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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
24/11/2010 |
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Data da última atualização: |
23/05/2011 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
RIBEIRO, C.; TOGAWA, R. C.; NESHICH, I. A. P.; MAZONI, I.; MANCINI, A. L.; MINARDI, R. C. de M.; SILVEIRA, C. H. da; JARDINE, J. G.; SANTORO, M. M.; NESHICH, G. |
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Afiliação: |
CRISTINA RIBEIRO, UFMG; ROBERTO C. TOGAWA, CENARGEN; IZABELLA A. P. NESHICH, Estagiária/CNPTIA; IVAN MAZONI, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; RAQUEL C. DE MELO MINARDI, UFMG; CARLOS H. DA SILVEIRA, UNIFEI; JOSE GILBERTO JARDINE, CNPTIA; MARCELO M. SANTORO, UFMG; GORAN NESHICH, CNPTIA. |
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Título: |
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
BMC Structural Biology, London, v. 10, n. 36, p. 1-16, 2010. |
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Idioma: |
Inglês |
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Conteúdo: |
Background: Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes. Results: We propose a novel method for describing binding properties and delineating serine proteases specificity by compiling an exhaustive table of interface forming residues (IFR) for serine proteases and their inhibitors. Currently, the Protein Data Bank (PDB) does not contain all the data that our analysis would require. Therefore, an in silico approach was designed for building corresponding complexes The IFRs are obtained by ?rigid body docking? among 70 structurally aligned, sequence wise non-redundant, serine protease structures with 3 inhibitors: bovine pancreatic trypsin inhibitor (BPTI), ecotine and ovomucoid third domain inhibitor. The table (matrix) of all amino acid positions at the interface and their respective occupancy is created. We also developed a new computational protocol for predicting IFRs for those complexes which were not deciphered experimentally so far, achieving accuracy of at least 0.97. Conclusions: The serine proteases interfaces prefer polar (including glycine) residues (with some exceptions). Charged residues were found to be uniquely prevalent at the interfaces between the ?miscellaneous-virus? subfamily and the three inhibitors. This prompts speculation about how important this difference in IFR characteristics is for maintaining virulence of those organisms. Our work here provides a unique tool for both structure/function relationship analysis as well as a compilation of indicators detailing how the specificity of various serine proteases may have been achieved and/or could be altered. It also indicates that the interface forming residues which also determine specificity of serine protease sub-family can not be presented in a canonical way but rather as a matrix of alternative populations of amino acids occupying variety of IFR positions. MenosBackground: Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes. Results: We propose a novel method for describing binding properties and delineating serine proteases specificity by compiling an exhaustive table of interface forming residues (IFR) for serine proteases and their inhibitors. Currently, the Protein Data Bank (PDB) does not contain all the data that our analysis would require. Therefore, an in silico approach was designed for building corresponding complexes The IFRs are obtained by ?rigid body docking? among 70 structurally aligned, sequence wise non-redundant, serine protease structures with 3 inhibitors: bovine pancreatic trypsin inhibitor (BPTI), ecotine and ovomuco... Mostrar Tudo |
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Palavras-Chave: |
Enzimas; Interface Forming Residues; Propriedades ligantes; Proteases. |
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Thesaurus Nal: |
Binding properties; Enzymes. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/23695/1/1472-6807-10-36.pdf
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Marc: |
LEADER 03631naa a2200301 a 4500
001 1867859
005 2011-05-23
008 2010 bl uuuu u00u1 u #d
100 1 $aRIBEIRO, C.
245 $aAnalysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.$h[electronic resource]
260 $c2010
520 $aBackground: Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes. Results: We propose a novel method for describing binding properties and delineating serine proteases specificity by compiling an exhaustive table of interface forming residues (IFR) for serine proteases and their inhibitors. Currently, the Protein Data Bank (PDB) does not contain all the data that our analysis would require. Therefore, an in silico approach was designed for building corresponding complexes The IFRs are obtained by ?rigid body docking? among 70 structurally aligned, sequence wise non-redundant, serine protease structures with 3 inhibitors: bovine pancreatic trypsin inhibitor (BPTI), ecotine and ovomucoid third domain inhibitor. The table (matrix) of all amino acid positions at the interface and their respective occupancy is created. We also developed a new computational protocol for predicting IFRs for those complexes which were not deciphered experimentally so far, achieving accuracy of at least 0.97. Conclusions: The serine proteases interfaces prefer polar (including glycine) residues (with some exceptions). Charged residues were found to be uniquely prevalent at the interfaces between the ?miscellaneous-virus? subfamily and the three inhibitors. This prompts speculation about how important this difference in IFR characteristics is for maintaining virulence of those organisms. Our work here provides a unique tool for both structure/function relationship analysis as well as a compilation of indicators detailing how the specificity of various serine proteases may have been achieved and/or could be altered. It also indicates that the interface forming residues which also determine specificity of serine protease sub-family can not be presented in a canonical way but rather as a matrix of alternative populations of amino acids occupying variety of IFR positions.
650 $aBinding properties
650 $aEnzymes
653 $aEnzimas
653 $aInterface Forming Residues
653 $aPropriedades ligantes
653 $aProteases
700 1 $aTOGAWA, R. C.
700 1 $aNESHICH, I. A. P.
700 1 $aMAZONI, I.
700 1 $aMANCINI, A. L.
700 1 $aMINARDI, R. C. de M.
700 1 $aSILVEIRA, C. H. da
700 1 $aJARDINE, J. G.
700 1 $aSANTORO, M. M.
700 1 $aNESHICH, G.
773 $tBMC Structural Biology, London$gv. 10, n. 36, p. 1-16, 2010.
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Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 178 | |
| 101. |  | GRYNBERG, P.; TOGAWA, R. C.; FREITAS, L. D. de; ANTONINO, J. D.; RANCUREL, C.; COSTA, M. M. do C.; GROSSI-DE-SA, M. F.; MILLER, R. N. G.; BRASILEIRO, A. C. M.; GUIMARAES, P. M.; DANCHIN, E. G. J. Comparative genomics reveals novel target genes towards specific control of plant-parasitic nematodes. Genes, v. 11, 1347, 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 102. | | NORIEGA, D. D.; ARRAES, F. B. M.; ANTONINO, J. D.; MACEDO, L. L. P.; FONSECA, F. C. A.; TOGAWA, R. C.; GRYNBERG, P.; SILVA, M. C. M.; NEGRISOLI JUNIOR, A. S.; MORGANTE, C. V.; GROSSI-DE-SA, M. F. Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source. PLoS ONE, v. 15, n. 8, e0235575, 2020.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia; Embrapa Semiárido; Embrapa Tabuleiros Costeiros. |
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| 103. | | MOTA, A. P. Z.; VIDIGAL, B.; DANCHIN, E. G. J.; TOGAWA, R. C.; BERTIOLI, S. C. de M. L.; BERTIOLI, D. J.; ARAUJO, A. C. G. de; BRASILEIRO, A. C. M.; GUIMARAES, P. M. Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. BMC Plant Biology, v. 18, n. 1, 159, 2018. Na publicação: Soraya C. M. Leal-Bertioli; Ana Claudia Guerra Araujo e Patricia Messenberg Guimaraes.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 104. | | FALCAO, L. L.; WERNECK, J. O. S.; ALBUQUERQUE, P. S. B.; ALVES, R. M.; GRYNBERG, P.; TOGAWA, R. C.; COSTA, M. M. do C.; BRIGIDO, M. M.; MARCELLINO, L. H. Comparative transcriptomics of cupuassu (Theobroma grandiflorum) offers insights into the early defense mechanism to Moniliophthora perniciosa, the causal agent of witches' broom disease. Journal of Plant Interactions, v. 17, n. 1, p. 991-1005, 2022. Na publicação; Joseilde Oliveira Silva-Werneck.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Amazônia Oriental; Embrapa Recursos Genéticos e Biotecnologia. |
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| 105. | | CRAVEIRO, S. R.; INGLIS, P. W.; MONTEIRO, L. L. S.; SANTOS, L. A. V. M.; TOGAWA, R. C.; RIBEIRO, Z. M. A.; RIBEIRO, B. M.; CASTRO, M. E. B. Complete genome sequences of seven new Chrysodeixis includens nucleopolyhedrovirus isolates from Minas Gerais and Mato Grosso States in Brazil. Microbiology Resource Announcements, v. 9, n. 8, e01501-19, 2020.| Tipo: Nota Técnica/Nota Científica |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 106. | | SANTOS, M. P. dos; MOTA, A. P. Z.; TOGAWA, R. C.; MARTINS, N. F.; NASCIMENTO, E. F. de M. B. do; LUCENA, V. S.; CASTELLANI, M. A.; FREIRE, E. V. S. A.; HILLIOU, F. The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily. Scientific Reports, v. 14,7119, 2024. Na publicação: Erika Valéria Saliba Albuquerque.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agroindústria Tropical; Embrapa Recursos Genéticos e Biotecnologia. |
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| 107. | | CARVALHO, N.; LEITE, P. H. dos S.; CANELA, F. M.; DUSI, D. M. de A.; TOGAWA, R. C.; AMARAL, Z. P. de S.; CHIARI, L.; CARNEIRO, V. T. de C.; BUSO, G. S. C. Caracterização e otimização de Primers SSR para B.brizantha, B.humidicola e B.decumbens. In: CONGRESSO BRASILEIRO DE RECURSOS GENÉTICOS, 4., 2016, Curitiba. Recursos genéticos no Brasil: a base para o desenvolvimento sustentável: anais. Brasília, DF: Sociedade Brasileira de Recursos Genéticos, 2016.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 108. | | SARTOR, T.; FALAVIGNA, V. da S.; CATTANI, A. M.; SILVEIRA, C. P.; MALABARBA, J.; PORTO, D. D.; GRYNBERG, P.; TOGAWA, R. C.; COSTA, M. M. do C.; SANTOS, H. P. dos; PASQUALI, G.; REVERS, L. F. Caracterização da função do gene FLC-LIKE durante a transição da ENDO- para dormência na macieira. In: SIMPÓSIO BRASILEIRO DE GENÉTICA MOLECULAR DE PLANTAS, 8, 2023, Florianópolis, SC. Anais...FLorianópolis: SBG, 30 de maio a 2 de junho de 2023. p. 67| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Uva e Vinho. |
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| 109. | | SARTOR, T.; FALAVIGNA, V. da S.; CATTANI, A. M.; SILVEIRA, C. P.; MALABARBA, J.; PORTO, D. D.; GRYNBERG, P.; TOGAWA, R. C.; COSTA, M. M. do C.; SANTOS, H. P. dos; PASQUALI, G.; REVERS, L. F. Caracterização da função do gene FLC-LIKE durante a transição da Endo- para ecodormencia na macieira. In: SIMPÓSIO BRASILEIRO DE GENÉTICA MOLECULAR DE PLANTAS, 8, 2023, Florianópolis, SC. Anais...Florianópolis: SBG, 2023. p. 67.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia; Embrapa Semiárido. |
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| 110. | | ARAÚJO, J. F.; CASTRO, A. R. de; COSTA, M. M. do C.; TOGAWA, R. C.; PAPPAS JUNIOR, G. J.; QUIRINO, B. F.; BUSTAMANTE, M. M. C.; WILLIAMSON, L.; HANDELSMAN, J.; KRUGER, R. H. Characterization of soil bacterial assemblies in Brazilian Savanna-Like vegetation reveals acidobacteria dominance. Microbial Ecology, v. 64, p. 760-770, 2012.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 5 |
| Biblioteca(s): Embrapa Agroenergia; Embrapa Recursos Genéticos e Biotecnologia. |
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| 111. | | HIGA, R. H.; MONTAGNER, A. J.; TOGAWA, R. C.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; MANCINI, A. L.; PAPPAS JUNIOR, G.; MIURA, R. T.; HORITA, L. G.; NESHICH, G. ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure. Bioinformatics, v. 20, n. 12, p. 1983-1985, 2004. Na publicação: P. R. Kuser.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 112. | | FIRMINO, A. A. P.; FONSECA, F. C. A.; MACEDO, L. L. P.; TOGAWA, R. C.; SILVA JUNIOR, O. B. da; PAPPAS JUNIOR, G. J.; SA, M. F. G. de. Cotton boll weevil (Anthonomus Grandis) transcriptome pyrosequencing and insect-pest control by RNAI gene silencing. In: CONGRESSO BRASILEIRO DE BIOTECNOLOGIA, 3., 2010, Fortaleza. Programa e resumos. Brasília, DF: SBBiotec, 2010. p. 279.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 113. | | HIGA, R. H.; OLIVEIRA, A. G.; HORITA, L. G.; MIURA, R. T.; INOUE, M. K.; FALCAO, P. R. K.; MANCINI, A. L.; YAMAGISHI, M. E. B.; TOGAWA, R. C.; NESHICH, G. Defining 3D residue environment in protein structures using SCORPION and FORMIGA. Bioinformatics, v. 20, n. 12, p. 1989-1991, 2004. Na publicação: P. R. Kuser.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 114. | | MOTA, A. P. Z.; BRASILEIRO, A. C. M.; VIDIGAL, B.; OLIVEIRA, T. N.; MARTINS, A. da C. Q.; SARAIVA, M. A. de P.; ARAUJO, A. C. G. de; TOGAWA, R. C.; SA, M. F. G. de; GUIMARAES, P. M. Defining the combined stress response in wild Arachis. Scientific Reports, v. 11, n. 1, 11097, 2021. Na publicação: Maria Fatima Grossi-de-Sá.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 115. | | MATOS, C. B.; FRAGOSO, R. da R.; ANDRADE, L. R. M. de; CORDEIRO, M. C. R.; SILVA, M. S.; TOGAWA, R. C.; ALMEIDA, J. D. de; BARROS, L. M. G. Estratégia para identificação de genes de resistência ao alumínio em planta nativa do cerrado sclerolobium paniculatum. In: ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 14., 2009, Brasília, DF. [Resumos...] Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Cerrados. |
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| 116. | | SALGADO, F. F.; VIEIRA, L. R.; SILVA, V. N. B.; LEAO, A. P.; GRYNBERG, P.; COSTA, M. M. do C.; TOGAWA, R. C.; SOUSA, C. A. F. de; SOUZA JUNIOR, M. T. Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress. BMC Plant Biology, v. 21, n. 518, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agroenergia; Embrapa Meio-Norte. |
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| 117. | | SALGADO, F. F.; VIEIRA, L. R.; SILVA, V. N. B.; LEAO, A. P.; GRYNBERG, P.; COSTA, M. M. do C.; TOGAWA, R. C.; SOUSA, C. A. F. de; SOUZA JUNIOR, M. T. Expression analysis of miRNAs and their putative target genes confrm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress. BMC Plant Biology, v. 21, 518, 2021.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 118. | | MARTEL, C. M.; WARRILOW, A. G. S.; JACKSON, C. J.; MULLINS, J. G. L.; TOGAWA, R. C.; PARKER, J. E.; MORRIS, M. S.; DONNISON, I. S.; KELLY, D. E.; KELLY, S. L. Expression, purification and use of the soluble domain of Lactobacillus paracasei beta-fructosidase to optimise production of bioethanol from grass fructans. Bioresource Technology, v. 101, p. 4395-4402, 2010.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 119. | | RABELLO, A. R.; RANGEL, P. H. N.; GUIMARÃES, C. M.; SALES, R. M. O. B.; SILVA, F. R.; COSTA, M. M. C.; TOGAWA, R. C.; FERREIRA, M. E.; MEHTA, A. Expressão diferencial em genótipos contrastantes de Oryza sativa para a tolerância a seca. In: ENCONTRO DO TALENTO ESTUDANTIL DA EMBRAPA RECURSOS GENÉTICOS E BIOTECNOLOGIA, 11., 2006, Brasília, DF. Anais: resumos dos trabalhos. Brasília, DF: Embrapa Recursos Genéticos e Biotecnologia, 2006. p. 77.| Tipo: Resumo em Anais de Congresso | Circulação/Nível: -- - -- |
| Biblioteca(s): Embrapa Arroz e Feijão; Embrapa Recursos Genéticos e Biotecnologia. |
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| 120. | | SANTOS, L. F. dos; FREGAPANI, R. M.; FALCAO, L. L.; TOGAWA, R. C.; COSTA, M. M. do C.; LOPES, U. V.; GRAMACHO, K. P.; ALVES, R. M.; MICHELI, F.; MARCELLINO, L. H. First microsatellite markers developed from cupuassu ESTs: application in diversity analysis and cross-species transferability to cacao. PLoS ONE, v. 11, n. 3, e0151074, 2016.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Amazônia Oriental; Embrapa Recursos Genéticos e Biotecnologia. |
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| Registros recuperados : 178 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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