Force Field Comparison of GM1 in a DOPC Bilayer Validated with
AFM and FRET Experiments.

J 2019

Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments.

OWEN, Michael Christopher; Andreas KARNER; Radek ŠACHL; Johannes PREINER; Mariana AMARO et al.

Základní údaje

Originální název

Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments.

Autoři

OWEN, Michael Christopher; Andreas KARNER; Radek ŠACHL; Johannes PREINER; Mariana AMARO a Robert VÁCHA

Vydání

JOURNAL OF PHYSICAL CHEMISTRY B, Washington, D.C. American Chemical Society, 2019, 1520-6106

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

Full Text

Impakt faktor

Impact factor: 2.857

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/19:00107895

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

MOLECULAR-DYNAMICS; BRAIN GANGLIOSIDES; MEMBRANE-LIPIDS; CHOLERA-TOXIN; SIMULATIONS; GLYCOSPHINGOLIPIDS; CONFORMATIONS; GLYCOLIPIDS; EXTENSION; GLYCAM06

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 3. 2020 15:46, Mgr. Pavla Foltynová, Ph.D.

Anotace

V originále

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-GLYCAM06 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-sn-glycero-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.

Návaznosti

GA17-11571S, projekt VaV

Název: Amfifilní peptidy na fosfolipidových membránách

Investor: Grantová agentura ČR, Amphiphilic Peptides at Phospholipid Membranes

Citovat

OWEN, Michael Christopher; Andreas KARNER; Radek ŠACHL; Johannes PREINER; Mariana AMARO a Robert VÁCHA. Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. JOURNAL OF PHYSICAL CHEMISTRY B. Washington, D.C.: American Chemical Society, 2019, roč. 123, č. 35, s. 7504-7517. ISSN 1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.9b05095.

@article{1597056,
   author = {Owen, Michael Christopher and Karner, Andreas and Šachl, Radek and Preiner, Johannes and Amaro, Mariana and Vácha, Robert},
   article_location = {Washington, D.C.},
   article_number = {35},
   doi = {https://doi.org/10.1021/acs.jpcb.9b05095},
   keywords = {MOLECULAR-DYNAMICS; BRAIN GANGLIOSIDES; MEMBRANE-LIPIDS; CHOLERA-TOXIN; SIMULATIONS; GLYCOSPHINGOLIPIDS; CONFORMATIONS; GLYCOLIPIDS; EXTENSION; GLYCAM06},
   language = {eng},
   issn = {1520-6106},
   journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
   title = {Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments.},
   url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b05095},
   volume = {123},
   year = {2019}
}

TY  - JOUR
ID  - 1597056
AU  - Owen, Michael Christopher - Karner, Andreas - Šachl, Radek - Preiner, Johannes - Amaro, Mariana - Vácha, Robert
PY  - 2019
TI  - Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments.
JF  - JOURNAL OF PHYSICAL CHEMISTRY B
VL  - 123
IS  - 35
SP  - 7504-7517
EP  - 7504-7517
PB  - American Chemical Society
SN  - 15206106
KW  - MOLECULAR-DYNAMICS
KW  - BRAIN GANGLIOSIDES
KW  - MEMBRANE-LIPIDS
KW  - CHOLERA-TOXIN
KW  - SIMULATIONS
KW  - GLYCOSPHINGOLIPIDS
KW  - CONFORMATIONS
KW  - GLYCOLIPIDS
KW  - EXTENSION
KW  - GLYCAM06
UR  - https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b05095
L2  - https://pubs.acs.org/doi/abs/10.1021/acs.jpcb.9b05095
N2  - 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-GLYCAM06 (in bilayers comprising SLIPIDS and LIPID14 lipids) force fields in bilayers comprising 1,2-dioleoyl-sn-glycero-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.
ER  -

OWEN, Michael Christopher; Andreas KARNER; Radek ŠACHL; Johannes PREINER; Mariana AMARO a Robert VÁCHA. Force Field Comparison of GM1 in a DOPC Bilayer Validated with AFM and FRET Experiments. \textit{JOURNAL OF PHYSICAL CHEMISTRY B}. Washington, D.C.: American Chemical Society, 2019, roč.~123, č.~35, s.~7504-7517. ISSN~1520-6106. Dostupné z: https://doi.org/10.1021/acs.jpcb.9b05095.

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