| |
|
|
| Registros recuperados : 80 | |
| 41. |  | FALCAO, P. R. K.; YAMAGISHI, M. E. B.; BORRO, L.; MANCINI, A. L.; HIGA, R. H.; NESHICH, G. Identification of folding essential residues by looking at an extensive DB of the structure descriptors in Diamond STING. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 13., 2005, Detroit. Program... Detroit: ISCB, 2005. p. 71. Na publicação: Paula Kuser; Michel Yamagishi; Adauto Mancini; Roberto Higa; Goran Neshich. ISMB 2005. Poster A-47.| Biblioteca(s): Embrapa Agricultura Digital. |
|    |
| 42. | | HIGA, R. H.; CRUZ, S. A. B. da; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; FILETO, R.; MANCINI, A. L.; NESHICH, G. Building multiple sequence alignments with a flavour of HSSP alignments. In: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional, 2005. p. 28. X-meeting 2005. Presented Posters. Na publicação: Paula Regina Kuser.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 46. | | FALCAO, P. R. K.; TADA, S. F. de S.; SOUZA, A. P.; YAMAGISHI, M. E. B.; MANCINI, A. L.; FILETO, R.; HIGA, R. H.; NESHICH, G. Modelagem molecular da proteína small heat shock de Xylella fastidiosa. Campinas: Embrapa Informática Agropecuária, 2004. 5 p. (Embrapa Informática Agropecuária. Comunicado técnico, 64). Na publicação: Michel Eduardo Beleza Yamaghishi.| Biblioteca(s): Embrapa Agricultura Digital. |
|  |
| 50. | | JARDINE, J. G.; MAZONI, I.; MANCINI, A. L.; BORRO, L. C.; ALVARENGA, D.; CECÍLIO, P. L.; PELLIGRINELLI, T. V.; NESHICH, G. How did the structure function descriptors of proteins change with introduction of 'remediated' PDB files. In: RED IBEROAMERICANA DE BIOINFORMÁTICA CONGRESS, 5., 2008, Santiago. Program and abstracts... Santiago. Pontificia Universidade Católica de Chile, 2008. p. 15.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 51. | | MANCINI, A. L.; BARIONI, L. G.; LIMA, H. N.; SANTOS, J. W.; SILVA, R. D. R.; SANTOS, E. H. dos; DIAS, F. R. T. A compact and flexible C++ framework to support modular development of hierarchical dynamic systems simulators (wip): Embrapa agricultural informatics. In: SYMPOSIUM ON THEORY OF MODELING & SIMULATION, 2014, San Diego. Proceedings... San Diego: Society for Computer Simulation International, 2014. Não paginado.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pantanal. |
| |
| 55. | | MANCINI, A. L.; JARDINE, J. G.; MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; CECILIO, P. L.; PELLIGRINELLI, T. V.; NESHICH, G. Structure descriptors of chameleon sequences. In: RED IBEROAMERICANA DE BIOINFORMÁTICA CONGRESS, 5., 2008, Chile. Program and abstracts... Santiago: Pontificia Universidad Católica de Chile, 2008. Não paginado. RIB 2008.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 56. | | MANCINI, A. L.; HIGA, R. H.; OLIVEIRA, A.; DOMINIQUINI, F.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; TOGAWA, R. C.; NESHICH, G. Sting contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics, v. 20, n. 13, p. 2145-2147, 2004. Na publicação: P. R. Kuser.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 57. | | HIGA, R. H.; CRUZ, S. A. B. da; KUSER, P. R.; YAMAGISHI, M. E. B.; FILETO, R.; OLIVEIRA, S. R. de M.; MAZONI, I.; SANTOS, E. H. dos; MANCINI, A. L.; NESHICH, G. Building multiple sequence alignments with a flavor of HSSP alignments. Genetics and Molecular Research, v. 5, n. 1, p. 127-137, 2006.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 58. | | CRUZ, S. A. B. da; MAZONI, I.; OLIVEIRA, S. R. de M.; YAMAGISHI, M. E. B.; FALCAO, P. R. K.; SANTOS, E. H. dos; VIEIRA, F. D.; HIGA, R. H.; MANCINI, A. L.; NESHICH, G. JMOL and STING integration: a STING for multiple patforms. In: X-MEETING; INTERNATIONAL CONFERENCE OF THE AB3C, 1., 2005, Caxambu. [Proceedings...]. [S.l.]: Associação Brasileira de Bioinformática e Biologia Computacional, 2005. p. 86. Na publicação: Stanley R. M. Oliveira, Paula R. Kuser, Edgard H. Santos. X-meeting 2005. Presented Posters.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 59. | | MOURA, M. F.; MANCINI, A. L.; BENATTI, R. M.; RODRIGUES, L. N.; VICTORIA, D. de C.; ROMANI, L. A. S.; OLIVEIRA, S. R. de M.; SILVA, L. E. A.; BEZERRA, G. A.; FRANCIOLI, G. A. Um ambiente para uso de outorga compartilhada de água. In: CONGRESSO BRASILEIRO DE AGROINFORMÁTICA, 12., 2019, Indaiatuba. Anais... Ponta Grossa: SBIAGRO, 2019. p. 521-522. Na publicação: Daniel Victoria, Luciana Alvim Romani, Stanley R Medeiros Oliveira. Organizadores: Maria Fernanda Moura, Jayme Garcia Arnal Barbedo, Alaine Margarete Guimarães, Valter Castelhano de Oliveira. SBIAgro 2019.| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 60. | | YAMAGISHI, M. E. B.; FALCAO, P. R. K.; OLIVEIRA, S. R. de M.; HIGA, R. H.; SANTOS, E. H. dos; MAZONI, I.; VIEIRA, F. D.; MANCINI, A. L.; NESHICH, G. Rotâmeros raros no Java Protein Dossier. Campinas: Embrapa Informática Agropecuária, 2006. 6 p. (Embrapa Informática Agropecuária. Comunicado técnico, 76).| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| Registros recuperados : 80 | |
|
|
|
Registro Completo
|
Biblioteca(s): |
Embrapa Recursos Genéticos e Biotecnologia. |
|
Data corrente: |
05/01/2011 |
|
Data da última atualização: |
03/02/2023 |
|
Tipo da produção científica: |
Artigo em Periódico Indexado |
|
Circulação/Nível: |
B - 1 |
|
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. |
|
Afiliação: |
CRISTINA RIBEIRO, UFMG; ROBERTO COITI 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. |
|
Título: |
Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. |
|
Ano de publicação: |
2010 |
|
Fonte/Imprenta: |
BMC Structural Biology, London, v. 10, n. 36, p. 1-16, 2010. |
|
Idioma: |
Inglês |
|
Notas: |
Disponível em:.Acesso em: 5 jan. 2011. |
|
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 |
|
Palavras-Chave: |
Enzimas; Interface Forming Residues; Propriedades ligantes; Proteases. |
|
Thesaurus NAL: |
Binding properties; Enzymes. |
|
Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
|
URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/23695/1/1472-6807-10-36.pdf
|
|
Marc: |
LEADER 03733naa a2200313 a 4500
001 1871662
005 2023-02-03
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.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
Fechar
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
