BMC Genomics Proceedings Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin Nipa Jongkon1, Wanwimon Mokmak2, Daungmanee Chuakheaw1, Philip J Shaw2, Sissades Tongsima*2 and Chak Sangma*1 Addresses: 1Cheminformatics Research Unit, Department of Chemistry, Faculty of Science, Kasetsart University, Thailand and 2National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klongluang, Pathumthani 12120, Thailand E-mail: Nipa Jongkon - g5084005@ku.ac.th; Wanwimon Mokmak - wanwimon.mok@biotec.or.th; Daungmanee Chuakheaw - fscidnc@ku.ac.th; Philip J Shaw - philip@biotec.or.th; Sissades Tongsima* - sissades@biotec.or.th; Chak Sangma* - fscicsm@ku.ac.th *Corresponding author BioMed Central Open Access from Asia Pacific Bioinformatics Network (APBioNet) Eighth International Conference on Bioinformatics (InCoB2009) Singapore 7-11 September 2009 Published: 3 December 2009 BMC Genomics 2009, 10(Suppl 3):S24 doi: 10.1186/1471-2164-10-S3-S24 This article is available from: http://www.biomedcentral.com/1471-2164/10/S3/S24 © 2009 Jongkon et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barrier to viral transmission from birds to humans. However, strains may emerge with mutated hemagglutinin, potentially changing the receptor binding preference from avian to human-type. This hypothesis has been proven correct, since viral isolates from Vietnam and Thailand have been found which have increased selectivity toward the human cell receptor. The change in binding preference is due to mutation, which can be computationally modelled. The aim of this study is to further explore whether computational simulation could be used as a prediction tool for host type selectivity in emerging variants. Results: Molecular dynamics simulation was employed to study the interactions between receptor models and hemagglutinin proteins from H5N1 strains A/Duck/Singapore/3/97, mutated A/Duck/Singapore/3/97 (Q222L, G224S, Q222L/G224S), A/Thailand/1(KAN-1)/2004, and mutated A/Thailand/1(KAN-1)/2004 (L129V/A134V). The avian receptor was represented by Siaa(2,3)Gal substructure and human receptor by Siaa(2,6)Gal. The glycoside binding conformation was monitored throughout the simulations since high selectivity toward a particular host occurs when the sialoside bound with the near-optimized conformation. Page 1 of 9 (page number not for citation purposes)