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Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
2015 (English)In: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 29, no 1, 13-21 p.Article in journal (Refereed) Published
Abstract [en]

Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)(2), respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of +/- 0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.

Place, publisher, year, edition, pages
2015. Vol. 29, no 1, 13-21 p.
Keyword [en]
Binding energies, Expanded ensemble molecular dynamics, Carbohydrates, Docking
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-113551DOI: 10.1007/s10822-014-9792-5ISI: 000346913200002OAI: oai:DiVA.org:su-113551DiVA: diva2:786743
Note

AuthorCount:4;

Available from: 2015-02-06 Created: 2015-02-04 Last updated: 2017-12-04Bibliographically approved

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Lyubartsev, Alexander P.
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