Behavior of H-FABP-fatty acid complex in a protein crystal simulation

Autores
Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B?factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B?factors. Our results suggest that restrained MD simulations based in experimental B?factors produce lower simulated B?factors than simulations without restraints,leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.
Fil: Espinosa Silva, Yanis Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Carlevaro, Carlos Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Materia
H-FABP-fatty acid
protein crystal simulation
Principal Component Analysis
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/93833
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/93833
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Behavior of H-FABP-fatty acid complex in a protein crystal simulationEspinosa Silva, Yanis RicardoAlvarez, Hugo ArielHoward, Eduardo IgnacioCarlevaro, Carlos ManuelH-FABP-fatty acidprotein crystal simulationPrincipal Component Analysishttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B?factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B?factors. Our results suggest that restrained MD simulations based in experimental B?factors produce lower simulated B?factors than simulations without restraints,leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.Fil: Espinosa Silva, Yanis Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Carlevaro, Carlos Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaCornell University2018-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/93833Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Behavior of H-FABP-fatty acid complex in a protein crystal simulation; Cornell University; ArXiV; 6-2018; 1-302331-8422CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://arxiv.org/abs/1806.06102info:eu-repo/semantics/altIdentifier/url/https://www.zhuanzhi.ai/document/3d6eec7b205229493b7cae9d0a4bfac5info:eu-repo/semantics/altIdentifier/url/https://arxiv.org/abs/1806.06102info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:42:14Zoai:ri.conicet.gov.ar:11336/93833instacron: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 09:42:14.62CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title Behavior of H-FABP-fatty acid complex in a protein crystal simulation
spellingShingle Behavior of H-FABP-fatty acid complex in a protein crystal simulation
Espinosa Silva, Yanis Ricardo
H-FABP-fatty acid
protein crystal simulation
Principal Component Analysis
title_short Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_full Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_fullStr Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_full_unstemmed Behavior of H-FABP-fatty acid complex in a protein crystal simulation
title_sort Behavior of H-FABP-fatty acid complex in a protein crystal simulation
dc.creator.none.fl_str_mv Espinosa Silva, Yanis Ricardo
Alvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
author Espinosa Silva, Yanis Ricardo
author_facet Espinosa Silva, Yanis Ricardo
Alvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
author_role author
author2 Alvarez, Hugo Ariel
Howard, Eduardo Ignacio
Carlevaro, Carlos Manuel
author2_role author
author
author
dc.subject.none.fl_str_mv H-FABP-fatty acid
protein crystal simulation
Principal Component Analysis
topic H-FABP-fatty acid
protein crystal simulation
Principal Component Analysis
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B?factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B?factors. Our results suggest that restrained MD simulations based in experimental B?factors produce lower simulated B?factors than simulations without restraints,leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.
Fil: Espinosa Silva, Yanis Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Alvarez, Hugo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Carlevaro, Carlos Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
description Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the macromolecules and explore the microstates that the confined proteins can adopt in the crystalline network. In this paper, we explored different strategies to simulate a heart fatty acid binding proteins (H-FABP) crystal starting from high resolution coordinates obtained at room temperature, describing in detail the procedure to study protein crystals (in particular H-FABP) by means of Molecular Dynamics simulations, and exploring the role of ethanol as a co-solute that can modify the stability of the protein and facilitate the interchange of fatty acids. Also, we introduced crystallographic restraints in our crystal models, according to experimental isotropic B?factors and analyzed the H-FABP crystal motions using Principal Component Analysis, isotropic and anisotropic B?factors. Our results suggest that restrained MD simulations based in experimental B?factors produce lower simulated B?factors than simulations without restraints,leading to more accurate predictions of the temperature factors. However, the systems without positional restraints represent a higher microscopic heterogeneity in the crystal.
publishDate 2018
dc.date.none.fl_str_mv 2018-06
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/11336/93833
Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Behavior of H-FABP-fatty acid complex in a protein crystal simulation; Cornell University; ArXiV; 6-2018; 1-30
2331-8422
CONICET Digital
CONICET
url http://hdl.handle.net/11336/93833
identifier_str_mv Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Behavior of H-FABP-fatty acid complex in a protein crystal simulation; Cornell University; ArXiV; 6-2018; 1-30
2331-8422
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://arxiv.org/abs/1806.06102
info:eu-repo/semantics/altIdentifier/url/https://www.zhuanzhi.ai/document/3d6eec7b205229493b7cae9d0a4bfac5
info:eu-repo/semantics/altIdentifier/url/https://arxiv.org/abs/1806.06102
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
dc.publisher.none.fl_str_mv Cornell University
publisher.none.fl_str_mv Cornell University
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_ 1844613331089883136
score 13.069144

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