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Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments
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SYSNO ASEP 0508974 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments Tvůrce(i) Owen, M. C. (CZ)
Karner, A. (AT)
Šachl, Radek (UFCH-W) RID, ORCID
Preiner, J. (AT)
Amaro, Mariana (UFCH-W) RID, ORCID
Vácha, R. (CZ)Zdroj.dok. Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 123, č. 35 (2019), s. 7504-7517Poč.str. 14 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova molecular-dynamics ; brain gangliosides ; membrane-lipids ; cholera-toxin ; simulations ; glycosphingolipids ; conformations ; glycolipids ; extension ; glycam06 Vědní obor RIV CF - Fyzikální chemie a teoretická chemie Obor OECD Physical chemistry CEP GA18-04871S GA ČR - Grantová agentura ČR GA17-03160S GA ČR - Grantová agentura ČR Způsob publikování Omezený přístup Institucionální podpora UFCH-W - RVO:61388955 UT WOS 000484882800003 EID SCOPUS 85072335907 DOI 10.1021/acs.jpcb.9b05095 Anotace The great physiological relevance of glycolipids is being increasingly recognized, and glycolipid interactions have been shown to be central to cell-cell recognition, neuronal plasticity, protein-ligand recognition, and other important processes. However, detailed molecular-level understanding of these processes remains to be fully resolved. Molecular dynamics simulations could reveal the details of the glycolipid interactions, but the results may be influenced by the choice of the employed force field. Here, we have compared the behavior and properties of GM1, a common, biologically important glycolipid, using the CHARMM36, OPLS, GROMOS, and Amber99-GLYCAMO6 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-snglycero-3-phosphocholine lipids and compared the results to atomic force microscopy and fluorescence resonance energy transfer experiments. We found discrepancies within the GM1 behavior displayed between the investigated force fields. Based on a direct comparison with complementary experimental results derived from fluorescence and AFM measurements, we recommend using the Amber99-GLYCAM force field in bilayers comprising LIPID14 or SLIPIDS lipids followed by CHARMM36 and OPLS force fields in simulations. The GROMOS force field is not recommended for reproducing the properties of the GM1 head group. Pracoviště Ústav fyzikální chemie J.Heyrovského Kontakt Michaela Knapová, michaela.knapova@jh-inst.cas.cz, Tel.: 266 053 196 Rok sběru 2020 Elektronická adresa http://hdl.handle.net/11104/0299797
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