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Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints
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SYSNO ASEP 0576127 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints Author(s) Biriukov, Denys (UOCHB-X) ORCID, RID
Javanainen, Matti (UOCHB-X) RID, ORCIDSource Title Journal of Chemical Theory and Computation . - : American Chemical Society - ISSN 1549-9618
Roč. 19, č. 18 (2023), s. 6332-6341Number of pages 10 s. Language eng - English Country US - United States Keywords linear constraint solver ; particle mesh Ewald ; molecular dynamics OECD category Physical chemistry R&D Projects LX22NPO5103 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 001061517800001 EID SCOPUS 85171789848 DOI https://doi.org/10.1021/acs.jctc.3c00614 Annotation The 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. 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.3c00614
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