Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388955%3A_____%2F19%3A00508974" target="_blank" >RIV/61388955:_____/19:00508974 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/19:00107895
Result on the web
<a href="http://hdl.handle.net/11104/0299797" target="_blank" >http://hdl.handle.net/11104/0299797</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1021/acs.jpcb.9b05095" target="_blank" >10.1021/acs.jpcb.9b05095</a>
Alternative languages
Result language
angličtina
Original language name
Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
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Volume of the periodical
123
Issue of the periodical within the volume
35
Country of publishing house
US - UNITED STATES
Number of pages
14
Pages from-to
7504-7517
UT code for WoS article
000484882800003
EID of the result in the Scopus database
2-s2.0-85072335907