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Registro Completo |
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Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
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Data corrente: |
05/01/2011 |
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Data da última atualização: |
03/06/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
RIBEIRO; 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 COITI TOGAWA, CENARGEN; IZABELLA A. P. NESHICH; 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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Notas: |
Disponível em:.Acesso em: 5 jan. 2011. |
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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 03733naa a2200313 a 4500
001 1871662
005 2024-06-03
008 2010 bl uuuu u00u1 u #d
100 1 $aRIBEIRO
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
500 $aDisponível em:<http://www.biomedcentral.com/1472-6807/10/36>.Acesso em: 5 jan. 2011.
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 Recursos Genéticos e Biotecnologia (CENARGEN) |
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Registro Completo
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Biblioteca(s): |
Embrapa Unidades Centrais. |
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Data corrente: |
14/04/2014 |
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Data da última atualização: |
30/03/2023 |
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Autoria: |
CRUZ, M. F. A. da; BUENO, R. D.; SOUZA, F. B. de; MOREIRA, M. A.; BARROS, E. G. de. |
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Afiliação: |
Maria Fernanda Antunes da Cruz, Universidade Federal de Viçosa (UFV), Departamento de Biologia Geral; Rafael Delmond Bueno, UFV, Departamento de Bioquímica e Biologia Molecular; Franciele Barros de Souza, UFV, Departamento de Bioquímica e Biologia Molecular; Maurilio Alves Moreira, UFV, Departamento de Bioquímica e Biologia Molecular; Everaldo Gonçalves de Barros, Universidade Federal de Viçosa (UFV), Departamento de Biologia Geral. |
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Título: |
Identificação de SNPs para conteúdo de ácido graxos em soja pela técnica HRM. |
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Ano de publicação: |
2013 |
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Fonte/Imprenta: |
Pesquisa Agropecuária Brasileira, Brasília, DF, v. 48, n. 12, p. 1596-1600, dez. 2013. |
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Idioma: |
Português |
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Notas: |
Notas científicas.
Título em inglês: Identification of SNPs for fatty acid content in soybean by the HRM technique. |
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Conteúdo: |
O objetivo deste trabalho foi identificar SNPs em genes associados ao conteúdo de ácidos graxos em soja e implementar a metodologia ?high resolution melting? (HRM) para genotipagem desses SNPs. Os iniciadores HRM foram desenhados para discriminar os alelos SNPs em duas populações e mapeamento (RILs e F2) e seguiram o padrão esperado de segregação. Os SNPs do gene ABI associaram-se significativamente ao conteúdo de ácido esteárico (R2=12,14), e os do gene FAD3B , aos conteúdos de ácido oleico (R2=14,69) e linolênico (R2= 10,62). A técnica de genotipagem dos SNPs por HRM é eficiente na discriminação das classes genotípicas. |
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Palavras-Chave: |
Genotipagem; Molecular markers; Poliformismo de nucleotídeo único; Seleção assistida por marcadores. |
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Thesagro: |
Marcador molecular; Melhoramento vegetal; Polimorfismo. |
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Thesaurus NAL: |
Genotyping; Plant breeding. |
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Categoria do assunto: |
-- |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/101052/1/Identificacao-de-SNPs.pdf
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Marc: |
LEADER 01652naa a2200289 a 4500
001 1984498
005 2023-03-30
008 2013 bl uuuu u00u1 u #d
100 1 $aCRUZ, M. F. A. da
245 $aIdentificação de SNPs para conteúdo de ácido graxos em soja pela técnica HRM.$h[electronic resource]
260 $c2013
500 $aNotas científicas. Título em inglês: Identification of SNPs for fatty acid content in soybean by the HRM technique.
520 $aO objetivo deste trabalho foi identificar SNPs em genes associados ao conteúdo de ácidos graxos em soja e implementar a metodologia ?high resolution melting? (HRM) para genotipagem desses SNPs. Os iniciadores HRM foram desenhados para discriminar os alelos SNPs em duas populações e mapeamento (RILs e F2) e seguiram o padrão esperado de segregação. Os SNPs do gene ABI associaram-se significativamente ao conteúdo de ácido esteárico (R2=12,14), e os do gene FAD3B , aos conteúdos de ácido oleico (R2=14,69) e linolênico (R2= 10,62). A técnica de genotipagem dos SNPs por HRM é eficiente na discriminação das classes genotípicas.
650 $aGenotyping
650 $aPlant breeding
650 $aMarcador molecular
650 $aMelhoramento vegetal
650 $aPolimorfismo
653 $aGenotipagem
653 $aMolecular markers
653 $aPoliformismo de nucleotídeo único
653 $aSeleção assistida por marcadores
700 1 $aBUENO, R. D.
700 1 $aSOUZA, F. B. de
700 1 $aMOREIRA, M. A.
700 1 $aBARROS, E. G. de
773 $tPesquisa Agropecuária Brasileira, Brasília, DF$gv. 48, n. 12, p. 1596-1600, dez. 2013.
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Embrapa Unidades Centrais (AI-SEDE) |
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