatic interactions, as 150 mM NaCl abolished its inhibitory effect. Mo-CBP3 induced the production of reactive oxygen species and caused in F. solani cells a marked loss of asymmetry, deformations and deep wrinkles in comparison to control cells. Disorganisation of the endomembrane system and condensation and shrinkage of cytosol with increased vacuolation and the loss of normal structure and content were also observed. Mo-CBP3 did not show haemolytic activity and it was not capable to alter de viability of both MCF-7 and Caco-2 cells, suggesting that this protein is not toxic for human cells. Based on its high stability and broad-spectrum efficacy against important phytopathogenic fungi at low inhibitory concentrations and absence of cytotoxicity to human cells, Mo-CBP3 has great potential in the development of new antifungal drugs or in transgenic crops with enhanced resistance to fungi.
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Betz, Christine [Verfasser], and Oliver [Akademischer Betreuer] Einsle. "Structural characterization of the metal-binding ligands S100A8/S100A9 and S100B of the receptor for advanced glycation end products = Strukturelle Charakterisierung der metallbindenden Liganden S100A8/S100A9 und S100B des Rezeptors für Advanced Glycation End Products." Freiburg : Universität, 2013. http://d-nb.info/1115813455/34.
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Elison, Kalman Grim. "Purification, functional characterization and crystallization of the PerR peroxide sensor from Saccharopolyspora erythraea." Thesis, Uppsala universitet, Strukturbiologi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-387943.
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This report summarizes the work on the cloning, expression, and purification of PerR, a metal sensing regulator from Saccharopolyspora erythraea and the subsequent characterization using small angle X-ray scattering and other biochemical methods. The report aims to provide an insight into prokaryotic metal homeostasis, provide a better understanding of how PerR works and provide valuable information for the continued work on the crystallization of PerR.
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El, Masri Rana. "Remodeling of heparan sulfate : functional and structural characterization of human endosulfatase HSulf-2 The sweet side of extracellular sulfatases Expression and purification of recombinant extracellular sulfatase HSulf-2 allows deciphering of enzyme sub-domain coordinated role for the binding and 6-O-desulfation of heparan sulfate." Thesis, Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV037.
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Les Héparanes Sulfates (HS) sont de polysaccharides complexes impliqués dans de nombreux processus biologiques. La structure des HS est contrôlée à la surface cellulaire par une famille particulière d‟endosulfatases extracellulaires, les Sulfs. Les Sulfs modifient dramatiquement les propriétés fonctionnelles des HS et sont impliqués dans de nombreux processus physiopathologiques, notamment le cancer. Ces enzymes se composent de deux domaines: un domaine catalytique (CAT) contenant le site actif et un domaine basique hydrophile (HD) responsable de la liaison aux HS. Le but de mon projet de thèse est de caractériser les propriétés structurales et fonctionnelles de la forme humaine HSulf-2, qui demeure à ce jour très mal connues. Dans ce cadre, nous avons tout d‟abord étudié les mécanismes de reconnaissance enzyme/substrat et caractérisé deux nouveaux motifs de reconnaissance des HS sur ces enzymes, responsable de leur activité. En utilisant des oligosaccharides naturels et synthétiques, nous avons aussi démontré que le domaine HD n'est pas essentiel pour la reconnaissance des HS, mais est permet une désulfatation processive et orientée du polysaccharide. De plus, nous avons identifié un tétrasaccharide comme étant la taille oligosaccharidique minimale requise pour l'activité de HSulf-2. Nos résultats nous ont permis de proposer un nouveau modèle décrivant le processus de désulfatation du HS par HSulf-2. D'autre part, nous avons montré que HSulf-2 est un protéoglycane, car il contient une modification post-traductionnelle unique (chaîne CS de Chondoitin Sulfate) sur son domaine HD. Cette chaîne diminue l'activité enzymatique et la liaison aux HS in vitro. Dans le microenvironnement tumoral, en utilisant un modèle de tumeur mammaire orthotopique murin, nous avons montré que la chaîne CS est libérée par protéolyse, conduisant à l'activation de HSulf-2, augmentant la capacité des tumeurs à se développer et à se transformer en métastase. Finalement, nous avons réalisé une étude structurale des Sulfs. Nous avons choisi d‟étudier séparément les deux domaines (CAT et HD). Des essais de cristallogenèse ont été menés pour le domaine CAT afin de résoudre sa structure par cristallographie aux rayons X, mais n‟ont pu aboutir. En ce qui concerne le HD, nous avons mis en place un protocole de production et de purification de HD d‟une manière recombinante et nous avons initiés une étude par RMN ainsi que d'autres techniques biophysiques afin de caractériser structuralement le domaine et d'identifier les sites de liaison aux HS. Nos résultats préliminaires suggèrent que la HD est un domaine non structuré, à l'exception de ses parties N- et C-terminales. L‟ensemble de ces travaux devrait nous permettre de mieux comprendre ces importants mécanismes de régulation des HS et de d‟envisager de nouvelles stratégies anticancéreuses ciblant les SulfsHeparan Sulfate (HS) are complex polysaccharides involved in many biological processes. The structure of HS is regulated at the cell surface by unique extracellular endosulfatases, the Sulfs. Sulfs dramatically change HS functional properties, thereby being implicated in many physiopathological processes including cancer. Sulfs features two domains: a catalytic domain (CAT) that comprises the active site, and an hydrophilic basic domain (HD) responsible for HS binding. The aim of my PhD project is to characterize the structural and the functional properties of the human for HSulf-2, which remains poorly understood. In this context, we have first studied the enzyme/substrate recognition mechanisms. We identified two novel HS binding motifs on these enzymes implicated in their activity. In addition, using natural and synthetic oligosaccharides, we demonstrated that the HD is not essential for HS recognition, but is directs the processive and orientated desulfation of the polysaccharide. Moreover, we showed that a tetrasaccharide is the minimal oligosaccharide size required for HSulf-2 activity. Our results enabled us to propose a new model depicting the desulfation process of HS by the Sulfs. Second, we have shown that HSulf-2 is a proteoglycan, given that it harbors a unique PTM (Chondroitin Sulfate, CS chain) on its HD domain. This chain decreases enzyme activity and HS binding in vitro. In the tumoral microenvironment, using a murine orthotropic mammary tumor model, we showed that the CS chain is lost by proteolytic processing, leading to the activation of HSulf-2, and the promotion of tumor growth, vascularization and metastasis. Finally, we have undertaken the structural characterization of the Sulfs. For this, we decided to study separately the two domains found in these enzymes (CAT and HD). Crystallogenesis assays were undertaken for the CAT domain to solve its structure by X-ray crystallography, but were unsuccessful. Regarding the HD, we set up a protocol of production and purification of recombinant HD and we initiated NMR studies and other biophysics analyses in order to structurally characterize the domain and to identify the HS binding sites. Our preliminary results suggest that the HD is an unstructured domain, except for its N- and C-terminal parts. Overall, our data provide significant insights into this critical regulatory step of HS function
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Faris, Jonathan Scott. "Characterization of the DNA binding properties of the thyroid hormone receptor." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1996. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq21931.pdf.
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Baumgärtel, Thomas. "Binding and characterization of fluorescent nano-aggregates on structured surfaces." Doctoral thesis, Universitätsbibliothek Chemnitz, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-91552.
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Im Mittelpunkt dieser Arbeit steht die selektive Funktionalisierung von Siliziumoxidnanostrukturen auf alkyl-passivierten Siliziumoberflächen welche durch rasterkraftmikroskopisch induzierte lokale anodische Oxidation (LAO) erzeugt werden. Bei der gezielten Immobilisierung von funktionalen Molekülen auf den Strukturen werden zwei verschiedene Routen verfolgt – Anbindung von ionischen Farbstoffen über elektrostatische Wechselwirkungen sowie stufenweise kovalente chemische Anbindung von bi-funktionalen Verbindermolekülen und Farbstoffen. Eine Untersuchung der hergestellten funktionalen Strukturen erfolgt mittels Rasterkraftmikroskopie, Raster-Kelvin-Mikroskopie sowie zeitaufgelöster Fluoreszenzmikroskopie und-spektroskopie. Durch zwei unabhängige Methoden kann gezeigt werden dass die Ladungen im lokalen Oxide vergleichsweise stabil sind und die elektrostatische Anbindung somit auch noch nach Tagen möglich sein sollte. Das Verhalten der elektrostatisch angebundenen Farbstoffe hängt stark von deren Art ab. Während es bei Rhodamin 6G nur zu einer minimalen spektralen Änderung im Vergleich zur Lösung kommt so zeigen spermin-funktionalisierte Perylenbisimidfarbstoffe eine deutliche H-Aggregation und Ausbildung von Excimerzuständen. Diese Zustände sind eindeutig thermisch aktiviert und zeigen eine wesentlich höhere Aktivierungsenergie als bei allen anderen bisher untersuchten Perylenaggregaten sowie eine Hysterese bei Temperaturveränderung. Die physikalische Ursache für dieses Phänomen liegt allem Anschein nach in der elektrostatischen Anbindung selbst welche ein instabiles Gleichgewicht mit der Wechselwirkung der Moleküle untereinander bildet. Eine geordnete kovalente Anbindung von funktionalen Silanmolekülen an die mittels LAO erzeugten Strukturen erfordert sehr definierte Prozessparameter. Die spektroskopische Untersuchung von an die funktionalen Silane chemisch angebundenen Fluoresceinfarbstoffen lässt indirekte Schlüsse auf deren Belegungsdichte und damit die Qualität der Silanmonolage zu.
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Sun, Xueguang. "Characterization of E. coli HFQ structure and its RNA binding properties." Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-12052005-145342/.
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Thesis (Ph. D.)--Biology, Georgia Institute of Technology, 2006.Wartell Roger, Committee Chair ; Chernoff Yury, Committee Member ; Harvey Stephen, Committee Member ; Spiro Stephen, Committee Member ; Williams Loren, Committee Member.
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Sun, Xueguang. "Characterization of E coli Hfq structure and its RNA binding properties." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/10416.
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Hfq is a bacterial RNA-binding protein recently shown to contain the Sm motif, a characteristic of Sm proteins that function in RNA processing in archaea and eukaryotes. Hfq plays a major role in RNA-RNA interactions regulating translation. Comparative structural modeling and amino acid sequence alignment were used to predict the 3-D structure of Hfq and the model was in excellent agreement with the crystal structure which determined for S. aureus Hfq. The evolution of Hfq was explored by a BLAST search of microbial genomes followed by phyletic analysis. About half of the genomes examined contain at least one gene coding for Hfq. The presence and absence of Hfq closely followed major bacterial clades. The potential RNA binding residues on the two surfaces of the Hfq hexamer were proposed based on the bioinformatics studies and the mutant Hfq proteins with either single or double mutations on the two surfaces of the Hfq hexamer were generated. Their RNA binding properties was biophysically studied by gel-shift assay, fluorescence anisotropy and fluorescence quenching techniques. Results indicated that 1) point mutations on the distal surface of the Hfq hexamer, Y25A and K31A, have a major effect on A18 binding. Both reduce binding by about 1000 fold. Mutations on the proximal surface have a small or no influence on A18 binding. 2) Two mutations, F39A and R16A, on the proximal surface of the Hfq structure reduce binding to the DsrA domain II by 10 fold. Other mutations reduce binding by less than 2 fold. 3) An amino acid covariance was observed in L12 and F39. Mutation L12F can partially restore F39A in DsrA RNA binding. 4) It appears that two Hfq hexamers cooperatively bind one RNA for both DsrADII and A18.
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Carrick, Francine Ellen. "Characterization of bovine insulin like growth factor binding protein-2 : structure and function." Title page, abstract and contents only, 2001. http://web4.library.adelaide.edu.au/theses/09PH/09phc3158.pdf.
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Chinenov, Yurii. "Molecular characterization of transcription factor GABP : redox regulation, promoter structure, and mechanisms of assembly /." free to MU campus, to others for purchase, 1999. http://wwwlib.umi.com/cr/mo/fullcit?p9962509.
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Arbuckle, Janeen Lynnae. "Identification and characterization of domains in non-core RAG1." Oklahoma City : [s.n.], 2007.
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Kiesler, Eva. "Isolation and functional characterization of Hrp65-binding proteins in Chironomus tentans." Doctoral thesis, Stockholm : Institutionen för molekylärbiologi och funktionsgenomik, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-218.
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Alves, Carolina Alpalhão Mantero de Mendonça. "Characterization of the hepatitis delta virus small antigen: intracellular localization, structure, multimerization and RNA binding ability." Doctoral thesis, Instituto de Higiene e Medicina Tropical, 2013. http://hdl.handle.net/10362/19280.
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O vírus da hepatite delta (HDV) é o agente patogénico responsável por uma das formas mais severas de hepatite viral. O genoma consiste numa molécula circular de RNA de cadeia simples de polaridade negativa e apresenta uma única proteína viral, o antigénio delta pequeno (S-HDAg). Na sequência de um mecanismo de editing outra proteína viral é traduzida, o antigénio delta grande (L-HDAg). Apesar de partilharem grande parte da sua sequência, as duas proteínas desempenham funções distintas. O S-HDAg é essencial para a acumulação de RNAs virais enquanto o L-HDAg inibe a replicação viral e é necessário para o empacotamento. O HDV depende extensivamente de factores do hospedeiro para completar o seu ciclo de replicação. Pensa-se que a polymerase II (pol II) do hospedeiro é redireccionada para transcrever o RNA viral.
No presente trabalho procurou-se caracterizar o S-HDAg e clarificar o seu papel no ciclo de replicação do HDV.
Observamos que quando o S-HDAg é expresso na presença de replicação do RNA viral, o antigénio co-localiza com a pol II. Contudo, a co-localização com pol II verifica-se mesmo na presença de RNA viral incapaz de ser replicado e na ocorrência de inibição da replicação viral, sugerindo que o S-HDAg não participa directamente na transcrição do RNA viral. Assim, propomos que o S-HDAg é essencial para acumulação de RNAs virais protegendo ou estabilizando os RNAs. Observamos ainda que na ausência de RNA viral o S-HDAg co-localiza com a nucleolina nos nucléolos. Contudo, na presença de RNA incapaz de ser replicado, o antigénio desloca-se para o nucleoplasma mantendo-se a nucleolina nos nucléolos, sugerindo que o S-HDAg não interage directamente com a nucleolina.
Ao estudarmos as características estruturais do S-HDAg verificámos, utilizando um preditor de desordem intrínseca, que apresenta um elevado grau de desordem. A previsão foi confirmada in vitro por dicroísmo circular observando-se que apenas 30% dos amino ácidos adoptam uma conformação de hélice . A ausência de uma estrutura rígida pode conferir ao antigénio flexibilidade para se adaptar a diferentes parceiros e participar em vários passos do ciclo de replicação viral.
A multimerização do S-HDAg foi analisada por dispersão de luz dinâmica. Os resultados indicam que o antigénio recombinante purificado é capaz de formar multímeros de 12 moléculas. Adicionalmente, foram observados multímeros de seis a oito moléculas em gel de poliacrilamida desnaturante, após cross-linking. Os mesmos multímeros foram observados para S-HDAg presente em partículas virais sugerindo que a multimerização do antigénio ocorre in vivo.
Finalmente, estudamos a capacidade do S-HDAg interagir com ácidos nucleicos. Verificamos que multímeros e monómeros de S-HDAg são capazes de interagir in vitro com RNA e DNA. A falta de especificidade observada pode dever-se apenas a interacções electrostáticas entre o S-HDAg de carga positiva (+12) e ácidos nucleicos de carga negativa. Propomos que, in vivo, a fosforilação extensiva do S-HDAg reduza a carga positiva contribuindo para que a interacção seja específica para os RNAs virais.Hepatitis delta virus (HDV) is the causative agent of one of the most severe forms of viral hepatitis. It has a small single-stranded circular RNA genome of negative polarity and only one viral protein, the small delta antigen (S-HDAg). Following site-specific RNA editing, a second longer protein is translated, the large delta antigen (L-HDAg). Although these viral proteins share most of their sequence they play distinct roles. S-HDAg is essential for the accumulation of HDV RNAs whereas L-HDAg inhibits HDV replication and is necessary for viral assembly. With such a limited coding capacity HDV must rely extensively on host cell components to complete its replication cycle. The host DNA-directed RNA polymerase II (pol II) is thought to be re-directed to transcribe HDV RNAs. The objective of this study was to further characterize S-HDAg and clarify its role(s) during the HDV replication cycle. We observed that when S-HDAg was expressed in vivo along with replicating HDV RNA it co-located with host pol II. However, such co-localization was also observed in the presence of non-replicating HDV RNAs or when replication was inhibited by specific doses of -amanitin. Thus, we propose that S-HDAg is essential for HDV RNA accumulation by stabilizing or protecting the viral RNAs rather than acting as a direct player in HDV RNA transcription. Additionally, we observed that S-HDAg located in nucleolus when expressed in the absence of HDV RNA, and co-located with host nucleolin. However, in the presence of non-replicating HDV RNAs, S-HDAg moved to the nucleoplasm whereas nucleolin was unchanged. This suggests that S-HDAg is not interacting directly with nucleolin. In our examination of S-HDAg‟s structural features we applied a meta-predictor of intrinsic disorder, PONDR-FIT. It predicted that full-length S-HDAg has extensive intrinsic disorder. This result was confirmed in vitro by circular dichroism measurements that indicated no more than 30% of S-HDAg amino acids adopted an -helical structure. Such a lack of a well-defined rigid structure is expected to grant flexibility to the antigen allowing it to interact with several partners and perform distinct roles during the HDV replication cycle. Protein multimerization was studied by dynamic light scattering. Data analysis indicated that purified recombinant S-HDAg was able to assemble into homomultimers as high as dodecamers. Similarly, denaturing polyacrylamide gel electrophoresis with prior cross-linking indicated formation of at least hexamers and octamers. Similar multimers were observed for S-HDAg present in virus-like particles indicating that S-HDAg multimerization also occurs in vivo.Finally we examined the ability of S-HDAg to bind nucleic acids in vitro. Both multimers and monomers bound to conformations of both RNA and DNA. Such a lack of specificity was probably due to electrostatic interactions between the positively-charged S-HDAg (+12) and negatively-charged nucleic acids. We propose that in vivo, extensive post-translational phosphorylation of S-HDAg reduces the positive charge, thereby contributing to interactions more specific for HDV RNAs and possibly dependent upon protein multimerization. Despite our observations presented here, some issues relating to our aims remain unresolved.
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Mariotti, Paolo <1980>. "Characterization of the structure and iron uptake mechanisms of the Staphylococcus aureus ferric hydroxamate-binding lipoprotein FhuD2." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amsdottorato.unibo.it/4821/.
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The Reverse Vaccinology (RV) approach allows using genomic information for the delineation of new protein-based vaccines starting from an in silico analysis. The first powerful example of the application of the RV approach is given by the development of a protein-based vaccine against serogroup B Meningococcus. A similar approach was also used to identify new Staphylococcus aureus vaccine candidates, including the ferric hydroxamate-binding lipoprotein FhuD2. S. aureus is a widespread human pathogen, which employs various different strategies for iron uptake, including: (i) siderophore-mediated iron acquisition using the endogenous siderophores staphyloferrin A and B, (ii) siderophore-mediated iron acquisition using xeno-siderophores (the pathway exploited by FhuD2) and (iii) heme-mediated iron acquisition. In this work the high resolution crystal structure of FhuD2 in the iron (III)-siderophore-bound form was determined. FhuD2 belongs to the Periplasmic Binding Protein family (PBP ) class III, and is principally formed by two globular domains, at the N- and C-termini of the protein, that make up a cleft where ferrichrome-iron (III) is bound. The N- and C-terminal domains, connected by a single long α-helix, present Rossmann-like folds, showing a β-stranded core and an α-helical periphery, which do not undergo extensive structural rearrangement when they interact with the ligand, typical of class III PBP members. The structure shows that ferrichrome-bound iron does not come directly into contact with the protein; rather, the metal ion is fully coordinated by six oxygen donors of the hydroxamate groups of three ornithine residues, which, with the three glycine residues, make up the peptide backbone of ferrichrome. Furthermore, it was found that iron-free ferrichrome is able to subtract iron from transferrin. This study shows for the first time the structure of FhuD2, which was found to bind to siderophores ,and that the protein plays an important role in S. aureus colonization and infection phases.