Prediction of mutation position, mutated amino acid and timing in hemagglutinins from North America H1 influenza A virus


This study was trying to predict the mutations in H1 hemagglutinins of influenza A virus from North America including the predictions of mu-tation position, the predictions of would-be-mutated amino acids and the predictions of time of occurrence of mutations. The results paved a possible way for accurate, precise and reliable prediction of mutation in proteins from influenza A virus.

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Yan, S. and Wu, G. (2009) Prediction of mutation position, mutated amino acid and timing in hemagglutinins from North America H1 influenza A virus. Journal of Biomedical Science and Engineering, 2, 117-122. doi: 10.4236/jbise.2009.22021.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] G. Wu & S. Yan. (2008) Lecture Notes on Computational Muta-tion. Nova Science Publishers, New York.
[2] E. Ghedin, N. A. Sengamalay, M. Shumway, J. Zaborsky, T. Feldblyum, V. Subbu, D.J. Spiro, J. Sitz, H. Koo, P. Bolotov, D. Dernovoy, T. Tatusova, Y. Bao, K. St George, J. Taylor, D.J. Lipman, C.M. Fraser, J.K. Taubenberger & S.L. Salzberg. (2005) Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature, 437, 1162-1166.
[3] J. C. Obenauer, J. Denson, P. K. Mehta, X. Su, S. Mukatira, D. B. Finkelstein, X. Xu, J. Wang, J. Ma, Y. Fan, K.M. Rakestraw, R.G. Webster, E. Hoffmann, S. Krauss, J. Zheng, Z. Zhang & C.W. Naeve. (2006) Large-scale sequence analysis of avian in-fluenza isolates. Science, 311, 1576-1580.
[4] K. C. Chou. (2004) Structure bioinformatics and its impact to biomedical science. Curr. Med. Chem, 11, 2105-2134.
[5] K. C. Chou. (2004) Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem. Biophys. Res. Commun, 316, 636-642.
[6] K. C. Chou. Insights from modelling the 3D structure of extracel-lular domain of alpha 7 nicotinic acetylcholine receptor. Bio-chem. Biophys. Res. Commun, 319, 433-438.
[7] K. C. Chou. (2004) Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res. 2005, 4, 1681-1686.
[8] X. Xiao, S. Shao, Y. Ding, Z. Huang, X. Chen & K.C. Chou. (2005) An application of gene comparative image for predicting the effect on replication radio by HBV virus gene missense muta-tion. J. Theo. Biol, 235, 555-565.
[9] X. Xiao, S. H. Shao & K. C. Chou. (2006) A probability cellular automation model for hepatitis B viral infections. Biochem. Bio-phys. Res. Commun, 342, 605-610.
[10] S. Yan & G. Wu. (2008) Quantitative relationship between mu-tated amino-acid sequence of human copper-transporting AT-Pases and their related diseases. Mol. Divers, 12, 119-129.
[11] Q. S. Du, S.Q. Wang & K. C. Chou. (2007) Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase strcutre for trating drug-resistant H5N1 virus. Biochem. Bio-phys. Res. Commun, 363, 525-531.
[12] J. R. Schnell & J. J. Chou. (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 451, 591-595.
[13] S. Q. Wang, Q. S. Du & K. C. Chou. (2007) Study of drug resis-tance of chicken influenza A virus (H5N1) from homology-modeled 3D structure of neuraminidases. Biochem. Biophys. Res. Commun, 354, 634-640.
[14] D.Q. Wei, Q.S. Du, H. Sun & K.C. Chou. (2006) Insights from modeling the 3D structure of H5N1 influenza virus neuramini-dase and its binding interactions with ligands. Biochem. Bio-phys. Res. Commun, 344, 1048-1055.
[15] D. C. Wiley & J. J. Skehel. (1987) The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu. Rev. Biochem, 56, 365-394.
[16] Y. Kanegae, S. Sugita, K. F. Shortridge, Y. Yoshioka & K. Nerome. (1994) Origin and evolutionary pathways of the H1 hemagglutinin gene of avian, swine and human influenza vi-ruses: cocirculation of two distinct lineages of swine virus. Arch. Virol, 134: 17-28.
[17] A.H. Reid, T.G. Fanning, J.V. Hultin & J.K. Taubenberger. (1999) Origin and evolution of the 1918 "Spanish" influenza virus he-magglutinin gene. Proc. Natl. Acad. Sci. USA , 96, 1651-1656.
[18] J. K. Taubenberger, A. H. Reid, A. E. Krafft, K. E. Bijwaard & T. G. Fanning. (1997) Initial genetic characterization of the 1918 “Spanish” influenza virus. Science , 275, 1793-1796.
[19] Influenza virus resources. (2008) http://www.ncbi.nlm.nih. gov/genomes/FLU/Database/multiple.cgi.
[20] G. Wu & S. Yan. Randomness in the primary structure of pro-tein: methods and implications. Mol. Biol. Today 2002, 3: 55-69.
[21] G. Wu & S. Yan. (2006) Mutation trend of hemagglutinin of in-fluenza A virus: a review from computational mutation view-point. Acta Pharmacol. Sin, 27: 513-526.
[22] Amino-acid pair predictability. (2008) http://www.dreamscitech. com/Service/rationale.htm.
[23] G. Wu & S. Yan. (2000) Prediction of distributions of amino acids and amino acid pairs in human haemoglobin ?-chain and its seven variants causing ?-thalassemia from their occurrences according to the random mechanism. Comp. Haematol. Int, 10, 80-84.
[24] G. Wu & S. Yan. (2001) Analysis of distributions of amino ac-ids, amino acid pairs and triplets in human insulin precursor and four variants from their occurrences according to the random mechanism. J. Biochem. Mol. Biol. Biophys, 5, 293-300.
[25] G. Wu & S. Yan. (2001) Analysis of distributions of amino acids and amino acid pairs in human tumor necrosis factor precursor and its eight variants according to random mechanism. J. Mol. Model, 7, 318-323.
[26] G. Wu & S. Yan. (2002) Random analysis of presence and ab-sence of two-and three-amino-acid sequences and distributions of amino acids, two-and three-amino-acid sequences in bovine p53 protein. Mol. Biol. Today, 3: 31-37.
[27] G. Wu & S. Yan. (2002) Analysis of distributions of amino acids in the primary structure of apoptosis regulator Bcl-2 family ac-cording to the random mechanism. J. Biochem. Mol. Biol. Bio-phys, 6, 407-414.
[28] G. Wu & S. Yan. (2002) Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family accord-ing to the random mechanism. J. Mol. Model, 8, 191-198.
[29] G. Wu & S. Yan. (2004) Determination of sensitive positions to mutations in human p53 protein. Biochem. Biophys. Res. Com-mun, 321, 313-319.
[30] G. Wu & S. Yan. (2005) Searching of main cause leading to se-vere influenza A virus mutations and consequently to influenza pandemics/epidemics. Am. J. Infect. Dis., 1, 116-123.
[31] G. Wu & S. Yan. (2005) Prediction of mutation trend in hemag-glutinins and neuraminidases from influenza A viruses by means of cross-impact analysis. Biochem. Biophys. Res. Commun., 326, 475-482.
[32] W. Feller. (1968) An Introduction to Probability Theory and Its Applications. 3rd ed, Vol, I. Wiley, New York, p. 34-40.
[33] Amino-acid distribution probability. (2008) http://www.dream-scitech. com/Service/timing.htm.
[34] G. Wu & S. Yan. (2005) Determination of mutation trend in pro-teins by means of translation probability between RNA codes and mutated amino acids. Biochem. Biophys. Res. Commun, 337, 692-700.
[35] G. Wu & S. Yan. (2006) Determination of mutation trend in he-magglutinins by means of translation probability between RNA codons and mutated amino acids. Protein Pept. Lett, 13, 601-609.
[36] G. Wu & S. Yan. (2007) Translation probability between RNA codons and translated amino acids, and its applications to protein mutations. In: Leading-Edge Messenger RNA Research Commu-nications. ed. Ostrovskiy M. H. Nova Science Publishers, New York, Chapter 3, 47-65.
[37] Amino-acid mutating probability. (2008). http://www.dream-scitech. com/Service/lag.htm.
[38] MathWorks Inc. (2001) MatLab-The Language of Technical Computing (version, release 12.1), 1984-2001.
[39] Systat Software Inc. Systat for Windows, version 11.00.01. 2004.
[40] E. Andersson, S. Kühlmann-Berenzon, A. Linde, L. Schi?ler, S. Rubinova & M. Frisén. (2008) Predictions by early indicators of the time and height of the peaks of yearly influenza outbreaks in Sweden. Scand. J. Public Health, 36, 475-482.
[41] Y. T. Li, H. W. Zhang, H. Ren, J. Chen & Y. Wang. (2007) Appli-cation of time series analysis in the prediction of incidence trend of influenza-like illness in Shanghai. Zhonghua Yu Fang Yi Xue Za Zhi, 41, 496-498.
[42] J. Saltyte Benth & D. Hofoss. (2008) Modelling and prediction of weekly incidence of influenza A specimens in England and Wales. Epidemiol. Infect, 136, 1658-1666.
[43] R. Sebastian, D. M. Skowronski, M. Chong, J. Dhaliwal & J. S. Brownstein. (2008) Age-related trends in the timeliness and pre-diction of medical visits, hospitalizations and deaths due to pneumonia and influenza, British Columbia, Canada, 1998-2004. Vaccine, 4, 1397-1403.
[44] P. F. Craigmile, N. Kim, S. A. Fernandez & B. K. Bonsu. (2007) Modeling and detection of respiratory-related outbreak signa-tures. BMC Med. Inform. Decis. Mak, 7: 28.
[45] P. M. Polgreen, F. D. Nelson & G. R. Neumann. (2007) Use of prediction markets to forecast infectious disease activity. Clin. Infect. Dis, 44: 272-279.
[46] R. G. Webster. (1997) Predictions for future human influenza pandemics. J. Infect. Dis, 176 (Suppl 1): S14-S19.A. Suhrbier, C. Schmidt & A. Fernan. (1993) Prediction of an HLA B8-restricted influenza epitope by motif. Immunology, 79, 171-173.
[47] A. Suhrbier, C. Schmidt & A. Fernan. Prediction of an HLA B8-restricted influenza epitope by motif. Immunology. 1993, 79: 171-173.
[48] P. Somvanshi, V Singh & P. K. Seth. (2008) Prediction of epi-topes in hemagglutinin and neuraminidase proteins of influenza A virus H5N1 strain: a clue for diagnostic and vaccine develop-ment. OMICS, 12, 61-69.
[49] P. Gogolák, A. Simon, A. Horváth, B. Réthi, I. Simon, K. Berkics, E. Rajnav?lgyi & G.K. Tóth. (2000) Mapping of a pro-tective helper T cell epitope of human influenza A virus hemagglutinin. Biochem. Biophys. Res. Commun, 270: 190-198.
[50] M. Young, K. Kirshenbaum, K. A. Dill & S. Highsmith. (1999) Predicting conformational switches in proteins. Protein Sci, 8, 1752-1764.

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