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Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites

[Image: see text] Despite the central role of lipids in many biophysical functions, the molecular mechanisms that dictate macroscopic lipid behavior remain elusive to both experimental and computational approaches. As such, there has been much interest in the development of low-resolution, implicit-...

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Autores principales: Pak, Alexander J., Dannenhoffer-Lafage, Thomas, Madsen, Jesper J., Voth, Gregory A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416712/
https://www.ncbi.nlm.nih.gov/pubmed/30702887
http://dx.doi.org/10.1021/acs.jctc.8b01033
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author Pak, Alexander J.
Dannenhoffer-Lafage, Thomas
Madsen, Jesper J.
Voth, Gregory A.
author_facet Pak, Alexander J.
Dannenhoffer-Lafage, Thomas
Madsen, Jesper J.
Voth, Gregory A.
author_sort Pak, Alexander J.
collection PubMed
description [Image: see text] Despite the central role of lipids in many biophysical functions, the molecular mechanisms that dictate macroscopic lipid behavior remain elusive to both experimental and computational approaches. As such, there has been much interest in the development of low-resolution, implicit-solvent coarse-grained (CG) models to dynamically simulate biologically relevant spatiotemporal scales with molecular fidelity. However, in the absence of solvent, a key challenge for CG models is to faithfully emulate solvent-mediated forces, which include both hydrophilic and hydrophobic interactions that drive lipid aggregation and self-assembly. In this work, we provide a new methodological framework to incorporate semiexplicit solvent effects through the use of virtual CG particles, which represent structural features of the solvent-lipid interface. To do so, we leverage two systematic coarse-graining approaches, multiscale coarse-graining (MS-CG) and relative entropy minimization (REM), in a hybrid fashion to construct our virtual-site CG (VCG) models. As a proof-of-concept, we focus our efforts on two lipid species, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), which adopt a liquid-disordered and gel phase, respectively, at room temperature. Through our analysis, we also present, to our knowledge, the first direct comparison between the MS-CG and REM methods for a complex biomolecule and highlight each of their strengths and weaknesses. We further demonstrate that VCG models recapitulate the rich biophysics of lipids, which enable self-assembly, morphological diversity, and multiple phases. Our findings suggest that the VCG framework is a powerful approach for investigation into macromolecular biophysics.
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spelling pubmed-64167122019-03-18 Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites Pak, Alexander J. Dannenhoffer-Lafage, Thomas Madsen, Jesper J. Voth, Gregory A. J Chem Theory Comput [Image: see text] Despite the central role of lipids in many biophysical functions, the molecular mechanisms that dictate macroscopic lipid behavior remain elusive to both experimental and computational approaches. As such, there has been much interest in the development of low-resolution, implicit-solvent coarse-grained (CG) models to dynamically simulate biologically relevant spatiotemporal scales with molecular fidelity. However, in the absence of solvent, a key challenge for CG models is to faithfully emulate solvent-mediated forces, which include both hydrophilic and hydrophobic interactions that drive lipid aggregation and self-assembly. In this work, we provide a new methodological framework to incorporate semiexplicit solvent effects through the use of virtual CG particles, which represent structural features of the solvent-lipid interface. To do so, we leverage two systematic coarse-graining approaches, multiscale coarse-graining (MS-CG) and relative entropy minimization (REM), in a hybrid fashion to construct our virtual-site CG (VCG) models. As a proof-of-concept, we focus our efforts on two lipid species, 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), which adopt a liquid-disordered and gel phase, respectively, at room temperature. Through our analysis, we also present, to our knowledge, the first direct comparison between the MS-CG and REM methods for a complex biomolecule and highlight each of their strengths and weaknesses. We further demonstrate that VCG models recapitulate the rich biophysics of lipids, which enable self-assembly, morphological diversity, and multiple phases. Our findings suggest that the VCG framework is a powerful approach for investigation into macromolecular biophysics. American Chemical Society 2019-01-31 2019-03-12 /pmc/articles/PMC6416712/ /pubmed/30702887 http://dx.doi.org/10.1021/acs.jctc.8b01033 Text en Copyright © 2019 American Chemical Society This is an open access article published under an ACS AuthorChoice License (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) , which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
spellingShingle Pak, Alexander J.
Dannenhoffer-Lafage, Thomas
Madsen, Jesper J.
Voth, Gregory A.
Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title_full Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title_fullStr Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title_full_unstemmed Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title_short Systematic Coarse-Grained Lipid Force Fields with Semiexplicit Solvation via Virtual Sites
title_sort systematic coarse-grained lipid force fields with semiexplicit solvation via virtual sites
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416712/
https://www.ncbi.nlm.nih.gov/pubmed/30702887
http://dx.doi.org/10.1021/acs.jctc.8b01033
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