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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
26/11/2009 |
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Data da última atualização: |
15/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
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Autoria: |
NESHICH, I. A. P.; MORAES, F. R. de; SALIM, J. A.; MAZONI, I.; MANCINI, A.; JARDINE, J. G.; NESHICH, G. |
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Afiliação: |
IZABELLA AGOSTINHO PENA NESHICH, Estagiária/CNPTIA; FABIO ROGERIO DE MORAES, Bolsista/CNPTIA; JOSÉ AUGUSTO SALIM, Estagiário/CNPTIA; IVAN MAZONI, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; JOSE GILBERTO JARDINE, CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Surface hydrophobicity index (SHI): insight into the mechanisms of protein-protein associations. |
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Ano de publicação: |
2009 |
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Fonte/Imprenta: |
In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB, 2009. |
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Páginas: |
Não paginado. |
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Idioma: |
Inglês |
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Notas: |
X-Meeting 2009 |
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Conteúdo: |
It is widely accepted that hydrophobic interaction (HI), the effective attraction between nonpolar (sub)molecular groups in water, play a central role in protein folding leading to stability of protein structures. In addition, the HI is also supposed to be related with formation of protein complexes, where molecular association involves entropy loss of the subunits and entropy gain of solvent. Janin and coworkers have estimated such (unfavorable) entropic cost at 20-30 kcal/mol and suggested that the burial, upon complexation, of exposed hydrophobic surface area is the main force for oligomerization (because it increases water entropy). This conclusion is supported by analyses first done by Argos and colleagues, which revealed that interface region of monomers has also been found to be more hydrophobic than the rest of solvent-exposed surface. Interested on properties, in particular into the hydropobicity, of protein surface in complexes and their isolated subunits, we decided to introduce a parameter, derived from the known scales (such as Kyte-Doollittle, Eisenberg and Engelman), normalizing aminoacid Hydropathy by their effective accessible surface area: the Aminoacid Normalized Hydrophobicity Index (ANHI). The accessible surface area per residue is calculated using SurfV program. In addition, we created a new parameter reported in a "per chain? fashion: Surface Hydrophobicity Index (SHI). SHI describes the cumulative surface Hydrophobicity for a selected chain in two flavors: isolated chain and chain in complex with another chain. SHI is calculated as the sum of all normalized ANHI of Hydrophobic (HB) residues (i.e. the aminoacids with positive values of Kyte-Doollittle hydropathy scale) divided by the sum of ANHI of all Hydrophilic (HL) residues of a PDB chain (SHI = ΣANHIHB/ΣANHIHL). Thus, low SHI values are indicators of the hydrophilic protein surfaces while high SHI values indicate more hydrophobic protein surfaces. Applying our method to the PDB containing only protein chains we could test Argos? (and ours) hypothesis. We found that 96.7% of oligomeric proteins in PDB have their SHI value in isolation higher (more hydrophobic) than in complex. This data suggests that protein association (for the data mart we examined) is effectively driven by hydrophobic effect where more hydrophobic portions at surface are buried upon complexes formation. In addition, another hypothesis has been proposed: monomer SHI values should be lower (more hydrophilic) than the SHI values of complex subunits alone. We hypothesized that, if oligomerization is driven by hydrophobic patches at surface, the establishment of monomers as "monomers? during evolution is related to the minimization of such patches on their surfaces. Our corresponding datamart shows that on average the SHI value for monomeric proteins with structure deciphered by X ray, is 0.28, against 0.37 for complex subunits alone. These results are important to help understand fully about protein complexes formation and consolidation of oligomers during evolution. We also believe that some other, yet to be defined features, can be deduced through SHI analysis, reinforcing how useful this index is to protein studies. MenosIt is widely accepted that hydrophobic interaction (HI), the effective attraction between nonpolar (sub)molecular groups in water, play a central role in protein folding leading to stability of protein structures. In addition, the HI is also supposed to be related with formation of protein complexes, where molecular association involves entropy loss of the subunits and entropy gain of solvent. Janin and coworkers have estimated such (unfavorable) entropic cost at 20-30 kcal/mol and suggested that the burial, upon complexation, of exposed hydrophobic surface area is the main force for oligomerization (because it increases water entropy). This conclusion is supported by analyses first done by Argos and colleagues, which revealed that interface region of monomers has also been found to be more hydrophobic than the rest of solvent-exposed surface. Interested on properties, in particular into the hydropobicity, of protein surface in complexes and their isolated subunits, we decided to introduce a parameter, derived from the known scales (such as Kyte-Doollittle, Eisenberg and Engelman), normalizing aminoacid Hydropathy by their effective accessible surface area: the Aminoacid Normalized Hydrophobicity Index (ANHI). The accessible surface area per residue is calculated using SurfV program. In addition, we created a new parameter reported in a "per chain? fashion: Surface Hydrophobicity Index (SHI). SHI describes the cumulative surface Hydrophobicity for a selected chain in two fla... Mostrar Tudo |
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Palavras-Chave: |
Bioinformática; Hidrofobicidade; Índice de hidrofobicidade superficial (SHI); Mecanismos de associação entre proteínas; Protein. |
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Thesagro: |
Proteína. |
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Thesaurus Nal: |
Bioinformatics. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 04236nam a2200289 a 4500
001 1576265
005 2020-01-15
008 2009 bl uuuu u00u1 u #d
100 1 $aNESHICH, I. A. P.
245 $aSurface hydrophobicity index (SHI)$binsight into the mechanisms of protein-protein associations.$h[electronic resource]
260 $aIn: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 5., 2009, Angra dos Reis. Abstracts book... Angra dos Reis: ABBCB$c2009
300 $aNão paginado.
500 $aX-Meeting 2009
520 $aIt is widely accepted that hydrophobic interaction (HI), the effective attraction between nonpolar (sub)molecular groups in water, play a central role in protein folding leading to stability of protein structures. In addition, the HI is also supposed to be related with formation of protein complexes, where molecular association involves entropy loss of the subunits and entropy gain of solvent. Janin and coworkers have estimated such (unfavorable) entropic cost at 20-30 kcal/mol and suggested that the burial, upon complexation, of exposed hydrophobic surface area is the main force for oligomerization (because it increases water entropy). This conclusion is supported by analyses first done by Argos and colleagues, which revealed that interface region of monomers has also been found to be more hydrophobic than the rest of solvent-exposed surface. Interested on properties, in particular into the hydropobicity, of protein surface in complexes and their isolated subunits, we decided to introduce a parameter, derived from the known scales (such as Kyte-Doollittle, Eisenberg and Engelman), normalizing aminoacid Hydropathy by their effective accessible surface area: the Aminoacid Normalized Hydrophobicity Index (ANHI). The accessible surface area per residue is calculated using SurfV program. In addition, we created a new parameter reported in a "per chain? fashion: Surface Hydrophobicity Index (SHI). SHI describes the cumulative surface Hydrophobicity for a selected chain in two flavors: isolated chain and chain in complex with another chain. SHI is calculated as the sum of all normalized ANHI of Hydrophobic (HB) residues (i.e. the aminoacids with positive values of Kyte-Doollittle hydropathy scale) divided by the sum of ANHI of all Hydrophilic (HL) residues of a PDB chain (SHI = ΣANHIHB/ΣANHIHL). Thus, low SHI values are indicators of the hydrophilic protein surfaces while high SHI values indicate more hydrophobic protein surfaces. Applying our method to the PDB containing only protein chains we could test Argos? (and ours) hypothesis. We found that 96.7% of oligomeric proteins in PDB have their SHI value in isolation higher (more hydrophobic) than in complex. This data suggests that protein association (for the data mart we examined) is effectively driven by hydrophobic effect where more hydrophobic portions at surface are buried upon complexes formation. In addition, another hypothesis has been proposed: monomer SHI values should be lower (more hydrophilic) than the SHI values of complex subunits alone. We hypothesized that, if oligomerization is driven by hydrophobic patches at surface, the establishment of monomers as "monomers? during evolution is related to the minimization of such patches on their surfaces. Our corresponding datamart shows that on average the SHI value for monomeric proteins with structure deciphered by X ray, is 0.28, against 0.37 for complex subunits alone. These results are important to help understand fully about protein complexes formation and consolidation of oligomers during evolution. We also believe that some other, yet to be defined features, can be deduced through SHI analysis, reinforcing how useful this index is to protein studies.
650 $aBioinformatics
650 $aProteína
653 $aBioinformática
653 $aHidrofobicidade
653 $aÍndice de hidrofobicidade superficial (SHI)
653 $aMecanismos de associação entre proteínas
653 $aProtein
700 1 $aMORAES, F. R. de
700 1 $aSALIM, J. A.
700 1 $aMAZONI, I.
700 1 $aMANCINI, A.
700 1 $aJARDINE, J. G.
700 1 $aNESHICH, G.
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Embrapa Agricultura Digital (CNPTIA) |
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| Registros recuperados : 31 | |
| 5. |  | RODRIGUES, H. P.; SILVA, D. C. G. da; FERREIRA, E. G. C.; MARCELINO-GUIMARÃES, F. C. Otimização de ensaios de PCR Multiplex para a amplificação de alvos de interesse para o melhoramento genético da Soja. In: JORNADA ACADÊMICA DA EMBRAPA SOJA, 15., 2020, Londrina. Resumos expandidos... Londrina: Embrapa Soja, 2020. 244 p. (Embrapa Soja. Documentos, 429). p. 202-210 (Embrapa Soja. Documentos, 429). Artigo de acesso aberto.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
|    |
| 6. | | AVELINO, B. B.; FERREIRA, E. G. C.; SILVA, D. C. G. da; MARCELINO-GUIMARÃES, F. C. Otimização de um método de extração de DNA de sementes de soja não destrutivo. In: JORNADA ACADÊMICA DA EMBRAPA SOJA, 15., 2020, Londrina. Resumos expandidos... Londrina: Embrapa Soja, 2020. 244 p. (Embrapa Soja. Documentos, 429). p. 234-243 (Embrapa Soja. Documentos, 429). Artigo de acesso aberto.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 7. | | SOARES, R. M.; MEYER, M. C.; FERREIRA, E. G. C.; MARCELINO-GUIMARÃES, F. C.; FANTINATO, G. G. P.; ÁVILA, W. Primeiro relato de ocorrência da mancha bacteriana marrom no Estado do Pará. In: REUNIÃO DE PESQUISA DE SOJA, 36., 2017, Londrina, PR. Resumos expandidos... Londrina: Embrapa Soja, 2017. p. 81-83. (Embrapa Soja. Documentos, 388). Editado por Alvadi Antonio Balbinot Junior, Fernando Augusto Henning, Regina Maria Villas Bôas de Campos Leite.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
|  |
| 8. | | SOUZA JUNIOR, H. de; SILVA, A. C.; AVELINO, B. B.; FERREIRA, E. G. C.; CASTANHO, F. M.; ISEPPON, A. M. B.; MARCELINO-GUIMARÃES, F. C. Avaliação da resistência do feijão-caupi (Vigna unguiculata (L.) Walp) à um isolado virulento de Phakopsora pachyrhizi. In: JORNADA ACADÊMICA DA EMBRAPA SOJA, 15., 2020, Londrina. Resumos expandidos... Londrina: Embrapa Soja, 2020. 244 p. (Embrapa Soja. Documentos, 429). P. 113-118 (Embrapa Soja. Documentos, 429). Artigo de acesso aberto.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 9. | | BISSI, R. B.; CARDOSO, R.; FERREIRA, E. G. C.; CAITAR, V. L.; FLORO, D. L.; SILVA, D. C. G.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Genome Wide Association Study of resistance to Phakopsora pachyrhizi in soybean breeding materials (Estudo de Associação Genômica Ampla da Resistência a Ferrugem Asiática da Soja em linhagens de soja de programa de melhoramento genético). In: CONGRESSO BRASILEIRO DE FITOPATOLOGIA, 51., 2019, Recife. Anais... Brasília, DF: SBF, 2019. p. 165.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 10. | | FERREIRA, E. G. C.; PEREIRA, A. A.; CATELLI, L. L.; AOYAGI, L. N.; CARVALHO, V. P.; BELZILE, F.; MARCELINO-GUIMARÃES, F. C.; ABDELNOOR, R. V. Mapeamento Genético de um locus de resistência a oídio mediado por Erysiphe diffusa em soja.Genetic mapping of powdery mildew resistance locus mediated by Erysiphe diffusa in soybean. In: CONGRESSO BRASILEIRO DE FITOPATOLOGIA, 51., 2019, Recife. Anais... Brasília, DF: SBF, 2019. p. 722.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 11. | | AVELINO, B. B.; BARROS, L. G.; SILVA, D. C. G. da; FERREIRA, E. G. C.; ARIAS, C. A. A.; MARCELINO-GUIMARÃES, F. C. Refinamento do mapa do locus de resistência a ferrugem da soja na PI 594756 por montagem genômica de novo. In: CONGRESSO BRASILEIRO DE MELHORAMENTO DE PLANTAS, 12., 2023, Caxambu, MG. Anais... Piracicaba: Sociedade Brasileira de Melhoramento de Plantas, 2023. Título em inglês: Refinement of the resistance locus to soybean rust in PI 594756 by de novo genome assembly.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 12. | | FERREIRA, E. G. C.; GOMES, D. F.; DELAI, C. V.; BARREIROS, M. A. B.; GRANGE, L.; RODRIGUES, E. P.; MERTZ-HENNING, L. M.; BARCELLOS, F. G.; HUNGRIA, M. Revealing potential functions of hypothetical proteins induced by genistein in the symbiosis island of Bradyrhizobium japonicum commercial strain SEMIA 5079 (= CPAC 15). BMC Microbiology, v. 22, 122, 2022. 20 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 13. | | SANTOS, J. V. M. dos; FERREIRA, E. G. C.; PASSIANOTTO, A. L. L.; BRUMER, B. B.; SANTOS, A. B. dos; SOARES, R. M.; TORKAMANEH, D.; ARIAS, C. A. A.; BELZILE, F.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development. BMC Genomics, v. 20, n. 798, 2019. 13 p.| Tipo: Artigo em Periódico Indexado |
| Biblioteca(s): Embrapa Soja. |
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| 14. | | ALEKCEVETCH, J. C.; PASSIANOTTO, A. L. de L.; FERREIRA, E. G. C.; SANTOS, A. B. dos; SILVA, D. C. G. da; DIAS, W. P.; BELZILE, F.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Genome-wide association study for resistance to the Meloidogyne javanica causing root-knot nematode in soybean. Theoretical and Applied Genetics, v. 134, p. 777-792, 2021. Artigo de acesso aberto.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Soja. |
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| 16. | | SILVA, A. C. da; SILVA, D. C. G. da; FERREIRA, E. G. C.; ABDELNOOR, R. V.; BORÉM, A.; ARIAS, C. A.; OLIVEIRA, M. F.; FERREIRA, M. E.; MARCELINO-GUIMARÃES, F. C. Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars. PLoS ONE, v. 20, n. 1, e0313151, 2025. 26 p.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Recursos Genéticos e Biotecnologia; Embrapa Soja. |
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| 17. | | AOYAGI, L. N.; FERREIRA, E. G. C.; AVELINO, B. B.; SILVA, D. C. G. da; LOPES-CAITAR, V. S.; ABDELNOOR, R. V.; SOUTO, E. R. de; MARCELINO-GUIMARÃES, F. C. Haplotypes in the RPP1 locus conferring resistance to asian soybean rust. In: INTERNATIONAL CONGRESS OF THE BRAZILIAN GENETICS SOCIETY, 69., 2024, Campos do Jordão. Emerging roles of DNA. e-book... Ribeirão Preto: SBG, 2024. p. 693.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 18. | | FERREIRA, E. G. C.; JANUARIO, N. C. G.; BROWSER, N. D.; GUERRA, W. D.; CAMPOS, H. D.; UTIAMADA, C. M.; SEIXAS, C. D. S.; SOARES, R. M.; MARCELINO-GUIMARÃES, F. C. Caracterização de isolados do complexo Diaporthe/Phomopsis obtidos de locais com suspeita de cancro-da-haste. In: CONGRESSO BRASILEIRO DE SOJA, 8., 2018, Goiânia. Inovação, tecnologias digitais e sustentabilidade da soja: anais. Brasília, DF: Embrapa, 2018. p. 584-586.| Tipo: Artigo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 19. | | SILVA, A. C.; SILVA, D. C. G. da; FERREIRA, E. G. C.; BORÉM, A.; FERREIRA, M. E.; ARIAS, C. A. A.; OLIVEIRA, M. F. de; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Development of the 1K SNP panel for genetics and breeding applications for the Brazilian soybean germplasm. In: WORLD SOYBEAN RESEARCH CONFERENCE, 11., 2023, Vienna. Soybean Research for Sustainable Development. abstracts. Vienna: University of Natural Resources and Life Sciences, 2023. 11 p.224. WSRC 2023| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| 20. | | RAMIREZ, L. M. A.; SILVA, D. C. G. da; FERREIRA, E. G. C.; AOYAGI, L. N.; BISSI, R. B.; AVELINO, B. B.; CATELLI, L.; ABDELNOOR, R. V.; MARCELINO-GUIMARÃES, F. C. Fine mapping of RPP5 gene in soybean PI200487. In: INTERNATIONAL CONGRESS OF THE BRAZILIAN GENETICS SOCIETY, 69., 2024, Campos do Jordão. Emerging roles of DNA. e-book... Ribeirão Preto: SBG, 2024. p. 685. 69 CBG 2024.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Soja. |
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| Registros recuperados : 31 | |
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| Nenhum registro encontrado para a expressão de busca informada. |
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