Modelling of beta-D-glucopyranose ring distortion in different force fields: a metadynamics study

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F10%3A00024204" target="_blank" >RIV/60461373:22330/10:00024204 - isvavai.cz</a>
Result on the web
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DOI - Digital Object Identifier
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Result language
angličtina
Original language name
Modelling of beta-D-glucopyranose ring distortion in different force fields: a metadynamics study
Original language description
Modelling of carbohydrate conformations is a challenging task for force field developers. Three carbohydrate force fields, namely GLYCAM06, GROMOS 45a4 and OPLS were evaluated. Free energies of different ring conformations of beta-D-glucopyranose were calculated using metadynamics in vacuum as well as in explicitly modelled water. All three force fields model the (4)C(1) conformation as the most stable by at least 6kJ/mol, as compared to other conformations. Interconversion from the (4)C(1) to any otherconformation is associated with a barrier of no lower than 26kJ/mol. The free energy surface calculated in the GLYCAM06 force field is in remarkably good agreement with the recent Car-Parrinello metadynamics study. The effect of a water environment is relatively low and analogous in all tested force fields. Namely, the presence of water stabilizes the upper-left ((3,O)B) versus bottom-right (B(3,O)) area of Stoddard's plot, relative to the situation in vacuum. Comparison of free and pot
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CE - Biochemistry
OECD FORD branch
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Publication year
2010
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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