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ImprovedCoarse-GrainedModeling ofCholesterol-Containing Lipid Bilayers Michael D. DailyBrett N. OlsenPaul H. Schlesinger2014 год

Improved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
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Полный текстСтраница публикацииПубликация в OpenAlex
Аннотация: Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond timescales, it is essential to develop accurate coarse-grained simulation models that can reach these timescales. Cholesterol has been shown experimentally to thicken the membrane and increase phospholipid tail order between 0-40% cholesterol, above which these effects plateau or slightly decrease. Here, we showed that the published MARTINI coarse-grained force-field for phospholipid (POPC) and cholesterol fails to capture these effects. Using reference atomistic simulations, we systematically modified POPC and cholesterol bonded parameters in MARTINI to improve its performance. We showed that the corrections to pseudo-bond angles between glycerol and the lipid tails and around the oleoyl double bond particle (the "angle-corrected model") slightly improves the agreement of MARTINI with experimentally measured thermal, elastic, and dynamic properties of POPC membranes. The angle-corrected model improves prediction of the thickening and ordering effects up to 40% cholesterol but overestimates these effects at higher cholesterol concentration. In accordance with prior work that showed the cholesterol rough face methyl groups are important for limiting cholesterol self-association, we revised the coarse-grained representation of these methyl groups to better match cholesterol-cholesterol radial distribution functions from atomistic simulations. In addition, by using a finer-grained representation of the branched cholesterol tail than MARTINI, we improved predictions of lipid tail order and bilayer thickness across a wide range of concentrations. Finally, transferability testing shows that a model incorporating our revised parameters into DOPC outperforms other CG models in a DOPC/cholesterol simulation series, which further argues for its efficacy and generalizability. These results argue for the importance of systematic optimization for coarse-graining biologically important molecules like cholesterol with complicated molecular structure.
Год издания: 2014
Авторы: Michael D. Daily, Brett N. Olsen, Paul H. Schlesinger, Daniel S. Ory, Nathan Baker
Издательство: American Chemical Society
Источник: Journal of Chemical Theory and Computation
Ключевые слова: Lipid Membrane Structure and Behavior, Protein Structure and Dynamics, Metabolomics and Mass Spectrometry Studies
Другие ссылки: Journal of Chemical Theory and Computation (PDF)
Journal of Chemical Theory and Computation (HTML)
PubMed Central (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
PubMed (HTML)