Large scale analysis of protein conformational transitions from aqueous to non-aqueous media
- Autores
- Velez Rueda, Ana Julia; Monzón, Alexander; Ardanaz, Sebastián Mario; Iglesias, Luis Emilio; Parisi, Gustavo Daniel
- Año de publicación
- 2018
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- Background: Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results: Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions: Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers.
Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Monzón, Alexander. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina
Fil: Ardanaz, Sebastián Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; Argentina
Fil: Iglesias, Luis Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; Argentina
Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina - Materia
-
BIOCATALYSIS
CONFORMATIONAL DIVERSITY
ORGANIC SOLVENTS
PROTEIN DYNAMICS - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/117604
Ver los metadatos del registro completo
id |
CONICETDig_f0149636172ea3b1039bc9f56b703853 |
---|---|
oai_identifier_str |
oai:ri.conicet.gov.ar:11336/117604 |
network_acronym_str |
CONICETDig |
repository_id_str |
3498 |
network_name_str |
CONICET Digital (CONICET) |
spelling |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous mediaVelez Rueda, Ana JuliaMonzón, AlexanderArdanaz, Sebastián MarioIglesias, Luis EmilioParisi, Gustavo DanielBIOCATALYSISCONFORMATIONAL DIVERSITYORGANIC SOLVENTSPROTEIN DYNAMICShttps://purl.org/becyt/ford/1.2https://purl.org/becyt/ford/1Background: Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results: Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions: Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers.Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Monzón, Alexander. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Ardanaz, Sebastián Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; ArgentinaFil: Iglesias, Luis Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; ArgentinaFil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaBioMed Central2018-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/117604Velez Rueda, Ana Julia; Monzón, Alexander; Ardanaz, Sebastián Mario; Iglesias, Luis Emilio; Parisi, Gustavo Daniel; Large scale analysis of protein conformational transitions from aqueous to non-aqueous media; BioMed Central; BMC Bioinformatics; 19; 1; 1-2018; 1-101471-2105CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2044-2info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-018-2044-2info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:08:01Zoai:ri.conicet.gov.ar:11336/117604instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:08:01.756CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
title |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
spellingShingle |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media Velez Rueda, Ana Julia BIOCATALYSIS CONFORMATIONAL DIVERSITY ORGANIC SOLVENTS PROTEIN DYNAMICS |
title_short |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
title_full |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
title_fullStr |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
title_full_unstemmed |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
title_sort |
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media |
dc.creator.none.fl_str_mv |
Velez Rueda, Ana Julia Monzón, Alexander Ardanaz, Sebastián Mario Iglesias, Luis Emilio Parisi, Gustavo Daniel |
author |
Velez Rueda, Ana Julia |
author_facet |
Velez Rueda, Ana Julia Monzón, Alexander Ardanaz, Sebastián Mario Iglesias, Luis Emilio Parisi, Gustavo Daniel |
author_role |
author |
author2 |
Monzón, Alexander Ardanaz, Sebastián Mario Iglesias, Luis Emilio Parisi, Gustavo Daniel |
author2_role |
author author author author |
dc.subject.none.fl_str_mv |
BIOCATALYSIS CONFORMATIONAL DIVERSITY ORGANIC SOLVENTS PROTEIN DYNAMICS |
topic |
BIOCATALYSIS CONFORMATIONAL DIVERSITY ORGANIC SOLVENTS PROTEIN DYNAMICS |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.2 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Background: Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results: Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions: Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers. Fil: Velez Rueda, Ana Julia. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Monzón, Alexander. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina Fil: Ardanaz, Sebastián Mario. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; Argentina Fil: Iglesias, Luis Emilio. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigación en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres". Grupo Vinculado al INGEBI- Laboratorio de Biocatálisis y Biotransformaciones - LBB - UNQUI; Argentina Fil: Parisi, Gustavo Daniel. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina |
description |
Background: Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results: Using proteins' experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions: Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-01 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
format |
article |
status_str |
publishedVersion |
dc.identifier.none.fl_str_mv |
http://hdl.handle.net/11336/117604 Velez Rueda, Ana Julia; Monzón, Alexander; Ardanaz, Sebastián Mario; Iglesias, Luis Emilio; Parisi, Gustavo Daniel; Large scale analysis of protein conformational transitions from aqueous to non-aqueous media; BioMed Central; BMC Bioinformatics; 19; 1; 1-2018; 1-10 1471-2105 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/117604 |
identifier_str_mv |
Velez Rueda, Ana Julia; Monzón, Alexander; Ardanaz, Sebastián Mario; Iglesias, Luis Emilio; Parisi, Gustavo Daniel; Large scale analysis of protein conformational transitions from aqueous to non-aqueous media; BioMed Central; BMC Bioinformatics; 19; 1; 1-2018; 1-10 1471-2105 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2044-2 info:eu-repo/semantics/altIdentifier/doi/10.1186/s12859-018-2044-2 |
dc.rights.none.fl_str_mv |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/2.5/ar/ |
eu_rights_str_mv |
openAccess |
rights_invalid_str_mv |
https://creativecommons.org/licenses/by/2.5/ar/ |
dc.format.none.fl_str_mv |
application/pdf application/pdf application/pdf application/pdf application/pdf application/pdf |
dc.publisher.none.fl_str_mv |
BioMed Central |
publisher.none.fl_str_mv |
BioMed Central |
dc.source.none.fl_str_mv |
reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
reponame_str |
CONICET Digital (CONICET) |
collection |
CONICET Digital (CONICET) |
instname_str |
Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.name.fl_str_mv |
CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas |
repository.mail.fl_str_mv |
dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
_version_ |
1844613946142621696 |
score |
13.070432 |