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Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints

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    SYSNO ASEP0576127
    Document TypeJ - Journal Article
    R&D Document TypeJournal Article
    Subsidiary JČlánek ve WOS
    TitleEfficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
    Author(s) Biriukov, Denys (UOCHB-X) ORCID, RID
    Javanainen, Matti (UOCHB-X) RID, ORCID
    Source TitleJournal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
    Roč. 19, č. 18 (2023), s. 6332-6341
    Number of pages10 s.
    Languageeng - English
    CountryUS - United States
    Keywordslinear constraint solver ; particle mesh Ewald ; molecular dynamics
    OECD categoryPhysical chemistry
    R&D ProjectsLX22NPO5103 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
    Method of publishingOpen access
    Institutional supportUOCHB-X - RVO:61388963
    UT WOS001061517800001
    EID SCOPUS85171789848
    DOI https://doi.org/10.1021/acs.jctc.3c00614
    AnnotationThe routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.
    WorkplaceInstitute of Organic Chemistry and Biochemistry
    Contactasep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418
    Year of Publishing2024
    Electronic addresshttps://doi.org/10.1021/acs.jctc.3c00614
Number of the records: 1  

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