CPL - Chalmers Publication Library
| Utbildning | Forskning | Styrkeområden | Om Chalmers | In English In English Ej inloggad.

Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations

Chaitanya A. K. Koppisetty (Institutionen för data- och informationsteknik, Datavetenskap, Bioinformatik (Chalmers)) ; M. Frank ; A. P. Lyubartsev ; P. G. Nyholm
Journal of Computer-Aided Molecular Design (0920-654X). Vol. 29 (2015), 1, p. 13-21.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: Binding energies; Expanded ensemble molecular dynamics; Carbohydrates; Docking

Denna post skapades 2015-01-29.
CPL Pubid: 211729


Läs direkt!

Länk till annan sajt (kan kräva inloggning)