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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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Esconder MarcMostrar Marc Completo |
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Registro original: |
Embrapa Recursos Genéticos e Biotecnologia (CENARGEN) |
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| Registros recuperados : 186 | |
| 141. |  | 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.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 142. | | NESHICH, G.; NESHICH, I. A. P.; MORAES, F.; SALIM, J. A.; BORRO, L.; YANO, I. H.; MAZONI, I.; JARDINE, J. G.; ROCCHIA, W. Using structural and physical-chemical parameters to identify, classify, and predict functional districts in proteins-the role of electrostatic potential. In: ROCCHIA, W.; SPAGNUOLO, M. (Ed.). Computational electrostatics for biological applications: geometric and numerical approaches to the description of electrostatic interaction between macromolecules. Cham: Springer, 2015. Chapter 12. p. 227-254.| Tipo: Capítulo em Livro Técnico-Científico |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 144. | | 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. |
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| 146. | | SILVA, M. C. M. da; TEIXEIRA, F. R.; CRUZ, C. C. M. da; TOGAWA, R. C.; NESHICH, G.; SA, M. F. G. de. In vitro molecular evolution of bean alpha-amylase inhibitors to investigate specificity of binding to alpha-amylases. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. [Proceedings...]. Detroit: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster LB-28.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 147. | | NARCISO, M. G.; YAMAGISHI, M. E. B.; NESHICH, G.; FALCAO, P.; HENRIQUE, E.; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I. Transformação de imagens 3D para 2D para análise de proteínas usando o software Sting. In: CONGRESSO DE COMPUTAÇÃO DO SUL DE MATO GROSSO, 2., 2006, Rondonópolis. Computação e educação: anais. Rondonópolis: UFMT, 2006. p. 176-184. COMPSULMT 2006.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 148. | | BEZERRA, I. C.; ALMEIDA, E. R. P. de; CASTRO, L. A. B. de; NESHICH, G.; VALLE, M.; MONTE-NESHICH, D. de C. Two globulin isoforms codified by a single precursor gene from taro (Colocasia esculenta L.). In: ENCONTRO BRASILEIRO DE BIOTECNOLOGIA VEGETAL, 1., 1993, Brasilia.Programa e resumos. Brasilia: EMBRAPA-CENARGEN, 1993. Poster 011. Resumo| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 149. | | NESHICH, I. A. P.; MORAES, F. R. de; MARANGONI, S.; MARTINS, D.; SALIM, J. A.; MAZONI, I.; MANCINI, A.; NESHICH, G.; JARDINE, J. G. Xylella fastidiosa hexameric pilus retraction motor PILT interfaces are maintained by non-hydrophobic contacts. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. Não paginado. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 150. | | YAMAGISHI, M. E. B.; FALCAO, P. R. K.; BORRO, L. C.; OLIVEIRA, S. R. de M.; SANTOS, E. H. dos; JARDINE, J. G.; VIEIRA, F. D.; MAZONI, I.; NARCISO, M. G.; NESHICH, G. Analysing protein-protein interface using JPIV. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster I-14. Na publicação: Paula R. Kuser-Falcão, Stanley R. M. Oliveira, Edgard H. Santos.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 151. | | 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. Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. BMC Structural Biology, London, v. 10, n. 36, p. 1-16, 2010.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 152. | | 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. Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors. BMC Structural Biology, London, v. 10, n. 36, p. 1-16, 2010. Disponível em:.Acesso em: 5 jan. 2011.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: B - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 153. | | 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. |
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| 154. | | NESHICH, I. A. P.; NISHIMURA, L.; MORAES, F. R. de; SALIM, J. A.; VILLALTA-ROMERO, F.; BORRO, L.; YANO, I. H.; MAZONI, I.; TASIC, L.; JARDINE, J. G.; NESHICH, G. Computational Biology tools for identifying specific ligand binding residues for novel agrochemical and drug design. Current Protein and Peptide Science, v. 16, n. 8, p. 701-717, 2015.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 2 |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 155. | | YAMAGISHI, M. E. B.; FALCAO, P. R. K.; HIGA, R. H.; SANTOS, E. H. dos; JARDINE, J. G.; MAZONI, I.; OLIVEIRA, S. R. de M.; MANCINI, A. L.; NESHICH, G. Identificando Pockets na superfície protéica usando o Java Protein Dossier - JPD. Campinas: Embrapa Informática Agropecuária, 2005. 4 p. (Embrapa Informática Agropecuária. Comunicado técnico, 67).| Biblioteca(s): Embrapa Agricultura Digital. |
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| 156. | | CARDOSO, C. M. Y.; MORAES, F. R. de; NESHICH, G.; MOREIRA, E. C. de O.; COSTA, C. de N. M.; SANTOS, R. C. dos; SOUZA, C. R. B. de. Identification of cDNA sequences coding for bZIP regulatory proteins predicted to interact with putative cis-acting elements from Be2S1 gene. In: CONGRESSO BRASILEIRO DE BIOTECNOLOGIA, 3., 2010, Forlaleza. Programas e resumos... Brasília, DF: Sociedade Brasileira de Biotecnologia, 2010. p. 212-213. Congresso da SBBiotec 2010.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 157. | | MARCELINO, L. H.; SOARES, F. X. S.; SILVA, C. M. da; ROCHA, T. L.; CARNEIRO, M.; GANDER, E. S.; SAMPAIO, M. A. M.; CASTRO, L. A. B. de; NESHICH, G. Introduction of tryptophan in the Brazil nut 2s storage albumins by site-directed mutagenesis. In: INTERNATIONAL SYMPOSIUM ON CRYSTALLOGRAPHY AND MOLECULAR BIOLOGY, 1990, Guaruja, SP, Abstracts.[S.l.]: Institute of Advanced Studies, Sao Carlos: Universidade Federal de Sao Carlos, 1990. PS1-03.| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia. |
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| 158. | | OLIVEIRA, S. R. de M.; ALMEIDA, G. V.; SOUZA, K. R. R.; RODRIGUES, D. N.; NESHICH, G.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G. An integrated database of structural parameters for protein analysis. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY, 14.; ANNUAL AB3C CONFERENCE, 2., 2006, Fortaleza. Conference Program... Fortaleza: ISCB, 2006. Não paginado. ISMB, X-MEETING 2006. Poster B-44. Na publicação: Stanley R. M. Oliveira, Paula R. Kuser-Falcão, Edgard H. Santos.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 159. | | 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.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
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| 160. | | 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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| Registros recuperados : 186 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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