Novel Rapid  Molecular Modeling Method Based on Evolutional Tree for Human Adenovirus Hexon Proteins Family

Chem. J. Chinese Universities ›› 2011, Vol. 32 ›› Issue (8): 1838.

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Novel Rapid Molecular Modeling Method Based on Evolutional Tree for Human Adenovirus Hexon Proteins Family

YUAN Xiao-Hui^1,2, WANG Ying-Chen², QU Zhang-Yi^2*, REN Jia-Yi^1,3, WANG Jing-Fei⁴, GUO Ying-Ying⁴, WANG Ya-Xian³, HUA Dong³, WU Xiao-Min⁵, YANG Zhi-Wei⁵, GAO Hong²

1. Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China;
2. Department of Hygienic Microbiology, School of Public Health, Harbin Medical University, Harbin 150081, China;
3. Department of Microbiology and Immunology, Institute of Basic Medicine, Heilongjiang University of Chinese Medicine, Harbin 150040, China;
4. Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150040, China;
5. Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China

Received:2010-09-27 Revised:2010-12-03 Online:2011-08-10 Published:2011-07-19
Contact: QU Zhang-Yi E-mail:qurainbow@yahoo.com.cn
Supported by:
国家自然科学基金(批准号: 30771909)、教育部博士点联合资助项目(批准号: 20070226007)、黑龙江省自然科学基金重点项目(批准号: ZJY0701)和黑龙江省教育厅科学技术项目(批准号: 11521172) 资助.

Abstract

Abstract: Human Adenoviruses (HAdVs) are responsible for many infectious diseases. 54 different serotypes of HAdVs have been identified so far, and the diversity of HAdVs has brought some difficulties to clinical diagnosis and therapy. In this study a novel rapid modeling method for proteins family has been developed on the basis of evolutionary tree, and by this method 7 hexon homologous proteins from D sub-specie Human Adenoviruses (HAdVs) were modeled. An evolutionary tree of these 7 hexon protein amino acid sequences was constructed by neighbor-joining (NJ) algorithm; Based on the information from the evolutional tree, an optimal modeling route was determined to accelerate the modeling of these hexons; And then, rapid modeling of hexons was automatically completed using homology modeling method within MODELER and CHARMM program; and the sturcures were proved to be acceptable by two assessment methods. Compared with the traditional scheme, this novel method can significantly reduce the amount of calculation. Every hexon structure model produced by this novel rapid modelling method could be reliably superimposed to the corresponding model produced by the traditional method. The rapid modeling of HAdVs hexon protein is very important to the molecular designing of HAdVs vaccines and the development of rapid HAdVs diagnostic typing agents.

Key words: Homology modeling, Evolutional tree, Human Adenovirus(HAdV), Hexon proteins family

CLC Number:

O641
R373.1

TrendMD:

YUAN Xiao-Hui, WANG Ying-Chen, QU Zhang-Yi*, REN Jia-Yi, WANG Jing-Fei, GUO Ying-Ying, WANG Ya-Xian, HUA Dong, WU Xiao-Min, YANG Zhi-Wei, GAO Hong. Novel Rapid Molecular Modeling Method Based on Evolutional Tree for Human Adenovirus Hexon Proteins Family[J]. Chem. J. Chinese Universities, 2011, 32(8): 1838.

References

[1] Madisch, I., et al., J Virol, 2005. 79(24). 15265-15276. [2] Kaneko, H., et al., J Gen Virol, 2009. 90(Pt 6). 1471-1476. [3] Zhang Hong-Yan (张鸿彦), et al., International Journal of Immunology (国际免疫学杂志), 2006. 29(2). 126-128. [4] Lu, X. and D.D. Erdman, Arch Virol, 2006. 151(8). 1587-1602. [5] Okada, M., et al., Arch Virol, 2007. 152(1). 1-9. [6] Berman, H.M., et al., Nucleic Acids Research, 2000. 28(1). 235-242. [7] Rux, J.J., P.R. Kuser, and R.M. Burnett, J Virol, 2003. 77(17). 9553-9566. [8] Pichla-Gollon, S.L., et al., J Virol, 2007. 81(4). 1680-1689. [9] YUAN Xiao-Hui (袁晓辉), QU Zhang-Yi (曲章义), and Wu Xiao-Min (吴晓敏), Chem. J. Chinese Universities (高等学校化学学报), 2009. 30(8). 1636-1640. [10] Yuan, X., et al., Vaccine, 2009. 27(37). 5103-5110. [11] ZHANG Yuan (张媛), et al., Chem. J. Chinese Universities (高等学校化学学报), 2005. 26(01). [12] ZHANG Lu-Jia (张鲁嘉), et al., Chem. J. Chinese Universities (高等学校化学学报), 2008. 29(05). 977-980. [13] Larkin, M.A., et al., Bioinformatics, 2007. 23(21). 2947-2948. [14] Tamura, K., et al., Mol Biol Evol, 2007. 24(8). 1596-1599. [15] Tang, K., et al., PLoS One. 5(7). e11604. [16] GUO Ying-Ying (郭莹莹), WU Chun-Yan (吴春艳), and WANG Jing-Fei (王靖飞), Chinese Journal of Preventive Veterinary Medicine (中国预防兽医学报), 2010. 32(3). 171-174. [17] Eswar, N., et al., Curr Protoc Bioinformatics, 2006. Chapter 5. Unit 5 6. [18] Gao Xue-Feng (高雪峰), et al., Chem. J. Chinese Universities (高等学校化学学报), 2003. 24(12). 2279-2281. [19] Van Der Spoel, D., et al., J Comput Chem, 2005. 26(16). 1701-1718. [20] Pr Bjelkmar, et al., J. Chem. Theory Comput, 2010. 6(2). 459–466. [21] Brooks, B.R., et al., J Comput Chem, 2009. 30(10). 1545-1614. [22] Sarzynska, J., et al., Biopolymers, 2008. 89(9). 732-746. [23] U. Essmann, L. Perera, and M.L. Berkowitz, J. Chem. Phys, 1995. 103. 8577-8529. [24] B. Hess, H. Bekker, and H.J.C. Berendsen, J. Comput. Chem, 1997. 18. 1463-1472. [25] Morris AL, et al., Proteins, 1992. 12. 345-364.

Novel Rapid Molecular Modeling Method Based on Evolutional Tree for Human Adenovirus Hexon Proteins Family

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