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Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions

[Image: see text] Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular leve...

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Autores principales: Javanainen, Matti, Heftberger, Peter, Madsen, Jesper J., Miettinen, Markus S., Pabst, Georg, Ollila, O. H. Samuli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10536986/
https://www.ncbi.nlm.nih.gov/pubmed/37616238
http://dx.doi.org/10.1021/acs.jctc.3c00648
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author Javanainen, Matti
Heftberger, Peter
Madsen, Jesper J.
Miettinen, Markus S.
Pabst, Georg
Ollila, O. H. Samuli
author_facet Javanainen, Matti
Heftberger, Peter
Madsen, Jesper J.
Miettinen, Markus S.
Pabst, Georg
Ollila, O. H. Samuli
author_sort Javanainen, Matti
collection PubMed
description [Image: see text] Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C–H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.
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spelling pubmed-105369862023-09-29 Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions Javanainen, Matti Heftberger, Peter Madsen, Jesper J. Miettinen, Markus S. Pabst, Georg Ollila, O. H. Samuli J Chem Theory Comput [Image: see text] Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C–H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches. American Chemical Society 2023-08-24 /pmc/articles/PMC10536986/ /pubmed/37616238 http://dx.doi.org/10.1021/acs.jctc.3c00648 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Javanainen, Matti
Heftberger, Peter
Madsen, Jesper J.
Miettinen, Markus S.
Pabst, Georg
Ollila, O. H. Samuli
Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title_full Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title_fullStr Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title_full_unstemmed Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title_short Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC–Cholesterol Interactions
title_sort quantitative comparison against experiments reveals imperfections in force fields’ descriptions of popc–cholesterol interactions
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10536986/
https://www.ncbi.nlm.nih.gov/pubmed/37616238
http://dx.doi.org/10.1021/acs.jctc.3c00648
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