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| Registros recuperados : 77 | |
| 2. |  | MAZONI, I.; NESHICH, G. DIPN: a dictionary of the internal proteins nanoenvironments and their potential for transformation into agricultural assets. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; OLIVEIRA, S. R. de M.; MEIRA, C. A. A.; LUCHIARI JUNIOR, A.; BOLFE, E. L. (ed.). Digital agriculture: research, development and innovation in production chains. Brasília, DF: Embrapa, 2023. cap. 9, p. 165-177.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 3. | | MAZONI, I.; NESHICH, G. DPIN: um dicionário dos nanoambientes internos das proteínas e seu potencial para transformação em ativos para a agricultura. In: MASSRUHÁ, S. M. F. S.; LEITE, M. A. de A.; OLIVEIRA, S. R. de M.; MEIRA, C. A. A.; LUCHIARI JUNIOR, A.; BOLFE, E. L. (Ed.). Agricultura digital: pesquisa, desenvolvimento e inovação nas cadeias produtivas. Brasília, DF: Embrapa, 2020. cap. 9, p. 218-232.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 10. | | JARDINE, J. G.; MAZONI, I.; BORRO, L. C.; ALVARENGA, D.; NESHICH, G. Signature contact coordination patterns for secondary structure elements in protein structures. 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: SBBq, 2008. Não paginado. PABMB.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 11. | | 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.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 12. | | 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.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Territorial. |
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| 14. | | 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| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Recursos Genéticos e Biotecnologia. |
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| 15. | | PENA, I.; MANCINI, A. L.; MAZONI, I.; JARDINE, J. G.; NESHICH, G.; ORTEGA, J. M. Identification of philogenetic relationship between GDPD and SMaseD proteins based on active site amino acid physical chemical properties. In: INTERNATIONAL CONFERENCE OF BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 4., 2008, Salvador. Proceedings... Salvador: AB³C, 2008. Não paginado. X-Meeting 2008.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 16. | | BORRO, L. C.; SALIM, J. A.; MAZONI, I.; YANO, I.; JARDINE, J. G.; NESHICH, G. Improving binding affinity prediction by using a rule-based model with physical-chemical and structural descriptors of the nano-environment for protein-ligand interactions. In: CONGRESS OF THE INTERNATIONAL UNION FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 23.; ANNUAL MEETING OF THE BRAZILIAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, 44., 2015, Foz do Iguaçu. Biochemistry for a better world: abstracts book. [Foz do Iguaçu]: SBBq, 2015. p. 153. C.047.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 18. | | MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JUNIOR, W. Protein structure topology comparison based on contact maps. 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-5.| Biblioteca(s): Embrapa Agricultura Digital. |
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| 19. | | MELO, R. C.; MAZONI, I.; NESHICH, G.; SANTORO, M. M.; MEIRA JÚNIOR, W. Contacts as the key elements for comparing two protein structures. 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-6.| Biblioteca(s): Embrapa Agricultura Digital. |
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| Registros recuperados : 77 | |
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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. |
Registro Completo
|
Biblioteca(s): |
Embrapa Agricultura Digital. |
|
Data corrente: |
26/11/2009 |
|
Data da última atualização: |
15/01/2020 |
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Tipo da produção científica: |
Resumo em Anais de Congresso |
|
Autoria: |
JARDINE, J. G.; NESHICH, I. A. P.; MORAES, F. R. de; MAZONI, I.; MANCINI, A.; SALIM, J. A.; NESHICH, G. |
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Afiliação: |
JOSE GILBERTO JARDINE, CNPTIA; IZABELLA AGOSTINHO PENA NESHICH, Estagiária/CNPTIA; FABIO ROGERIO DE MORAES, Bolsista/CNPTIA; IVAN MAZONI, CNPTIA; ADAUTO LUIZ MANCINI, CNPTIA; JOSÉ AUGUSTO SALIM, Estagiário/CNPTIA; GORAN NESHICH, CNPTIA. |
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Título: |
Generation of lipase B mutants with increased surface hydrophobicity in order to improve biodiesel catalysis. |
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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. |
|
Idioma: |
Inglês |
|
Notas: |
X-Meeting 2009. |
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Conteúdo: |
Biodiesel is a mixture of mono-alkyl esters of long-chain fatty acids and is considered to be a promise as an alternative fuel considering its favorable properties. The industrial production of biodiesel is generally based on transesterification of vegetal oils, in the presence of non-selective inorganic base or acid catalysts. It has been used for decades, but associated problems such as removal of catalysts, excessive energy requirements and the difficulties for purification of glycerol, still have not been solved. An alternative for the high cost to produce Biodiesel is based on enzymatic processes using Lipases as biocatalysts, a methodology that is undergoing a rapid development in accordance with the world demand for clean and selective processes. The use of Lipases as biocatalysts allows easy recovery of glycerol without purification or chemical waste production. Nevertheless, the yield of the process is lower than the one which uses inorganic catalysts. In order to create enzymes more suitable for this procedure, we hypothesized that a Lipase with a more hydrophobic surface would interact better with the substrate in the conversion of oil to biodiesel in a solvent-free system, generating a higher production compared to normal Lipases. Thus, we used the structure of Lipase Novozyme 435 from Candida Antarctica (PDB: 1TCB), which is widely used for this purpose and studied the accessibility to solvent, contact patterns and hydrophobicity of structure. We aimed to identify surface hydrophilic aminoacids which do not neighbor catalytic site nor do they influence important structural features. This enabled us to create mutant proteins with more surface Hydrophobicity. First, using Blue Star STING, we selected hydrophilic aminoacids which are located at surface with high solvent exposure (more than 40% of their total areas) and without contacts with other residues. The selected aminoacids were: Ser5, Thr244 and Arg309 which have, respectively, 111.8, 141.38 and 167.82 °A2 of exposed area at surface. We replaced these hydrophilic aminoacids by hydrophobic ones which have similar total area. The Serine 5 was substituted by an Alanine, the Threonine 244 by a Valine and the Arginine 309 by a Methionine. Finally, we created four modeled mutants using Modeller: the LIP1, which has the Ser5Ala mutation; the LIP2 with the Thr244Val mutation; LIP3, with Arg309Met; and LIP4 with the three mutations together: Ser5Ala, Thr244Val and Arg309Met. Models were validated with Ramanchandran plot analysis and ProSA web. We used the program SurfV to calculate solvent accessibility of the aminoacids, and calculated the Surface Hydrophobicity Index (SHI) with our new (unpublished) methodology using Perl scripts and MySQL. Java Protein Dossier was used to get contacts data and perform select procedure based on multiple selection conditions. We found that these mutations have no consequence on the internal contacts pattern of Lipase and we predict that probably they will not have an influence on catalytic site. Analysis of HSI revealed that the LIP4 mutant had the highest Hydrophobicity on surface (SHI: 0.839) compared to the other mutants and the wild type 1TCB (SHI: 0.712). We suggest LIP4 mutant as a good candidate for experimental test. In addition, the ratio of volume to surface (in A° ) is similar between mutants and wild type, showing there are no significant alterations in volume and total area of protein. Considering the percentage of surface occupied by each group of aminoacids, the LIP4 mutant has 47.4% of surface occupied by hydrophobic aminoacids, and wild type (1TCB) has 43.2%. Hence, we suggest using LIP4 mutant as biocatalyst for Biodiesel production and we expect that it will have a higher efficiency than the wild type. MenosBiodiesel is a mixture of mono-alkyl esters of long-chain fatty acids and is considered to be a promise as an alternative fuel considering its favorable properties. The industrial production of biodiesel is generally based on transesterification of vegetal oils, in the presence of non-selective inorganic base or acid catalysts. It has been used for decades, but associated problems such as removal of catalysts, excessive energy requirements and the difficulties for purification of glycerol, still have not been solved. An alternative for the high cost to produce Biodiesel is based on enzymatic processes using Lipases as biocatalysts, a methodology that is undergoing a rapid development in accordance with the world demand for clean and selective processes. The use of Lipases as biocatalysts allows easy recovery of glycerol without purification or chemical waste production. Nevertheless, the yield of the process is lower than the one which uses inorganic catalysts. In order to create enzymes more suitable for this procedure, we hypothesized that a Lipase with a more hydrophobic surface would interact better with the substrate in the conversion of oil to biodiesel in a solvent-free system, generating a higher production compared to normal Lipases. Thus, we used the structure of Lipase Novozyme 435 from Candida Antarctica (PDB: 1TCB), which is widely used for this purpose and studied the accessibility to solvent, contact patterns and hydrophobicity of structure. We aimed to identi... Mostrar Tudo |
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Palavras-Chave: |
Catálise de biodiesel; Hidrofobicidade; Modeller; Mutantes de lipase B. |
|
Thesaurus NAL: |
Biodiesel; Hydrophobicity; Mutants. |
|
Categoria do assunto: |
-- |
|
Marc: |
LEADER 04751nam a2200289 a 4500
001 1576258
005 2020-01-15
008 2009 bl uuuu u00u1 u #d
100 1 $aJARDINE, J. G.
245 $aGeneration of lipase B mutants with increased surface hydrophobicity in order to improve biodiesel catalysis.$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 $aBiodiesel is a mixture of mono-alkyl esters of long-chain fatty acids and is considered to be a promise as an alternative fuel considering its favorable properties. The industrial production of biodiesel is generally based on transesterification of vegetal oils, in the presence of non-selective inorganic base or acid catalysts. It has been used for decades, but associated problems such as removal of catalysts, excessive energy requirements and the difficulties for purification of glycerol, still have not been solved. An alternative for the high cost to produce Biodiesel is based on enzymatic processes using Lipases as biocatalysts, a methodology that is undergoing a rapid development in accordance with the world demand for clean and selective processes. The use of Lipases as biocatalysts allows easy recovery of glycerol without purification or chemical waste production. Nevertheless, the yield of the process is lower than the one which uses inorganic catalysts. In order to create enzymes more suitable for this procedure, we hypothesized that a Lipase with a more hydrophobic surface would interact better with the substrate in the conversion of oil to biodiesel in a solvent-free system, generating a higher production compared to normal Lipases. Thus, we used the structure of Lipase Novozyme 435 from Candida Antarctica (PDB: 1TCB), which is widely used for this purpose and studied the accessibility to solvent, contact patterns and hydrophobicity of structure. We aimed to identify surface hydrophilic aminoacids which do not neighbor catalytic site nor do they influence important structural features. This enabled us to create mutant proteins with more surface Hydrophobicity. First, using Blue Star STING, we selected hydrophilic aminoacids which are located at surface with high solvent exposure (more than 40% of their total areas) and without contacts with other residues. The selected aminoacids were: Ser5, Thr244 and Arg309 which have, respectively, 111.8, 141.38 and 167.82 °A2 of exposed area at surface. We replaced these hydrophilic aminoacids by hydrophobic ones which have similar total area. The Serine 5 was substituted by an Alanine, the Threonine 244 by a Valine and the Arginine 309 by a Methionine. Finally, we created four modeled mutants using Modeller: the LIP1, which has the Ser5Ala mutation; the LIP2 with the Thr244Val mutation; LIP3, with Arg309Met; and LIP4 with the three mutations together: Ser5Ala, Thr244Val and Arg309Met. Models were validated with Ramanchandran plot analysis and ProSA web. We used the program SurfV to calculate solvent accessibility of the aminoacids, and calculated the Surface Hydrophobicity Index (SHI) with our new (unpublished) methodology using Perl scripts and MySQL. Java Protein Dossier was used to get contacts data and perform select procedure based on multiple selection conditions. We found that these mutations have no consequence on the internal contacts pattern of Lipase and we predict that probably they will not have an influence on catalytic site. Analysis of HSI revealed that the LIP4 mutant had the highest Hydrophobicity on surface (SHI: 0.839) compared to the other mutants and the wild type 1TCB (SHI: 0.712). We suggest LIP4 mutant as a good candidate for experimental test. In addition, the ratio of volume to surface (in A° ) is similar between mutants and wild type, showing there are no significant alterations in volume and total area of protein. Considering the percentage of surface occupied by each group of aminoacids, the LIP4 mutant has 47.4% of surface occupied by hydrophobic aminoacids, and wild type (1TCB) has 43.2%. Hence, we suggest using LIP4 mutant as biocatalyst for Biodiesel production and we expect that it will have a higher efficiency than the wild type.
650 $aBiodiesel
650 $aHydrophobicity
650 $aMutants
653 $aCatálise de biodiesel
653 $aHidrofobicidade
653 $aModeller
653 $aMutantes de lipase B
700 1 $aNESHICH, I. A. P.
700 1 $aMORAES, F. R. de
700 1 $aMAZONI, I.
700 1 $aMANCINI, A.
700 1 $aSALIM, J. A.
700 1 $aNESHICH, G.
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