51 research outputs found
The ionized methylene transfer from the distonic radical cation +CH2-O-CH2 to heterocyclic compounds. A pentaquadrupole mass spectrometric study
No full textIon-molecule reactions of the mass-selected distonic radical cation +CH2-O-CH2 (1) with several heterocyclic compounds have been investigated by multiple stage mass spectro- metric experiments performed in a pentaquadrupole mass spectrometer. Reactions with pyridine, 2-, 3-, and 4-ethyl, 2-methoxy, and 2-n-propyl pyridine occur mainly by transfer of CH2+ to the nitrogen, which yields distonic N-methylene-pyridinium radical cations. The MS3 spectra of these products display very characteristic collision-induced dissociation chemistry, which is greatly affected by the position of the substituent in the pyridine ring. Ortho isomers undergo a δ-cleavage cyclization process induced by the free-radical character of the N-methylene group that yields bicyclic pyridinium cations. On the other hand, extensive CH2+ transfer followed by rapid hydrogen atom loss, that is, a net CH+ transfer, occurs not to the heteroatoms, but to the aromatic ring of furan, thiophene, pyrrole, and N-methyl pyrrole. The reaction proceeds through five- to six-membered ring expansion, which yields the pyrilium, thiapyrilium, N-protonated, and N-methylated pyridine cations, respectively, as indicated by MS3 scans. Ion 1 fails to transfer CH2+ to tetrahydrofuran, whereas a new α-distonic sulfur ion is formed in reactions with tetrahydrothiophene. Unstable N-methylene distonic ions, likely formed by transfer of CH2+ to the nitrogen of piperidine and pyrrolidine, undergo rapid fragmentation by loss of the α-NH hydrogen to yield closed-shell immonium cations. The most thermodynamically favorable products are formed in these reactions, as estimated by ab initio calculations at the MP2/6-31G(d,p)//6- 31G(d,p) + ZPE level of theory
TopoLink: A software to validate structural models using chemical crosslinking constraints
No full textAlgoritmo para identificação de peptídeos covalentemente ligados e analisados por espectrometria de massas
No full textO estudo de estruturas e interações proteicas é uma importante área de pesquisa para se entender as funções das proteínas. No entanto, essa é também uma das áreas de grandes desafios experimentais, devido à inerente complexidade atômica de proteínas e peptídeos. Os métodos de elucidação estrutural de alta resolução (e.g. difração de raios-X e RMN) são hoje os considerados “padrões-ouro” para esses tipos
de estudos. No entanto, uma grande parte das proteínas e seus respectivos complexos não são passíveis de serem resolvidos por esses métodos, motivando o desenvolvimento de novas técnicas para a caracterização estrutural de proteínas e seus complexos. Neste sentido, a espectrometria de massas acoplada à técnica de crosslinking (XL-MS) é uma grande promessa, devido às suas características intrínsecas, tais como alta sensibilidade e ampla aplicabilidade. Neste trabalho, desenvolveu-se um software com aplicações pioneiras, denominado SIM-XL, capaz de identificar peptídeos covalentemente ligados e analisados por espectrometria de massas, a fim de caracterizar estruturas de proteínas, bem como de complexos proteínas-proteínas e proteína-peptídeo. Esse software faz uso de técnicas de reconhecimento de padrões para resolver um gargalo na modelagem proteica e interação proteína-proteína. Portanto, o algoritmo aqui apresentado, traz benefícios imediatos nas áreas de biologia e biotecnologia e indiretamente, em diversas outras áreas, como por exemplo, no desenvolvimento de novos fármacos.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de
Desenvolvimento Científico e Tecnológico (CNPq), Programa de Apoio à Pesquisa Estratégica em Saúde (Papes) da Fiocruz, Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Microsoft Research.The study of protein structures and interactions is an important area of development for understanding the function of proteins. However, this is also an area of great experimental challenge, due to the inherent atomic complexity of proteins and peptides. The methods of structural elucidation of high-resolution (e.g. X-ray
diffraction and NMR) are currently considered the “gold standard” for these types of studies. However, many proteins are not amendable to being solved by these methods; thus motivating the development of new techniques for structural characterization of proteins and their complexes. In this regard, mass spectrometry coupled by crosslinking technique (XL-MS) poses as a promise to overcome these limitations as it
provides a high sensitivity and wide applicability. Here we present SIM-XL, a software pioneer in many ways, capable of identifying cross-linked peptides analyzed by mass spectrometry and thus ultimately aiding in structural characterization and in determining protein-protein interactions. Our software uses pattern recognition strategies to address a bottleneck in protein modeling and protein-protein interaction.
As such, various fields related to biology and biotechnology suffer an immediate benefit from this work, and other areas, say, the development of new drugs, are indirectly benefited as well
Algoritmo para identificação de peptídeos covalentemente ligados e analisados por espectrometria de massas
No full textCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Conselho Nacional de
Desenvolvimento Científico e Tecnológico (CNPq), Programa de Apoio à Pesquisa Estratégica em Saúde (Papes) da Fiocruz, Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), Microsoft Research.Instituto Carlos Chagas, Fiocruz-PR, Curitiba, PR, BrasilO estudo de estruturas e interações proteicas é uma importante área de pesquisa para se entender as funções das proteínas. No entanto, essa é também uma das áreas de grandes desafios experimentais, devido à inerente complexidade atômica de proteínas e peptídeos. Os métodos de elucidação estrutural de alta resolução (e.g. difração de raios-X e RMN) são hoje os considerados “padrões-ouro” para esses tipos
de estudos. No entanto, uma grande parte das proteínas e seus respectivos complexos não são passíveis de serem resolvidos por esses métodos, motivando o desenvolvimento de novas técnicas para a caracterização estrutural de proteínas e seus complexos. Neste sentido, a espectrometria de massas acoplada à técnica de crosslinking (XL-MS) é uma grande promessa, devido às suas características intrínsecas, tais como alta sensibilidade e ampla aplicabilidade. Neste trabalho, desenvolveu-se um software com aplicações pioneiras, denominado SIM-XL, capaz de identificar peptídeos covalentemente ligados e analisados por espectrometria de massas, a fim de caracterizar estruturas de proteínas, bem como de complexos proteínas-proteínas e proteína-peptídeo. Esse software faz uso de técnicas de reconhecimento de padrões para resolver um gargalo na modelagem proteica e interação proteína-proteína. Portanto, o algoritmo aqui apresentado, traz benefícios imediatos nas áreas de biologia e biotecnologia e indiretamente, em diversas outras áreas, como por exemplo, no desenvolvimento de novos fármacos.The study of protein structures and interactions is an important area of development for understanding the function of proteins. However, this is also an area of great experimental challenge, due to the inherent atomic complexity of proteins and peptides. The methods of structural elucidation of high-resolution (e.g. X-ray
diffraction and NMR) are currently considered the “gold standard” for these types of studies. However, many proteins are not amendable to being solved by these methods; thus motivating the development of new techniques for structural characterization of proteins and their complexes. In this regard, mass spectrometry coupled by crosslinking technique (XL-MS) poses as a promise to overcome these limitations as it
provides a high sensitivity and wide applicability. Here we present SIM-XL, a software pioneer in many ways, capable of identifying cross-linked peptides analyzed by mass spectrometry and thus ultimately aiding in structural characterization and in determining protein-protein interactions. Our software uses pattern recognition strategies to address a bottleneck in protein modeling and protein-protein interaction.
As such, various fields related to biology and biotechnology suffer an immediate benefit from this work, and other areas, say, the development of new drugs, are indirectly benefited as well
Proteomic analysis of papaya fruit ripening using 2DE-DIGE
No full textCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Papayas have a very short green life as a result of their rapid pulp softening as well as their susceptibility to physical injury and mold growth. The ripening-related changes take place very quickly, and there is a continued interest in the reduction of postharvest losses. Proteins have a central role in biological processes, and differential proteomics enables the discrimination of proteins affected during papaya ripening. A comparative analysis of the proteomes of climacteric and pre-climacteric papayas was performed using 2DE-DIGE. Third seven proteins corresponding to spots with significant differences in abundance during ripening were submitted to MS analysis, and 27 proteins were identified and classified into six main categories related to the metabolic changes occurring during ripening. Proteins from the cell wall (alpha-galactosidase and invertase), ethylene biosynthesis (methionine synthase), climacteric respiratory burst, stress response, synthesis of carotenoid precursors (hydroxymethylbutenyl 4-diphosphate synthase, GcpE), and chromoplast differentiation (fibrillin) were identified. There was some correspondence between the identified proteins and the data from previous transcript profiling of papaya fruit, but new, accumulated proteins were identified, which reinforces the importance of differential proteomics as a tool to investigate ripening and provides potentially useful information for maintaining fruit quality and minimizing postharvest losses. (C) 2011 Elsevier B.V. All rights reserved.75414281439Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq
Proteomic analysis of papaya fruit ripening using 2DE-DIGE
No full textPapayas have a very short green life as a result of their rapid pulp softening as well as their susceptibility to physical injury and mold growth. The ripening-related changes take place very quickly, and there is a continued interest in the reduction of postharvest losses. Proteins have a central role in biological processes, and differential proteomics enables the discrimination of proteins affected during papaya ripening. A comparative analysis of the proteomes of climacteric and pre-climacteric papayas was performed using 2DE-DIGE. Third seven proteins corresponding to spots with significant differences in abundance during ripening were submitted to MS analysis, and 27 proteins were identified and classified into six main categories related to the metabolic changes occurring during ripening. Proteins from the cell wall (alpha-galactosidase and invertase), ethylene biosynthesis (methionine synthase), climacteric respiratory burst, stress response, synthesis of carotenoid precursors (hydroxymethylbutenyl 4-diphosphate synthase, GcpE), and chromoplast differentiation (fibrillin) were identified. There was some correspondence between the identified proteins and the data from previous transcript profiling of papaya fruit, but new, accumulated proteins were identified, which reinforces the importance of differential proteomics as a tool to investigate ripening and provides potentially useful information for maintaining fruit quality and minimizing postharvest losses75414281439CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPSem informação2008/52447-
Evaluation of some effects on plant metabolism through proteins and enzymes in transgenic and non-transgenic soybeans after cultivation with silver nanoparticles
No full textTo evaluate the effects of silver nanoparticles (AgNP) exposition, transgenic (through gene cp4EPSPS) and non-isogenic non-transgenic soybeans were cultivated in the presence or absence of AgNP or silver nitrate (AgNO3) at 50 mg/kg of silver. Physiological aspects of the plants including mass production and development of roots, proteomics such as protein amount and differential proteins, enzymes and lipid peroxidation were determined after exposition. The mass production of non-transgenic plants treated with AgNP or AgNO3 was decreased by 25 and 19%, respectively, on their mass based, while for transgenic soybean this effect was observed for AgNP cultivation only. Fifty-nine proteins were identified from the differentially abundant spots by two-dimensional difference gel electrophoresis and nano-electrospray ionization liquid chromatography coupled tandem mass spectrometry. Identified species as ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), ATP synthase, superoxide dismutase (SOD), related to plant metabolism were less abundant for the cultivation with either AgNP and AgNO3 than the control. Finally, this work demonstrated significant correlation as evidenced by changes in lipid peroxidation content and catalase activity, which were a result of exposure to either AgNP or AgNO3 cultivations. Further, necrotic areas in the basal part of the stems and damage or chlorotic areas were found in the leaves. Significance: Once nanoparticles have been employed for several applications in recent years and they can be released in the environmental matrices, this study highlights proteomic and enzymatic alterations in transgenic and non-transgenic soybeans, an important crop, after cultivation with silver nanoparticles. Such strategy employing proteomic and enzymatic approaches to evaluate soybeans exposed to silver nanoparticles has not yet been reported. Therefore, the results obtained in this study can expand the information concerning the effects of silver nanoparticles in soybean plants19188106CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP401170/2016-0sem informação2016/07384-7; 2013/15646-
Proteomic analysis of banana fruit reveals proteins that are differentially accumulated during ripening
No full textBananas (Musa spp.) are highly perishable fruit of notable economic and nutritional relevance. Because the identification of proteins involved in metabolic pathways could help to extend green-life and improve the quality of the fruit, this study aimed to compare the proteins of banana pulp at the pre-climacteric and climacteric stages. The use of two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed 50 differentially expressed proteins, and comparing those proteins to the Mass Spectrometry Protein Sequence Database (MSDB) identified 26 known proteins. Chitinases were the most abundant types of proteins in unripe bananas, and two isoforms in the ripe fruit have been implicated in the stress/defense response. In this regard, three heat shock proteins and isoflavone reductase were also abundant at the climacteric stage. Concerning fruit quality, pectate lyase, malate dehydrogenase, and starch phosphorylase accumulated during ripening. In addition to the ethylene formation enzyme amino cyclo carboxylic acid oxidase, the accumulation of S-adenosyl-L-homocysteine hydrolase was needed because of the increased ethylene synthesis and DNA methylation that occurred in ripening bananas. Differential analysis provided information on the ripening-associated changes that occurred in proteins involved in banana flavor, texture, defense, synthesis of ethylene, regulation of expression, and protein folding, and this analysis validated previous data on the transcripts during ripening. In this regard, the differential proteomics of fruit pulp enlarged our understanding of the process of banana ripening. (C) 2012 Elsevier B.V. All rights reserved.Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2008/52447-0]Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq
The SEB-1 Transcription Factor Binds to the STRE Motif in Neurospora crassa and Regulates a Variety of Cellular Processes Including the Stress Response and Reserve Carbohydrate Metabolism
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