Macromolecular diffusion in crowded media beyond the hard-sphere model

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shou...

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Autores: Blanco Andrés, Pablo M., Garcés, Josep Lluís, Madurga Díez, Sergio, Mas i Pujadas, Francesc
Tipo de documento: artigo
Estado:Versión aceptada para publicación
Data de publicação:2018
País:España
Recursos:Universidad de Barcelona
Repositório:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/121895
Acesso em linha:https://hdl.handle.net/2445/121895
Access Level:Acceso aberto
Palavra-chave:Macromolècules
Moviment brownià
Hidrodinàmica
Processos de difusió
Macromolecules
Brownian movements
Hydrodynamics
Diffusion processes
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spelling Macromolecular diffusion in crowded media beyond the hard-sphere modelBlanco Andrés, Pablo M.Garcés, Josep LluísMadurga Díez, SergioMas i Pujadas, FrancescMacromolèculesMoviment browniàHidrodinàmicaProcessos de difusióMacromoleculesBrownian movementsHydrodynamicsDiffusion processesThe effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlong versus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (a) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and a are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.Royal Society of Chemistry2018info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionapplication/pdfhttps://hdl.handle.net/2445/121895Articles publicats en revistes (Ciència dels Materials i Química Física)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésVersió postprint del document publicat a: https://doi.org/10.1039/C8SM00201KSoft Matter, 2018, vol. 14, p. 3105-3114https://doi.org/10.1039/C8SM00201Kinfo:eu-repo/grantAgreement/EC/H2020/692146(c) Blanco, Pablo M. et al., 2018info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/1218952026-05-27T06:46:51Z
dc.title.none.fl_str_mv Macromolecular diffusion in crowded media beyond the hard-sphere model
title Macromolecular diffusion in crowded media beyond the hard-sphere model
spellingShingle Macromolecular diffusion in crowded media beyond the hard-sphere model
Blanco Andrés, Pablo M.
Macromolècules
Moviment brownià
Hidrodinàmica
Processos de difusió
Macromolecules
Brownian movements
Hydrodynamics
Diffusion processes
title_short Macromolecular diffusion in crowded media beyond the hard-sphere model
title_full Macromolecular diffusion in crowded media beyond the hard-sphere model
title_fullStr Macromolecular diffusion in crowded media beyond the hard-sphere model
title_full_unstemmed Macromolecular diffusion in crowded media beyond the hard-sphere model
title_sort Macromolecular diffusion in crowded media beyond the hard-sphere model
dc.creator.none.fl_str_mv Blanco Andrés, Pablo M.
Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author Blanco Andrés, Pablo M.
author_facet Blanco Andrés, Pablo M.
Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author_role author
author2 Garcés, Josep Lluís
Madurga Díez, Sergio
Mas i Pujadas, Francesc
author2_role author
author
author
dc.subject.none.fl_str_mv Macromolècules
Moviment brownià
Hidrodinàmica
Processos de difusió
Macromolecules
Brownian movements
Hydrodynamics
Diffusion processes
topic Macromolècules
Moviment brownià
Hidrodinàmica
Processos de difusió
Macromolecules
Brownian movements
Hydrodynamics
Diffusion processes
description The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlong versus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (a) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and a are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.
publishDate 2018
dc.date.none.fl_str_mv 2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/121895
url https://hdl.handle.net/2445/121895
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Versió postprint del document publicat a: https://doi.org/10.1039/C8SM00201K
Soft Matter, 2018, vol. 14, p. 3105-3114
https://doi.org/10.1039/C8SM00201K
info:eu-repo/grantAgreement/EC/H2020/692146
dc.rights.none.fl_str_mv (c) Blanco, Pablo M. et al., 2018
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Blanco, Pablo M. et al., 2018
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Royal Society of Chemistry
publisher.none.fl_str_mv Royal Society of Chemistry
dc.source.none.fl_str_mv Articles publicats en revistes (Ciència dels Materials i Química Física)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15.300724

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