Title

Structural study of biologically significant ligands with major birch pollen allergen Betv1 by docking and molecular dynamics simulation

Authors

Sangeeta Kundu and Debjani Roy*

Affiliation

Bioinformatics Centre, Bose Institute, Kolkata, India, Debjani Roy Bioinformatics Centre, Bose Institute, Acharya J.C Bose Centenary Building, P- 1/12 C.I.T Scheme –VII M, Kolkata – 700054 India

Email

debjani@bic.boseinst.ernet.in

Article Type

Hypothesis

Date

Received October 20, 2009; Accepted November 24, 2009; Published January 24, 2010

Abstract

The major birch pollen allergen, Betv1 of Betula verrucosa is the main causative agent of birch pollen allergy in humans. Betv1 is capable of binding several physiological ligands including fatty acids, flavones, cytokinins and sterols. Until now, no structural information from crystallography or NMR is available regarding binding mode of any of these ligands into the binding pocket of Betv1. In the present study thirteen ligands have been successfully docked into the hydrophobic cavity of Betv1 and binding free energies of the complexes have been calculated using AutoDock 3.0.5. A linear relationship with correlation coefficient (R2) of 0.6 is obtained between ΔGbs values plotted against their corresponding IC50 values. The complex formed between Betv1 and the best docking pose for each ligand has been optimized by molecular dynamics simulation. Here, we describe the ligand binding of Betv1, which provides insight into the biological function of this protein. This knowledge is required for structural alteration or inhibition of some of these ligands in order to modify the allergenic properties of this protein.

Keywords

Betula verrucosa ; Birch pollen allergy; Docking; Molecular dynamics simulation

Citation

Lim et al., Bioinformation, 4 (7) 326-330 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.