Title: Development of Chemical Bond based Elastic Network Model and its application in identifying functional motions in H5N1 highly pathogenic avian influenza viruses

Authors: Yunho Jang, Xiu-Feng Wan

Addresses: Influenza Division, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA. ' Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA

Abstract: Here we proposed a Chemical Bond based Elastic Network Model (CB-ENM) method, which was demonstrated with a better performance in representing functional movements, especially the local motions, than the conventional normal mode analysis. CB-ENM was applied in characterising functional motions in surface glycoprotein Haemagglutinin (HA) of H5N1 highly pathogenic avian influenza virus. Eleven local peaks were identified amongst HA fluctuation spectrum, and eight of these peaks were correlated with the reported five antigenic binding sites and Receptor Binding Sites (RBS) in influenza viruses. Our study showed that CB-ENM has a potential in identifying functional residues in protein structure.

Keywords: CB-ENM; chemical bond based elastic network model; normal mode analysis; functional motion; influenza virus; flu virus; H5N1 highly pathogenic avian influenza virus; bird flu; haemagglutinin; receptor binding sites; antigenic binding sites.

DOI: 10.1504/IJBRA.2010.031288

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.1, pp.1 - 11

Published online: 27 Jan 2010 *

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