alexa Ab initio base fragment molecular orbital studies of in
ISSN: 1747-0862

Journal of Molecular and Genetic Medicine
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Short Article

Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors

Toshihiko Sawada1,2,*, Tomohiro Hashimoto3, Hiroaki Tokiwa1,4, Tohru Suzuki5, Hirofumi Nakano6, Hideharu Ishida7, Makoto Kiso1,7 ,Yasuo Suzuki1,2,8,*

1Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan,

2College of Life and Health Sciences, Chubu University, Kasugai, Aichi 487- 8501, Japan

3Faculty of Regional Studies, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan,

4Department of Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Tokyo 171-8501, Japan

5The United Graduate School of Agricultural Science, Gifu University, Japan,

6Department of Chemistry, Aichi University of Education, Kariya, Aichi 448-8542, Japan,

7Department of Applied Bioorganic Chemistry, Gifu University, Japan,

8Japan and Global COE Program for Innovation in Human Health Sciences, University of Shizuoka School of Pharmaceutical Sciences, 52-1 Yada, Shizuoka 422-8526, Japan

*Corresponding Author:
Toshihiko Sawada
Tel: +81 29 8613298
Fax: +81 29 8613171
Email: [email protected]
Yasuo Suzuki
Email: [email protected]
Tel/Fax: +81 568 516391

Received date: 26 July 2008, Revised date: 28 October 2008, Accepted date: 30 October 2008, Published online 26 November 2008

© Copyright The Authors:This is an open access article, published under the terms of the Creative Commons Attribution Non-Commercial License ( This license permits non- commercial use, distribution and reproduction of the article, provided the original work is appropriately acknowledged with correct citation details.



Mutations in avian influenza A viral hemagglutinin HA1 domain may alter the binding specificity of HA for F-sialosaccharide receptors, shifting the virus’s host range from birds to humans. The amino acid mutations can occur at the sialoside binding site, as well as the antigenic site, far from the binding site. Thus, a theoretical study involving the in silico prediction of HA-sialosaccharide binding may require quantum chemical analysis of HA1 full domain complexed with sialosides, balancing a computational cost with model size of HA1-sialoside complex. In addition, there is no insight to relationship between the model size of HA1-sialoside complex and its binding energy. In this study, H3 subtype HA1 full domains complexed with avian- and human-type Neu5AcF(2-3 and 2-6)Gal receptor analogs was investigated by ab initio based fragment molecular orbital (FMO) method at the level of second-order Møller–Plesset perturbation (MP2)/6- 31G. Using this approach, we found avian H3 HA1 to bind to avian F2-3 receptor more strongly than to human F2-6 receptor in gas phase, by a value of 15.3-16.5 kcal/mol. This binding benefit was larger than that in the small model complex. Analysis of the interfragment interaction energies (IFIEs) between Neu5Ac-Gal receptor and amino acid residues on the full domain of H3 HA1 also confirmed the higher avian H3-avian F2-3 binding specificity. It was particularly important to evaluate the IFIEs of amino acid residues in a 13Å radius around Neu5Ac-Gal to take account of long-range electrostatic interactions in the larger HA1- sialoside complex model. These results suggest suitable size of HA1-sialoside complex is significant to estimate HA1-sialoside binding energy and IFIE analysis with FMO method.


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