Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization

Autores
Paz, Sergio Alexis; Maragliano, Luca; Abrams, Cameron F.
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K + ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.
Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Maragliano, Luca. Fondazione Istituto Italiano Di Tecnologia; Italia
Fil: Abrams, Cameron F.. Drexel University; Estados Unidos
Materia
ION CHANNELS
FREE ENERGY
ACCELERATED DYNAMICS
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:11336/85197
Acceder
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network_name_str CONICET Digital (CONICET)
spelling Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrizationPaz, Sergio AlexisMaragliano, LucaAbrams, Cameron F.ION CHANNELSFREE ENERGYACCELERATED DYNAMICShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K + ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Maragliano, Luca. Fondazione Istituto Italiano Di Tecnologia; ItaliaFil: Abrams, Cameron F.. Drexel University; Estados UnidosAmerican Chemical Society2018-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/85197Paz, Sergio Alexis; Maragliano, Luca; Abrams, Cameron F.; Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization; American Chemical Society; Journal of Chemical Theory and Computation; 14; 5; 5-2018; 2743-27501549-96181549-9626CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/10.1021/acs.jctc.8b00024info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.8b00024info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:53:47Zoai:ri.conicet.gov.ar:11336/85197instacron: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 09:53:47.921CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
title Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
spellingShingle Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
Paz, Sergio Alexis
ION CHANNELS
FREE ENERGY
ACCELERATED DYNAMICS
title_short Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
title_full Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
title_fullStr Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
title_full_unstemmed Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
title_sort Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization
dc.creator.none.fl_str_mv Paz, Sergio Alexis
Maragliano, Luca
Abrams, Cameron F.
author Paz, Sergio Alexis
author_facet Paz, Sergio Alexis
Maragliano, Luca
Abrams, Cameron F.
author_role author
author2 Maragliano, Luca
Abrams, Cameron F.
author2_role author
author
dc.subject.none.fl_str_mv ION CHANNELS
FREE ENERGY
ACCELERATED DYNAMICS
topic ION CHANNELS
FREE ENERGY
ACCELERATED DYNAMICS
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K + ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.
Fil: Paz, Sergio Alexis. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentina
Fil: Maragliano, Luca. Fondazione Istituto Italiano Di Tecnologia; Italia
Fil: Abrams, Cameron F.. Drexel University; Estados Unidos
description We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to investigate the process of K + ions translocation inside the Kv1.2 channel. By comparing a series of two-dimensional free energy surfaces for ion movement calculated with different conditions on the intercalated water molecules, we first recapitulate the widely accepted knock-on mechanism for ion translocation and then confirm that permeation occurs with water molecules alternated among the ions, in accordance with the latest experimental findings. From a methodological standpoint, our new OTFP-2D algorithm demonstrates the excellent sampling acceleration of temperature-accelerated molecular dynamics and the ability to efficiently compute 2D free-energy surfaces. It will therefore be useful in large variety complex biomacromolecular simulations.
publishDate 2018
dc.date.none.fl_str_mv 2018-05
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/11336/85197
Paz, Sergio Alexis; Maragliano, Luca; Abrams, Cameron F.; Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization; American Chemical Society; Journal of Chemical Theory and Computation; 14; 5; 5-2018; 2743-2750
1549-9618
1549-9626
CONICET Digital
CONICET
url http://hdl.handle.net/11336/85197
identifier_str_mv Paz, Sergio Alexis; Maragliano, Luca; Abrams, Cameron F.; Effect of intercalated water on potassium ion transport through Kv1.2 channels studied via on-the-fly free-energy parametrization; American Chemical Society; Journal of Chemical Theory and Computation; 14; 5; 5-2018; 2743-2750
1549-9618
1549-9626
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://pubs.acs.org/doi/10.1021/acs.jctc.8b00024
info:eu-repo/semantics/altIdentifier/doi/10.1021/acs.jctc.8b00024
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
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
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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score 13.070432

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