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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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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
08/02/2012 |
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Data da última atualização: |
05/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
B - 4 |
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Autoria: |
CUNHA, F. F. da; RAMOS, M. M.; ALENCAR, C. A. B. de; OLIVEIRA, R. A. de; ARAÚJO, R. A. S.; CECON, P. R.; MARTINS, C. E.; CÓSER, A. C. |
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Afiliação: |
FERNANDO FRANÇA DA CUNHA, UFMS; MÁRCIO MOTA RAMOS, UFV; CARLOS AUGUSTO BRASILEIRO DE ALENCAR, Universidade Vale do Rio Doce; RUBENS ALVES DE OLIVEIRA, UFV; RODRIGO ANTÔNIO SILVA ARAÚJO, Universidade Vale do Rio Doce; PAULO ROBERTO CECON, UFV; CARLOS EUGENIO MARTINS, CNPGL; ANTÔNIO CARLOS CÓSER, Pesquisador aposentado do CNPGL. |
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Título: |
Número de folhas do capim-xaraés em diferentes manejos e doses de adubação, intervalos de desfolha e estações anuais. |
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Ano de publicação: |
2011 |
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Fonte/Imprenta: |
Bioscience Journal, v. 27, n. 2, p. 271-282, 2011. |
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Idioma: |
Português |
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Conteúdo: |
Objetivou-se avaliar os efeitos de diferentes manejos e doses de adubação, intervalos de desfolha e estações anuais sobre as características morfogênicas do capim-xaraés. O experimento foi conduzido em esquema de parcelas sub-subdivididas, tendo nas parcelas um esquema fatorial 2 x 2, duas estações anuais (inverno e verão) e dois manejos de adubação (convencional e fertirrigação), nas subparcelas quatro intervalos de desfolha (21, 28, 35 e 42 dias) e nas sub-subparcelas seis doses de adubação (0, 15, 39, 64, 83 e 100% das doses de 700 e 560 kg de N e K2O, respectivamente), no delineamento inteiramente casualizado, com quatro repetições. As características morfogênicas foram estudadas por meio dos números de folhas emergentes (NFEm), expandidas (NFEx) e vivas (NFV). O capim-xaraés quando cultivado no inverno e adubado de forma convencional apresentou maior NFEx e NFV no intervalo de desfolha de 34 dias. Nas demais condições, o intervalo de desfolha proporcionou aumento linear no NFEx e NFV. O intervalo de desfolha não afetou o NFEm. O manejo da adubação não afetou e a estação verão e o aumento da dose de adubação proporcionaram aumento nas características morfogênicas. |
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Thesagro: |
Brachiaria Brizantha; Fertirrigação; Morfogênese. |
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Categoria do assunto: |
F Plantas e Produtos de Origem Vegetal |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/53652/1/Artigo-meta-2011-BioscJ-Caca-60313-6945.pdf
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Marc: |
LEADER 01966naa a2200241 a 4500
001 1914756
005 2024-02-05
008 2011 bl uuuu u00u1 u #d
100 1 $aCUNHA, F. F. da
245 $aNúmero de folhas do capim-xaraés em diferentes manejos e doses de adubação, intervalos de desfolha e estações anuais.$h[electronic resource]
260 $c2011
520 $aObjetivou-se avaliar os efeitos de diferentes manejos e doses de adubação, intervalos de desfolha e estações anuais sobre as características morfogênicas do capim-xaraés. O experimento foi conduzido em esquema de parcelas sub-subdivididas, tendo nas parcelas um esquema fatorial 2 x 2, duas estações anuais (inverno e verão) e dois manejos de adubação (convencional e fertirrigação), nas subparcelas quatro intervalos de desfolha (21, 28, 35 e 42 dias) e nas sub-subparcelas seis doses de adubação (0, 15, 39, 64, 83 e 100% das doses de 700 e 560 kg de N e K2O, respectivamente), no delineamento inteiramente casualizado, com quatro repetições. As características morfogênicas foram estudadas por meio dos números de folhas emergentes (NFEm), expandidas (NFEx) e vivas (NFV). O capim-xaraés quando cultivado no inverno e adubado de forma convencional apresentou maior NFEx e NFV no intervalo de desfolha de 34 dias. Nas demais condições, o intervalo de desfolha proporcionou aumento linear no NFEx e NFV. O intervalo de desfolha não afetou o NFEm. O manejo da adubação não afetou e a estação verão e o aumento da dose de adubação proporcionaram aumento nas características morfogênicas.
650 $aBrachiaria Brizantha
650 $aFertirrigação
650 $aMorfogênese
700 1 $aRAMOS, M. M.
700 1 $aALENCAR, C. A. B. de
700 1 $aOLIVEIRA, R. A. de
700 1 $aARAÚJO, R. A. S.
700 1 $aCECON, P. R.
700 1 $aMARTINS, C. E.
700 1 $aCÓSER, A. C.
773 $tBioscience Journal$gv. 27, n. 2, p. 271-282, 2011.
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