Polarizable water model for the coarse-grained MARTINI force field.

Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, whic...

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Autores principales:	Semen O Yesylevskyy, Lars V Schäfer, Durba Sengupta, Siewert J Marrink
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/0b3dcf3b8db8455d93aa0b827749fa7e
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spelling	oai:doaj.org-article:0b3dcf3b8db8455d93aa0b827749fa7e2021-12-02T19:58:22ZPolarizable water model for the coarse-grained MARTINI force field.1553-734X1553-735810.1371/journal.pcbi.1000810https://doaj.org/article/0b3dcf3b8db8455d93aa0b827749fa7e2010-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20548957/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.Semen O YesylevskyyLars V SchäferDurba SenguptaSiewert J MarrinkPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 6, Iss 6, p e1000810 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Semen O Yesylevskyy Lars V Schäfer Durba Sengupta Siewert J Marrink Polarizable water model for the coarse-grained MARTINI force field.
description	Coarse-grained (CG) simulations have become an essential tool to study a large variety of biomolecular processes, exploring temporal and spatial scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization, and thus a proper screening of interactions depending on the local environment, is absent. Given the important role of water as a ubiquitous solvent in biological systems, its treatment is crucial to the properties derived from simulation studies. Here, we parameterize a polarizable coarse-grained water model to be used in combination with the CG MARTINI force field. Using a three-bead model to represent four water molecules, we show that the orientational polarizability of real water can be effectively accounted for. This has the consequence that the dielectric screening of bulk water is reproduced. At the same time, we parameterized our new water model such that bulk water density and oil/water partitioning data remain at the same level of accuracy as for the standard MARTINI force field. We apply the new model to two cases for which current CG force fields are inadequate. First, we address the transport of ions across a lipid membrane. The computed potential of mean force shows that the ions now naturally feel the change in dielectric medium when moving from the high dielectric aqueous phase toward the low dielectric membrane interior. In the second application we consider the electroporation process of both an oil slab and a lipid bilayer. The electrostatic field drives the formation of water filled pores in both cases, following a similar mechanism as seen with atomistically detailed models.
format	article
author	Semen O Yesylevskyy Lars V Schäfer Durba Sengupta Siewert J Marrink
author_facet	Semen O Yesylevskyy Lars V Schäfer Durba Sengupta Siewert J Marrink
author_sort	Semen O Yesylevskyy
title	Polarizable water model for the coarse-grained MARTINI force field.
title_short	Polarizable water model for the coarse-grained MARTINI force field.
title_full	Polarizable water model for the coarse-grained MARTINI force field.
title_fullStr	Polarizable water model for the coarse-grained MARTINI force field.
title_full_unstemmed	Polarizable water model for the coarse-grained MARTINI force field.
title_sort	polarizable water model for the coarse-grained martini force field.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/0b3dcf3b8db8455d93aa0b827749fa7e
work_keys_str_mv	AT semenoyesylevskyy polarizablewatermodelforthecoarsegrainedmartiniforcefield AT larsvschafer polarizablewatermodelforthecoarsegrainedmartiniforcefield AT durbasengupta polarizablewatermodelforthecoarsegrainedmartiniforcefield AT siewertjmarrink polarizablewatermodelforthecoarsegrainedmartiniforcefield
_version_	1718375763314475008

Polarizable water model for the coarse-grained MARTINI force field.

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