Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment

Autores
Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel
Año de publicación
2020
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. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of Cα atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one Cα seems to be a good balance between giving flexibility to the system and preserving its structure.
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. Universidad Industrial Santander; Colombia
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. Universidad Nacional Arturo Jauretche; 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. Universidad Tecnológica Nacional; 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. Universidad Tecnológica Nacional; Argentina
Materia
H-FABP: heart fatty acid binding protein
MD: Molecular Dynamics
PDB: Protein Data Bank
POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PCA: principal component analysis
NVT: constant Number of atoms Volume and Temperature
NpT: constant Number of atoms pressure and Temperature
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/154311
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/154311
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environmentEspinosa Silva, Yanis RicardoAlvarez, Hugo ArielHoward, Eduardo IgnacioCarlevaro, Carlos ManuelH-FABP: heart fatty acid binding proteinMD: Molecular DynamicsPDB: Protein Data BankPOPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholinePCA: principal component analysisNVT: constant Number of atoms Volume and TemperatureNpT: constant Number of atoms pressure and Temperaturehttps://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. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of <i>Cα</i> atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one <i>Cα</i> seems to be a good balance between giving flexibility to the system and preserving its structure.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. Universidad Industrial Santander; ColombiaFil: 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. Universidad Nacional Arturo Jauretche; 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; Argentina. Universidad Tecnológica Nacional; 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; Argentina. Universidad Tecnológica Nacional; ArgentinaTaylor & Francis Ltd2020-06-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/154311Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment; Taylor & Francis Ltd; Journal Of Biomolecular Structure & Dynamics; 39; 11-6-2020; 3459-34680739-11021538-0254CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.tandfonline.com/doi/full/10.1080/07391102.2020.1773315info:eu-repo/semantics/altIdentifier/doi/10.1080/07391102.2020.1773315info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:05:45Zoai:ri.conicet.gov.ar:11336/154311instacron: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 10:05:46.267CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
title Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
spellingShingle Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
Espinosa Silva, Yanis Ricardo
H-FABP: heart fatty acid binding protein
MD: Molecular Dynamics
PDB: Protein Data Bank
POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PCA: principal component analysis
NVT: constant Number of atoms Volume and Temperature
NpT: constant Number of atoms pressure and Temperature
title_short Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
title_full Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
title_fullStr Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
title_full_unstemmed Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
title_sort Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment
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: heart fatty acid binding protein
MD: Molecular Dynamics
PDB: Protein Data Bank
POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PCA: principal component analysis
NVT: constant Number of atoms Volume and Temperature
NpT: constant Number of atoms pressure and Temperature
topic H-FABP: heart fatty acid binding protein
MD: Molecular Dynamics
PDB: Protein Data Bank
POPC: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
PCA: principal component analysis
NVT: constant Number of atoms Volume and Temperature
NpT: constant Number of atoms pressure and Temperature
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. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of <i>Cα</i> atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one <i>Cα</i> seems to be a good balance between giving flexibility to the system and preserving its structure.
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. Universidad Industrial Santander; Colombia
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. Universidad Nacional Arturo Jauretche; 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. Universidad Tecnológica Nacional; 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. Universidad Tecnológica Nacional; 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. We explored different strategies to simulate a heart fatty acid binding protein (H-FABP) crystal by means of Molecular Dynamics (MD) simulations. We evaluate the effect of introducing restraints according to experimental isotropic B-factors and we analyzed the H-FABP motions in the crystal using Principal Component Analysis (PCA), isotropic and anisotropic B-factors. We compared the behavior of the protein simulated in the crystal confinement versus in solution, and we observed the effect of that confinement in the mobility of the protein residues. Restraining one-third of <i>Cα</i> atoms based on experimental B-factors produce lower B-factors than simulations without restraints, showing that the position restraint of the atoms with the lowest experimental B-factor is a good strategy to maintain the geometry of the crystal with an obvious decrease in the degrees of motion of the protein. PCA shows that, as position restraint reduces the conformational space explored by the system, the motion of the crystal is better recovered, for an essential subspace of the same size, in the simulations without restraints. Restraining only one <i>Cα</i> seems to be a good balance between giving flexibility to the system and preserving its structure.
publishDate 2020
dc.date.none.fl_str_mv 2020-06-11
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/11336/154311
Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment; Taylor & Francis Ltd; Journal Of Biomolecular Structure & Dynamics; 39; 11-6-2020; 3459-3468
0739-1102
1538-0254
CONICET Digital
CONICET
url http://hdl.handle.net/11336/154311
identifier_str_mv Espinosa Silva, Yanis Ricardo; Alvarez, Hugo Ariel; Howard, Eduardo Ignacio; Carlevaro, Carlos Manuel; Molecular dynamics simulation of the heart type fatty acid binding protein in a crystal environment; Taylor & Francis Ltd; Journal Of Biomolecular Structure & Dynamics; 39; 11-6-2020; 3459-3468
0739-1102
1538-0254
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://www.tandfonline.com/doi/full/10.1080/07391102.2020.1773315
info:eu-repo/semantics/altIdentifier/doi/10.1080/07391102.2020.1773315
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Taylor & Francis Ltd
publisher.none.fl_str_mv Taylor & Francis Ltd
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
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