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Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC-Cholesterol Interactions
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SYSNO ASEP 0575757 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Quantitative Comparison against Experiments Reveals Imperfections in Force Fields’ Descriptions of POPC-Cholesterol Interactions Author(s) Javanainen, Matti (UOCHB-X) RID, ORCID
Heftberger, P. (AT)
Madsen, J. J. (US)
Miettinen, M. S. (DE)
Pabst, G. (AT)
Ollila, O. H. S. (FI)Source Title Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
Roč. 19, č. 18 (2023), s. 6342-6352Number of pages 11 s. Language eng - English Country US - United States Keywords molecular-dynamics simulations ; lipid-bilayer structure ; small-angle neutron OECD category Physical chemistry Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 001114790000001 EID SCOPUS 85169887479 DOI https://doi.org/10.1021/acs.jctc.3c00648 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2024 Electronic address https://doi.org/10.1021/acs.jctc.3c00648
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