| |
|
|
 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
|
Registro Completo |
|
Biblioteca(s): |
Embrapa Agricultura Digital. |
|
Data corrente: |
26/11/2009 |
|
Data da última atualização: |
15/01/2020 |
|
Tipo da produção científica: |
Resumo em Anais de Congresso |
|
Autoria: |
NESHICH, I. A. P.; MORAES, F. R. de; SALIM, J. A.; MAZONI, I.; MANCINI, A.; JARDINE, J. G.; NESHICH, G. |
|
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. |
|
Título: |
Surface hydrophobicity index (SHI): insight into the mechanisms of protein-protein associations. |
|
Ano de publicação: |
2009 |
|
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. |
|
Páginas: |
Não paginado. |
|
Idioma: |
Inglês |
|
Notas: |
X-Meeting 2009 |
|
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 |
|
Palavras-Chave: |
Bioinformática; Hidrofobicidade; Índice de hidrofobicidade superficial (SHI); Mecanismos de associação entre proteínas; Protein. |
|
Thesagro: |
Proteína. |
|
Thesaurus Nal: |
Bioinformatics. |
|
Categoria do assunto: |
-- |
|
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.
Download
Esconder MarcMostrar Marc Completo |
|
Registro original: |
Embrapa Agricultura Digital (CNPTIA) |
|
|
Biblioteca |
ID |
Origem |
Tipo/Formato |
Classificação |
Cutter |
Registro |
Volume |
Status |
URL |
Voltar
|
|
|
| Registros recuperados : 77 | |
| 21. |  | MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; JARDINE, J. G.; NESHICH, G. Studying structure function relationship of proteins using "remediated" PDB files. In: ANNUAL MEETING OF SBBQ, 37.; CONGRESS OF THE PAN-AMERICAN ASSOCIATION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 11, 2008, Águas de Lindóia. Program and index... Águas de Lindóia, Program and index... Águas de Lindóia: SBBq, 2008. Não paginado. PABMB.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
|    |
| 23. | | TOGAWA, R. C.; RIBEIRO, C.; MAZONI, I.; PELLIGRINELLI, T.; JARDINE, J. G.; NESHICH, G. The table of interface forming residues as the specificity indicator for serine proteases bound to different inhibitors. In: INTERNATIONAL CONFERENCE ON BIOINFORMATICS & COMPUTATIONAL BIOLOGY, 2008, Georgia. Las Vegas Nevada: CSREA, 2008, p. 811-817. BIOCOMP 2008. WORLDCOMP'08| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Recursos Genéticos e Biotecnologia. |
|  |
| 24. | | MAZONI, I.; BORRO, L. C.; JARDINE, J. G.; YANO, I. H.; SALIM, J. A.; NESHICH, G. Study of specific nanoenvironments containing [alfa]-helices in all-[alfa] and ([alfa]+[beta])+([alfa]/[beta]) proteins. Plos One, v. 13, n. 7, p. 1-25, 2018. Artigo e0200018.| Tipo: Artigo em Periódico Indexado | Circulação/Nível: A - 1 |
| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Territorial. |
| |
| 26. | | JARDINE, J. G.; NESHICH, I. A. P.; MORAES, F. R. de; MAZONI, I.; MANCINI, A.; SALIM, J. A.; NESHICH, G. Generation of lipase B mutants with increased surface hydrophobicity in order to improve biodiesel catalysis. 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. |
| |
| 27. | | SALIM, J. A.; MAZONI, I.; MANCINI, A. L.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. MSSP: a web-based application for analysis of selected parameter from multiple structures in a graphical manner. 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. |
| |
| 29. | | JARDINE, J. G.; NESHICH, G.; MAZONI, I.; MARTINS, D.; MARANGONI, S.; NOVELLO, J. C.; GATTAZ, W. F.; DIAS-NETO, E. Molecular modeling and structural analysis of the Myelin basic protein-Q65ZS4. In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 3., 2007, São Paulo. Proceedings... Campinas: Embrapa Informática Agropecuária, 2007. p. 138. X-meeting 2007.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 30. | | NESHICH, I. A. P.; MAZONI, I.; SALIM, J. A.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Pathogenic Prion Proteins (PrP) have higher electrostatic potential pattern than normal cellular prion protein in a specific region. In: ANNUAL MEETING OF THE SBBq, 40., 2011, Foz do Iguaçu. [Proceedings...]. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2011. Não paginado.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 32. | | NESHICH, I. A. P.; MORAES, F. de; SALIM, J. A.; MAZONI, I.; JARDINE, J. G.; NESHICH, G. Size matters: surface hydrophobicity index (SHI) describes the impact of the size of interface area on oligomerization driven by hydrophobic effect. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISMB, 2012. Não paginado. 3Dsig 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 33. | | NESHICH, I. A. P.; MORAES, F. R. de; SALIM, J. A.; MAZONI, I.; MANCINI, A.; JARDINE, J. G.; NESHICH, G. Surface hydrophobicity index (SHI): insight into the mechanisms of protein-protein associations. 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. |
| |
| 34. | | MAZONI, I.; SALIM, J. A; NESHICH, I. A. P.; MORAES, F. R. de; NISHIMURA, L.; JARDINE, J. G.; NESHICH, G. Structure function relationship de convoluted to a level of physical chemical descriptors: case study - lysozyme / lactalbumine differences. In: ANNUAL MEETING OF THE SBBq, 40., 2011, Foz do Iguaçu. [Proceedings...]. São Paulo, SP: Brazilian Society for Biochemistry and Molecular Biology, 2011. Não paginado.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 35. | | NARCISO, M. G.; YAMAGISHI, M. E. B.; QUINAGLIA, T.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I.; FALCAO, P. R. K.; NESHICH, G. Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma proteína qualquer. Campinas: Embrapa Informática Agropecuária, 2006. 4 p. (Embrapa Informática Agropecuária. Comunicado técnico, 77). Na publicação: Goran Neshich.| Tipo: Comunicado Técnico/Recomendações Técnicas |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 36. | | NARCISO, M. G.; NESHICH, G.; YAMAGISHI, M. E. B.; FALCÃO, P.; SANTOS, E. H. dos; VIEIRA, F. D.; JARDINE, J. G.; MAZONI, I. Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma proteína qualquer usando o software Sting. In: CONGRESSO DE COMPUTAÇÃO DO SUL DE MATO GROSSO, 2., 2006, Rondonópolis. Computação e educação: anais. Rondonópolis: UFMT, 2006. p. 166-175. COMPSULMT 2006.| Tipo: Artigo em Anais de Congresso / Nota Técnica |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 37. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. P.; NESHICH, G. Computational analysis of the secondary structure elements based on the physical chemical and geometrical descriptors and statistics data. 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. |
| |
| 38. | | SALIM, J. A.; VON ZUBEN, F. J.; MORAES, F. R. de; NESHICH, I. A. P.; MAZONI, I.; JARDINE, J.; NESHICH, G. Characterization of catalytic site residues using STING_DB structural descriptors. In: ANNUAL INTERNATIONAL CONFERENCE ON INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY; STRUCTURAL BIOINFORMATICS AND COMPUTATIONAL BIOPHYSICS CONFERENCE MEETING, 8., 2012, Long Beach, California. Abstracts... California: ISCB, 2012. Não paginado. Poster. 3DSIG 2012.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 39. | | MAZONI, I.; FALCÃO, P. R. K.; YAMAGISHI, M.; BORRO, L.; JARDINE, J. G.; SANTOS, E. H. dos; OLIVEIRA, S. R. de M.; NESHICH, G.; NARCISO, M. G. Comparisson of the amino acids co-evolution and the correlated structure descriptors. 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-51. Na publicação: Paula Kuser, Stanley R. M. Oliveira, Marcelo Narciso.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| 40. | | MAZONI, I.; BORRO, L. C.; MANCINI, A.; SALIM, J. A.; MORAES, F. R.; JARDINE, J. G.; NESHICH, I. A. P.; NESHICH, G. Comparison between physical chemical and geometrical characteristics of the amino acids present in alpha-helices and beta-sheets. 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 pagiando. X-Meeting 2009.| Tipo: Resumo em Anais de Congresso |
| Biblioteca(s): Embrapa Agricultura Digital. |
| |
| Registros recuperados : 77 | |
|
| Nenhum registro encontrado para a expressão de busca informada. |
|
|
