Estudio de la dinámica de agregación proteica con TRP-cage

Autores
Faundez, Cristian Leonel; Meyra, Ariel Germán; Ferrara, Carlos Gastón
Año de publicación
2018
Idioma
español castellano
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In this work we propose a domain decomposition method based on Robin type boundary con- ditions that is suitable to solve the porous media equations on very large reservoirs. In order to reduce the algebraic systems to be solved to affordable sizes, a multiscale formulation is considered in which the coupling variables between subdomains, namely, pressures and normal fluxes, are seek in low dimen- sional spaces on the skeleton of the decomposition, while considering the permeability heterogeneities in the original fine grid for the local problems. In the new formulation, a non-dimensional parameter in the Robin condition is introduced such that we may transit smoothly from two well known formulations, namely, the Multiscale Mortar Mixed and the Multiscale Hybrid Mixed finite element methods. In the proposed formulation the interface spaces for pressure and fluxes can be selected independently. This has the potential to produce more accurate results by better accommodating local features of the exact solution near subdomain boundaries. Several numerical examples which exhibit highly heterogeneous permeability fields and channelized regions are solved with the new formulation and results compared to the aforementioned multiscale methods.
We studied by molecular dynamics (MD) aggregating two mini proteins such as TRP-cage (TRP) in neutral pH conditions and with explicit solvent. The results correspond to two different systems, the first with 3952 water molecules and one TRP and the second with 7654 water molecules and two TRPs. Both systems were simulated in NVT and NPT ensembles, with T = 300 K and P = 1 bar. The results show the formation of stable dimers in short simulation times. The analyzes made from the surface accessible to the solvent show that the main mechanism or driver of the formation of these dimers at neutral pH is the hydrophobic interaction between different sectors of the protein (hydrophobic amino acids).
Instituto de Física de Líquidos y Sistemas Biológicos
Materia
Bioquímica
Proteínas
TRP-cage
Superficie Accesible al Solvente (SASA)
Proteins
Solvent Accessible Surface (SASA)
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/96208

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network_name_str SEDICI (UNLP)
spelling Estudio de la dinámica de agregación proteica con TRP-cageStudy of protein aggregation dynamics with TRP-cageFaundez, Cristian LeonelMeyra, Ariel GermánFerrara, Carlos GastónBioquímicaProteínasTRP-cageSuperficie Accesible al Solvente (SASA)ProteinsSolvent Accessible Surface (SASA)In this work we propose a domain decomposition method based on Robin type boundary con- ditions that is suitable to solve the porous media equations on very large reservoirs. In order to reduce the algebraic systems to be solved to affordable sizes, a multiscale formulation is considered in which the coupling variables between subdomains, namely, pressures and normal fluxes, are seek in low dimen- sional spaces on the skeleton of the decomposition, while considering the permeability heterogeneities in the original fine grid for the local problems. In the new formulation, a non-dimensional parameter in the Robin condition is introduced such that we may transit smoothly from two well known formulations, namely, the Multiscale Mortar Mixed and the Multiscale Hybrid Mixed finite element methods. In the proposed formulation the interface spaces for pressure and fluxes can be selected independently. This has the potential to produce more accurate results by better accommodating local features of the exact solution near subdomain boundaries. Several numerical examples which exhibit highly heterogeneous permeability fields and channelized regions are solved with the new formulation and results compared to the aforementioned multiscale methods.We studied by molecular dynamics (MD) aggregating two mini proteins such as TRP-cage (TRP) in neutral pH conditions and with explicit solvent. The results correspond to two different systems, the first with 3952 water molecules and one TRP and the second with 7654 water molecules and two TRPs. Both systems were simulated in NVT and NPT ensembles, with T = 300 K and P = 1 bar. The results show the formation of stable dimers in short simulation times. The analyzes made from the surface accessible to the solvent show that the main mechanism or driver of the formation of these dimers at neutral pH is the hydrophobic interaction between different sectors of the protein (hydrophobic amino acids).Instituto de Física de Líquidos y Sistemas Biológicos2018-07info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdf17-22http://sedici.unlp.edu.ar/handle/10915/96208spainfo:eu-repo/semantics/altIdentifier/url/https://ri.conicet.gov.ar/11336/89284info:eu-repo/semantics/altIdentifier/issn/2027 6745info:eu-repo/semantics/altIdentifier/hdl/11336/89284info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2025-09-29T11:20:31Zoai:sedici.unlp.edu.ar:10915/96208Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292025-09-29 11:20:32.234SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv Estudio de la dinámica de agregación proteica con TRP-cage
Study of protein aggregation dynamics with TRP-cage
title Estudio de la dinámica de agregación proteica con TRP-cage
spellingShingle Estudio de la dinámica de agregación proteica con TRP-cage
Faundez, Cristian Leonel
Bioquímica
Proteínas
TRP-cage
Superficie Accesible al Solvente (SASA)
Proteins
Solvent Accessible Surface (SASA)
title_short Estudio de la dinámica de agregación proteica con TRP-cage
title_full Estudio de la dinámica de agregación proteica con TRP-cage
title_fullStr Estudio de la dinámica de agregación proteica con TRP-cage
title_full_unstemmed Estudio de la dinámica de agregación proteica con TRP-cage
title_sort Estudio de la dinámica de agregación proteica con TRP-cage
dc.creator.none.fl_str_mv Faundez, Cristian Leonel
Meyra, Ariel Germán
Ferrara, Carlos Gastón
author Faundez, Cristian Leonel
author_facet Faundez, Cristian Leonel
Meyra, Ariel Germán
Ferrara, Carlos Gastón
author_role author
author2 Meyra, Ariel Germán
Ferrara, Carlos Gastón
author2_role author
author
dc.subject.none.fl_str_mv Bioquímica
Proteínas
TRP-cage
Superficie Accesible al Solvente (SASA)
Proteins
Solvent Accessible Surface (SASA)
topic Bioquímica
Proteínas
TRP-cage
Superficie Accesible al Solvente (SASA)
Proteins
Solvent Accessible Surface (SASA)
dc.description.none.fl_txt_mv In this work we propose a domain decomposition method based on Robin type boundary con- ditions that is suitable to solve the porous media equations on very large reservoirs. In order to reduce the algebraic systems to be solved to affordable sizes, a multiscale formulation is considered in which the coupling variables between subdomains, namely, pressures and normal fluxes, are seek in low dimen- sional spaces on the skeleton of the decomposition, while considering the permeability heterogeneities in the original fine grid for the local problems. In the new formulation, a non-dimensional parameter in the Robin condition is introduced such that we may transit smoothly from two well known formulations, namely, the Multiscale Mortar Mixed and the Multiscale Hybrid Mixed finite element methods. In the proposed formulation the interface spaces for pressure and fluxes can be selected independently. This has the potential to produce more accurate results by better accommodating local features of the exact solution near subdomain boundaries. Several numerical examples which exhibit highly heterogeneous permeability fields and channelized regions are solved with the new formulation and results compared to the aforementioned multiscale methods.
We studied by molecular dynamics (MD) aggregating two mini proteins such as TRP-cage (TRP) in neutral pH conditions and with explicit solvent. The results correspond to two different systems, the first with 3952 water molecules and one TRP and the second with 7654 water molecules and two TRPs. Both systems were simulated in NVT and NPT ensembles, with T = 300 K and P = 1 bar. The results show the formation of stable dimers in short simulation times. The analyzes made from the surface accessible to the solvent show that the main mechanism or driver of the formation of these dimers at neutral pH is the hydrophobic interaction between different sectors of the protein (hydrophobic amino acids).
Instituto de Física de Líquidos y Sistemas Biológicos
description In this work we propose a domain decomposition method based on Robin type boundary con- ditions that is suitable to solve the porous media equations on very large reservoirs. In order to reduce the algebraic systems to be solved to affordable sizes, a multiscale formulation is considered in which the coupling variables between subdomains, namely, pressures and normal fluxes, are seek in low dimen- sional spaces on the skeleton of the decomposition, while considering the permeability heterogeneities in the original fine grid for the local problems. In the new formulation, a non-dimensional parameter in the Robin condition is introduced such that we may transit smoothly from two well known formulations, namely, the Multiscale Mortar Mixed and the Multiscale Hybrid Mixed finite element methods. In the proposed formulation the interface spaces for pressure and fluxes can be selected independently. This has the potential to produce more accurate results by better accommodating local features of the exact solution near subdomain boundaries. Several numerical examples which exhibit highly heterogeneous permeability fields and channelized regions are solved with the new formulation and results compared to the aforementioned multiscale methods.
publishDate 2018
dc.date.none.fl_str_mv 2018-07
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
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info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://sedici.unlp.edu.ar/handle/10915/96208
url http://sedici.unlp.edu.ar/handle/10915/96208
dc.language.none.fl_str_mv spa
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dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://ri.conicet.gov.ar/11336/89284
info:eu-repo/semantics/altIdentifier/issn/2027 6745
info:eu-repo/semantics/altIdentifier/hdl/11336/89284
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
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