In the first part of the thesis, protein-ligand interactions were investigated using the chaperone LcrH, from Yersinia as target protein. The structure of a peptide encompassing the amphipathic domain (residue 278-300) of the protein YopD from Yersinia was determined by NMR in 40% TFE. The structure of YopD278-300 is a well defined α-helix with a β-turn at the C-terminus of the helix capping the structure. This turn is crucial for the structure as peptides lacking the residues involved in the turn are unstructured. NMR relaxation indicates that the peptide is not monomeric. This is supported by intermolecular NOEs found from residue Phe280 to Ile288 and Val292 indicative of a multimeric structure with the helical structures oriented in an antiparallel manner with hydrophobic residues forming the oligomer. The interaction with the chaperone LcrH was confirmed by 1H relaxation experiments and induced chemical shift changes in the peptide Protein-ligand interactions were investigated further in the second paper using a different approach. A wide range of substances were used in screening for affinity against the chaperones PapD and FimC from uropathogenic Escherichia coli using 1H relaxation NMR experiments, surface plasmon resonance and 19F NMR. Fluorine NMR proved to be advantageous as compared to proton NMR as it is straight forward to identify binding ligands due to the well resolved 19F NMR spectra. Several compounds were found to interact with PapD and FimC through induced line-broadening and chemical shift changes for the ligands. Data corroborate well with surface plasmon resonance and proton NMR experiments. However, our results indicate the substances used in this study to have poor specificity for PapD and FimC as the induced chemical shift is minor and hardly no competitive binding is observed. Paper III and IV is an investigation of the structural features of the allergenic 2S albumin Ber e 1 from Brazil nut. Ber e 1 is a 2S albumin previously identified as the major allergen of Brazil nut. Recent studies have demonstrated that endogenous Brazil nut lipids are required for an immune response to occur in vivo. The structure was obtained from 3D heteronuclear NMR experiments followed by simulated annealing using the software ARIA. Interestingly, the common fold of the 2S albumin family, described as a right-handed super helix with the core composed of a helix bundle, is not found in Ber e 1. Instead the C-terminal region is participating in the formation of the core between helix 3, 4 and 5. The dynamic properties of Ber e 1 were investigated using 15N relaxation experiments and data was analyzed using the model-free approach. The analysis showed that a few residues in the loop between helix 2 and 3 experience decreased mobility, compared to the rest of the loop. This is consistent with NOE data as long range NOEs were found from the loop to the core region of the protein. The anchoring of this loop is a unique feature of Ber e 1, as it is not found in any other structures of 2S albumins. Chemical shift mapping of Ber e 1 upon the addition of lipid extract from Brazil nut identified 4 regions in the protein where chemical shift perturbations were detected. Interestingly, all four structural clusters align along a cleft in the structure formed by helix 1-3 on one side and helix 4-5 on the other. This cleft is big enough to encompass a lipid molecule. It is therefore tempting to speculate whether this cleft is the lipid binding epitope in Ber e 1.

SOUZA, Pedro Filho Noronha de.Purificação, caracterização bioquímica e atividade antimicrobiana de uma nova albumina 2s da torta da mamoneira (Ricinus communis L.), com atividade inibitória contra tripsina. 2012. 114 f. Dissertação (Mestrado em Bioquímica) - Universidade Federal do Ceará, Fortaleza-CE, 2012. / Submitted by Eric Santiago (erichhcl@gmail.com) on 2016-06-27T14:14:02Z No. of bitstreams: 1 2012_dis_pfnsouza.pdf: 1847174 bytes, checksum: 6675a05ab248cfb741080071e366161c (MD5) / Approved for entry into archive by José Jairo Viana de Sousa (jairo@ufc.br) on 2016-08-02T20:11:34Z (GMT) No. of bitstreams: 1 2012_dis_pfnsouza.pdf: 1847174 bytes, checksum: 6675a05ab248cfb741080071e366161c (MD5) / Made available in DSpace on 2016-08-02T20:11:34Z (GMT). No. of bitstreams: 1 2012_dis_pfnsouza.pdf: 1847174 bytes, checksum: 6675a05ab248cfb741080071e366161c (MD5) Previous issue date: 2012 / Castor bean (Ricinus communis L.) is an important crop for the Northeast of Brazil, which recently has been used to produce biodiesel. Around 90% of the castor bean production in Brazil is concentrated at Northeast region and the state of Ceará is the second largest producer. During the oil extraction process from the castor bean seeds, a resulting residue, called castor cake, is underutilized. However, this byproduct is rich in protein and micronutrients such as nitrogen, phosphorus and potassium, an attribute that qualifies it as a stuff that could be used as organic fertilizer or as animal feed, for example, bringing added value to it. Unfortunately, its use as food has not been possible because of the presence of toxic elements and allergens (ricin, ricinine, complex allergens) in its composition, unless it were previously submitted to a detoxification process. To date, the existing technologies to this end are not economically viable on an industrial scale. Therefore, studies to add value to this abundant byproduct generated in the castor bean biodiesel productive chain is of paramount importance. Thus, in this context, this study was performed to identify, isolate, purify and characterize new bioactive molecules of de-oiled castor cake with biotechnological potential. Through extraction of soluble proteins with 50 mM Tris-HCl pH 7.5, fractionation with ammonium sulfate (50-75%), following by hydrophobic interaction chromatography in Phenyl-Sepharose column and ion exchange chromatography (DEAE-Sepharose), a protein, named Rc-2S-Alb, able to inhibit trypsin was purified. Rc-2S-Alb has a molecular mass of approximately 75.8 kDa, as determined by SDS-PAGE, and under reducing conditions showed a large and a small protein band of 15.8 kDa and 10.5 kDa, respectively. Its NH2-terminal sequence showed similarity with the following proteins: putative 2S albumin precursor (89%), chain A of RicC3 (89%), and chain A of mabilin-1 (89%), all from R. communis seeds; and with the short chain of a "napin-like" protein from Brassica napus (89%). In addition, these similar proteins have two highly conserved domains: QEVQRKDLS and YLRQS. Comparison of the partial primary structure of Rc-2S-Alb generated by the ESI-Q-TOF MS/MS analysis of 17 tryptic peptides, showed 43% similarity to Mabinlin-1 (pI/Mr 6.7 and 29.3 kDa) from R. communis. There were also high similarities among the three-dimensional structures of Rc-2S-Alb, RicC3 and Mabinlin-1. Rc-2S-Alb did not inhibit the spore germination of the phytopathogenic fungi Fusarium oxysporum and Rizoctonia solani, but promoted aggregation of their respective spores. Moreover, Rc-2S-Alb did not inhibit the mycelial growth of Fusarium oxysporum, Fusarium solani, Rizoctonia solani and Collethotricum gloeosporioides. Contrary, Rc-2S-Alb was effective in inhibiting the growth of the human pathogenic bacteria Pseudomonas aeruginosae, Klebsiella pneumoniae and Bacillus subtilis, at low concentrations. In conclusion, it was established a protocol to purify a new 2S albumin from castor bean cake, which inhibits trypsin and has important antibacterial activity. Thus, the Rc-2S-Alb should be further studied in order to verify its effectiveness as new alternative therapeutic agent against resistant bacteria to commercial antibiotics, which will contribute to improve the human health. / A mamoneira (Ricinus communis L.) é uma cultura importante para a região Nordeste do Brasil, onde, recentemente, tem sido utilizada para produção de biodiesel. O Nordeste detém 90% da produção brasileira de mamona, sendo o Ceará, o segundo maior produtor. No processo de extração de óleo das sementes de mamoneira para produção de biodiesel, o resíduo resultante, denominado de torta da mamona, representa um subproduto pouco utilizado. Apesar disso, essa torta é rica em proteínas e micronutrientes, como nitrogênio, fósforo e potássio, atributo que a qualifica como um insumo que poderia ser utilizado como adubo orgânico, ou mesmo como ração animal, o que lhe agregaria valor comercial. Todavia, seu uso como alimento não tem sido possível por causa da presença de elementos tóxicos e alergênicos (Ricina, Ricinina, Complexos Alergênicos) na sua composição, a não ser que passasse por processamento para sua destoxificação. Infelizmente, tecnologia economicamente viável para esse fim, em escala industrial, ainda é inexistente. Portanto, há necessidade de pesquisas que venham a agregar valor a esse subproduto abundante da cadeia produtiva do biodiesel. Assim, nesse contexto, o presente trabalho está inserido num projeto cujo objetivo maior é identificar, isolar, purificar e caracterizar novas moléculas bioativas da torta delipidada de sementes de mamoeira com potencial biotecnológico. Através de extração de proteínas solúveis com tampão Tris-HCl, 50 mM, pH 7,5, e fracionamento do extrato obtido com sulfato de amônio (50-75%), cromatografia de interação hidrofóbica em coluna Phenyl-Sepharose e cromatografia de troca iônica (DEAE-Sepharose) foi possível purificar uma albumina 2S, denominada Rc-2S-Alb, capaz de inibir tripsina. A Rc-2S-Alb apresentou massa molecular de, aproximadamente, 75,8 kDa, determinada por SDS-PAGE, mas, em condições redutoras, apareceu como uma banda maior de 15,8 kDa e outra menor com 10,5 kDa. Sua sequência NH2-terminal revelou haver similaridade (89%) com o precursor putativo da albumina 2S de R. communis já descrita, com a cadeia A da estrutura da RicC3 (89%), com a cadeia A da mabilin-1, ambas, também, de R. communis (89%), com a cadeia pequena de uma proteina “napin-like”de Brassica napus (89%). Em todas essas proteínas similares, dois domínios, QEVQRKDLS e YLRQS, são altamente conservados. Comparação da estrutura primária gerada por ESI-Q-TOF MS/MS, a apartir de 17 peptídeos trípticos da Rc-2S-Alb, mostrou similaridade de 43% com a Mabinlin-1 (pI/Mr de 6,7 e 29.3 kDa) de R. communis. Em relação à estrutura tridimensional da Rc-2S-Alb, ela apresentou similaridade com a de Ric C3 e Mabinlin-1. A Rc-2S-Alb foi incapaz de inibir a germinação de esporos dos fungos fitopatogênicos Fusarium oxysporum e Rizoctonia solani, mas foi capaz de promover a aglomeração dos mesmos. A Rc-2S-Alb também não foi capaz de inibir o crescimento micelial dos fungos Fusarium oxysporum, Fusarium solani, Rizoctonia solani e Collethotricum gloeosporioides. Por outro lado, a Rc-2S-Alb foi eficiente em inibir o crescimento de Pseudomonas aeruginosae, Klebsiella pneumoniae e Bacillus subtilis, todas as bactérias patogênicas a seres humanos, quando em baixas concentrações. Como conclusão, foi possível a purificação de uma nova albumina 2S da torta da mamona, capaz de inibir tripsina e com atividade antibacteriana importante. Assim, a Rc-2S-Alb deve ser explorada no sentido de verificar sua eficácia como um novo agente terapêutico alternativo no combate a bactérias resistentes aos produtos disponíveis, hoje, no mercado, o que, se confirmado, poderá contribuir para a melhoria da saúde humana.

CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior / Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico / FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico / Castor bean (Ricinus communis L.) is an important crop for the Northeast of Brazil, which recently has been used to produce biodiesel. Around 90% of the castor bean production in Brazil is concentrated at Northeast region and the state of Cearà is the second largest producer. During the oil extraction process from the castor bean seeds, a resulting residue, called castor cake, is underutilized. However, this byproduct is rich in protein and micronutrients such as nitrogen, phosphorus and potassium, an attribute that qualifies it as a stuff that could be used as organic fertilizer or as animal feed, for example, bringing added value to it. Unfortunately, its use as food has not been possible because of the presence of toxic elements and allergens (ricin, ricinine, complex allergens) in its composition, unless it were previously submitted to a detoxification process. To date, the existing technologies to this end are not economically viable on an industrial scale. Therefore, studies to add value to this abundant byproduct generated in the castor bean biodiesel productive chain is of paramount importance. Thus, in this context, this study was performed to identify, isolate, purify and characterize new bioactive molecules of de-oiled castor cake with biotechnological potential. Through extraction of soluble proteins with 50 mM Tris-HCl pH 7.5, fractionation with ammonium sulfate (50-75%), following by hydrophobic interaction chromatography in Phenyl-Sepharose column and ion exchange chromatography (DEAE-Sepharose), a protein, named Rc-2S-Alb, able to inhibit trypsin was purified. Rc-2S-Alb has a molecular mass of approximately 75.8 kDa, as determined by SDS-PAGE, and under reducing conditions showed a large and a small protein band of 15.8 kDa and 10.5 kDa, respectively. Its NH2-terminal sequence showed similarity with the following proteins: putative 2S albumin precursor (89%), chain A of RicC3 (89%), and chain A of mabilin-1 (89%), all from R. communis seeds; and with the short chain of a "napin-like" protein from Brassica napus (89%). In addition, these similar proteins have two highly conserved domains: QEVQRKDLS and YLRQS. Comparison of the partial primary structure of Rc-2S-Alb generated by the ESI-Q-TOF MS/MS analysis of 17 tryptic peptides, showed 43% similarity to Mabinlin-1 (pI/Mr 6.7 and 29.3 kDa) from R. communis. There were also high similarities among the three-dimensional structures of Rc-2S-Alb, RicC3 and Mabinlin-1. Rc-2S-Alb did not inhibit the spore germination of the phytopathogenic fungi Fusarium oxysporum and Rizoctonia solani, but promoted aggregation of their respective spores. Moreover, Rc-2S-Alb did not inhibit the mycelial growth of Fusarium oxysporum, Fusarium solani, Rizoctonia solani and Collethotricum gloeosporioides. Contrary, Rc-2S-Alb was effective in inhibiting the growth of the human pathogenic bacteria Pseudomonas aeruginosae, Klebsiella pneumoniae and Bacillus subtilis, at low concentrations. In conclusion, it was established a protocol to purify a new 2S albumin from castor bean cake, which inhibits trypsin and has important antibacterial activity. Thus, the Rc-2S-Alb should be further studied in order to verify its effectiveness as new alternative therapeutic agent against resistant bacteria to commercial antibiotics, which will contribute to improve the human health. / A mamoneira (Ricinus communis L.) à uma cultura importante para a regiÃo Nordeste do Brasil, onde, recentemente, tem sido utilizada para produÃÃo de biodiesel. O Nordeste detÃm 90% da produÃÃo brasileira de mamona, sendo o CearÃ, o segundo maior produtor. No processo de extraÃÃo de Ãleo das sementes de mamoneira para produÃÃo de biodiesel, o resÃduo resultante, denominado de torta da mamona, representa um subproduto pouco utilizado. Apesar disso, essa torta à rica em proteÃnas e micronutrientes, como nitrogÃnio, fÃsforo e potÃssio, atributo que a qualifica como um insumo que poderia ser utilizado como adubo orgÃnico, ou mesmo como raÃÃo animal, o que lhe agregaria valor comercial. Todavia, seu uso como alimento nÃo tem sido possÃvel por causa da presenÃa de elementos tÃxicos e alergÃnicos (Ricina, Ricinina, Complexos AlergÃnicos) na sua composiÃÃo, a nÃo ser que passasse por processamento para sua destoxificaÃÃo. Infelizmente, tecnologia economicamente viÃvel para esse fim, em escala industrial, ainda à inexistente. Portanto, hà necessidade de pesquisas que venham a agregar valor a esse subproduto abundante da cadeia produtiva do biodiesel. Assim, nesse contexto, o presente trabalho està inserido num projeto cujo objetivo maior à identificar, isolar, purificar e caracterizar novas molÃculas bioativas da torta delipidada de sementes de mamoeira com potencial biotecnolÃgico. AtravÃs de extraÃÃo de proteÃnas solÃveis com tampÃo Tris-HCl, 50 mM, pH 7,5, e fracionamento do extrato obtido com sulfato de amÃnio (50-75%), cromatografia de interaÃÃo hidrofÃbica em coluna Phenyl-Sepharose e cromatografia de troca iÃnica (DEAE-Sepharose) foi possÃvel purificar uma albumina 2S, denominada Rc-2S-Alb, capaz de inibir tripsina. A Rc-2S-Alb apresentou massa molecular de, aproximadamente, 75,8 kDa, determinada por SDS-PAGE, mas, em condiÃÃes redutoras, apareceu como uma banda maior de 15,8 kDa e outra menor com 10,5 kDa. Sua sequÃncia NH2-terminal revelou haver similaridade (89%) com o precursor putativo da albumina 2S de R. communis jà descrita, com a cadeia A da estrutura da RicC3 (89%), com a cadeia A da mabilin-1, ambas, tambÃm, de R. communis (89%), com a cadeia pequena de uma proteina ânapin-likeâde Brassica napus (89%). Em todas essas proteÃnas similares, dois domÃnios, QEVQRKDLS e YLRQS, sÃo altamente conservados. ComparaÃÃo da estrutura primÃria gerada por ESI-Q-TOF MS/MS, a apartir de 17 peptÃdeos trÃpticos da Rc-2S-Alb, mostrou similaridade de 43% com a Mabinlin-1 (pI/Mr de 6,7 e 29.3 kDa) de R. communis. Em relaÃÃo à estrutura tridimensional da Rc-2S-Alb, ela apresentou similaridade com a de Ric C3 e Mabinlin-1. A Rc-2S-Alb foi incapaz de inibir a germinaÃÃo de esporos dos fungos fitopatogÃnicos Fusarium oxysporum e Rizoctonia solani, mas foi capaz de promover a aglomeraÃÃo dos mesmos. A Rc-2S-Alb tambÃm nÃo foi capaz de inibir o crescimento micelial dos fungos Fusarium oxysporum, Fusarium solani, Rizoctonia solani e Collethotricum gloeosporioides. Por outro lado, a Rc-2S-Alb foi eficiente em inibir o crescimento de Pseudomonas aeruginosae, Klebsiella pneumoniae e Bacillus subtilis, todas as bactÃrias patogÃnicas a seres humanos, quando em baixas concentraÃÃes. Como conclusÃo, foi possÃvel a purificaÃÃo de uma nova albumina 2S da torta da mamona, capaz de inibir tripsina e com atividade antibacteriana importante. Assim, a Rc-2S-Alb deve ser explorada no sentido de verificar sua eficÃcia como um novo agente terapÃutico alternativo no combate a bactÃrias resistentes aos produtos disponÃveis, hoje, no mercado, o que, se confirmado, poderà contribuir para a melhoria da saÃde humana.