Prediction of mutations initiated by internal power in H3N2 hemagglutinins of influenza A virus from North America

International Journal of Peptide Research and Therapeutics

Volumn 14, Issue 1, 2008, Pages 41-51

  Wu, Guang ^a   Yan, Shaomin ^a  

^a DreamSciTech Consulting   (China)

Author keywords

Amino acid; Hemagglutinin; Influenza; Logistic regression; Mutation; Prediction

Indexed keywords

AMINO ACID; VIRUS HEMAGGLUTININ; VIRUS PROTEIN;

ARTICLE; CORRELATION ANALYSIS; INFLUENZA VIRUS A H3N2; LOGISTIC REGRESSION ANALYSIS; MATHEMATICAL MODEL; MUTATIONAL ANALYSIS; NONHUMAN; NORTH AMERICA; NUCLEOTIDE SEQUENCE; PREDICTION; QUANTITATIVE ANALYSIS; RANDOMIZATION; VIRUS MUTATION;

INFLUENZA A VIRUS;

EID: 40049092267     PISSN: 15733149     EISSN: 15733904     Source Type: Journal    
DOI: 10.1007/s10989-007-9104-1     Document Type: Article

References (114)

1. Abbottbase Pharmacokinetic System Operations Manual version 1.10, Abbott Laboratories, Abbott Park, IL (1992) 6:45-62
2. Althaus IW, Chou JJ, Gonzales AJ, Diebel MR, Chou KC, Kezdy FJ, Romero DL, Aristoff PA, Tarpley WG, Reusser F (1993a) Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. J Biol Chem 268:6119-6124
3. Althaus IW, Chou JJ, Gonzales AJ, Diebel MR, Chou KC, Kezdy FJ, Romero DL, Aristoff PA Tarpley WG, Reusser F (1993b) Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry 32:6548-6554
4. Althaus IW, Gonzales AJ, Chou JJ, Diebel MR, Chou KC, Kezdy FJ, Romero DL, Aristoff PA, Tarpley WG, Reusser F (1993c) The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J Biol Chem 268:14875-14880
5. Bean WJ, Schell M, Katz J, Kawaoka Y, Naeve C, Gorman O, Webster RG (1992) Evolution of the H3 influenza virus hemagglutinin from human and nonhuman hosts. J Virol 66:1129-1138
6. Chi XS, Bolar TV, Zhao P, Tam JS, Rappaport R, Cheng SM (2005) Molecular Evolution of Human Influenza A/H3N2 Virus in Asia and Europe from 2001 to 2003. J Clin Microbiol 43:6130-6132
7. Chou JJ (1993a) A formulation for correlating properties of peptides and its application to predicting human immunodeficiency virus protease-cleavable sites in proteins. Biopolymers 33:1405-1414
8. Chou JJ (1993b) Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach. J Protein Chem 12:291-302
9. Chou KC (1993) A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J Biol Chem 268:16938-16948
10. Chou KC (1996) Prediction of HIV protease cleavage sites in proteins. Anal Biochem 233:1-14
11. Chou KC (2004a) Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor. Biochem Biophys Res Commun 319:433-438
12. Chou KC (2004b) Insights from modelling the tertiary structure of BACE2. J Proteome Res 3:1069-1072
13. Chou KC (2004c) Molecular therapeutic target for type-2 diabetes. J Proteome Res 3:1284-1288
14. Chou KC (2004d) Structural bioinformatics and its impact to biomedical science. Curr Med Chem 11:2105-2134
15. Chou KC (2005) Modeling the tertiary structure of human cathepsin-E. Biochem Biophys Res Commun 331:56-60
16. Chou KC (2006) Modelling extracellular domains of GABA-A receptors: subtypes 1:2, 3, and 5. Biochem Biophys Res Commun 316:636-642
17. Chou KC, Jones D, Heinrikson RL (1997) Prediction of the tertiary structure and substrate binding site of caspase-8. FEBS Lett 419:49-54
18. Chou KC, Kezdy FJ, Reusser F (1994) Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Anal Biochem 221:217-230
19. Chou KC, Tomasselli AG, Heinrikson RL (2000) Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Lett 470:249-256
20. Chou KC, Watenpaugh KD, Heinrikson RL (1999) A Model of the complex between cyclin-dependent kinase 5(Cdk5) and the activation domain of neuronal Cdk5 activator. Biochem Biophys Res Commun 259:420-428
21. Chou KC, Wei DQ, Zhong WZ (2003) Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem Biophys Res Comm 308:148-151 (Erratum: ibid, 2003, 310, 675)
22. Chou KC, Wei DQ, Du QS, Sirois S, Zhong WZ (2006) Progress in computational approach to drug development against SARS. Curr Med Chem 13:3263-3270
23. Demuth H, Beale M (2001) Neural network toolbox for use with MatLab. version 4
24. Draper NR, Smith H (1981) Applied regression analysis, 2nd edn. Wiley, New York
25. Du QS, Mezey PG, Chou KC (2005) Heuristic molecular lipophilicity potential (HMLP): a 2D-QSAR study to LADH of molecular family pyrazole and derivatives. J Comput Chem 26:461-470
26. Du QS, Sun H, Chou KC (2007) Inhibitor design for SARS coronavirus main protease based on "distorted key theory". Med Chem 3:1-6
27. Elhammer AP, Poorman RA, Brown E, Maggiora LL, Hoogerheide JG, Kezdy FJ (1993) The specificity of UDP-GalNAc:polypeptide N- acetylgalactosaminyltransferase as inferred from a database of in vivo substrates and from the in vitro glycosylation of proteins and peptides. J Biol Chem 268:10029-10038
28. Everitt BS (1999) Chance rules: an informal guide to probability, risk, and statistics. Springer, New York
29. Feller W (1968) An introduction to probability theory and its applications, 3rd edn., vol I. Wiley, New York
30. Fitch WM, Bush RM, Bender CA, Cox NJ (1997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci USA 94:7712-7718
31. Fitch WM, Leiter JME, Xingqiang L, Palese P (1991) Positive Darwinian evolution in human influenza viruses. Proc Natl Acad Sci USA 88:4270-4274
32. Gan YR, Huang H, Huang YD, Rao CM, Zhao Y, Liu JS, Wu L, Wei DQ (2006) Synthesis and activity assess of an octapeptide inhibitor designed for SARS coronavirus main proteinase. Peptides 27:622-625
33. Gao WN, Wei DQ Li Y, Gao H, Xu WR, Li AX, Chou KC (2007) Agaritine and its derivatives are potential inhibitors against HIV proteases. Med Chem 3:221-226
34. Gao N, Yan S, Wu G (2006) Pattern of positions sensitive to mutations in human haemoglobin α-chain. Protein Pept Lett 13:101-107
35. Hay AJ, Douglas AR, Sparrow DB, Cameron KR, Skehel JJ (1994) Antigenic and genetic characterization of current influenza strains. Eur J Epidemiol 10:465-466
36. Healy MJR (1979) Outliers in clinical chemistry quality-control schemes. Clin Chem 25:675-677
37. Hope-Simpson RE, Golubev DB (1987) A new concept of the epidemic process of influenza A virus. Epidemiol Infect 99:5-54
38. Hosmer DW Jr, Lemeshow S (2000) Applied logistic regression, 2nd edn. Wiley, New York
39. Influenza virus resources. (2006) http://www.ncbi.nlm.nih.gov/genomes/ FLU/Database/multiple.cgi
40. Laver WG, Webster RG (1973) Studies on the origin of pandemic influenza III. Evidence implicating duck and equine influenza viruses as possible progenitors of the Hong Kong strain of human influenza. Virology 51:383-391
41. Lee MS, Chen JS (2004) Predicting antigenic variants of influenza A/H3N2 viruses. Emerg Infect Dis 10:1385-1390
42. Li L, Wei DQ, Wang JF, Chou KC (2007) Computational studies of the binding mechanism of calmodulin with chrysin. Biochem Biophys Res Comm 358:1102-1107
43. MathWorks Inc. (2001) MatLab - the language of technical computing (version 6.1.0.450, release 12.1) 1984-2001
44. Miller WG (2006) OpenStat4, version 13, release 3, http://www.statpages. org/miller/openstat
45. Nakajima K, Nobusawa E, Nagy A, Nakajima S (2005) Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution. J Virol 79:6472-6477
46. Plotkin JB, Dushoff J (2003) Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proc Natl Acad Sci USA 100:7152-7157
47. Plotkin JB, Dushoff J, Levin SA (2002) Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proc Natl Acad Sci USA 99:6263-6268
48. Poorman RA Tomasselli AG, Heinrikson RL, Kezdy FJ (1991) A cumulative specificity model for proteases from human immunodeficiency virus types 1 and 2, inferred from statistical analysis of an extended substrate data base. J Biol Chem 266:14554-14561
49. Potter CW (2001) A history of influenza. J Appl Microbiol 91:572-579
50. PROSITE (2002) A dictionary of protein sites and patterns user manual. http://www.expasy.ch/prosite/
51. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus AD, Fouchier RA (2004) Mapping the antigenic and genetic evolution of influenza virus. Science 305:371-376
52. SPSS Inc. SigmaStat for Windows, version 3.00. 1992-2003
53. SYSTAT Software Inc. (2004) Systat for Windows, version 11.00.01
54. Thompson TB Chou KC, Zheng C (1995) Neural network prediction of the HIV-1 protease cleavage sites. J Theor Biol 177:369-379
55. Wang JF, Wei DQ, Li L, Zheng SY, Li YX, Chou KC (2007a) 3D structure modeling of cytochrome P450 2C19 and its implication for personalized drug design. Biochem Biophys Res Commun 355:513-519 (Corrigendum: ibid, 2007, 357, 330)
56. Wang SQ, Du QS, Chou KC (2007b) Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem Biophys Res Comm 354:634-640
57. Wang JF, Wei DQ, Lin Y, Wang YH, Du HL, Chou KC (2007c) Insights from modeling the 3D structure of NAD(P)H-dependent D-xylose reductase of Pichia stipitis and its binding interactions with NAD and NADP. Biochem Biophys Res Comm 359:323-329
58. Wang M, Katz JM, Webster RG (1989) Extensive heterogeneity in the hemagglutinin of egg-grown influenza viruses from different patients. Virology 171:275-279
59. Wei DQ, Du QS, Sun H, Chou KC (2006) Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Biochem Biophys Res Comm 344:1048-1055
60. Wei H, Zhang R, Wang C, Zheng H, Chou KC, Wei DQ (2007) Molecular insights of SAH enzyme catalysis and their implication for inhibitor design. J Theor Biol 244:692-702
61. Wiley DC, Skehel JJ (1987) The structure and function of the hemagglutinin membrane glycoprotein of influenza virus. Annu Rev Biochem 56:365-394
62. 2 affinity. Comp Haematol Int 9:148-151
63. Wu G (2000a) Frequency and Markov chain analysis of amino-acid sequence of human glutathione reductase. Biochem Biophys Res Commun 268:823-826
64. Wu G (2000b) Frequency and Markov chain analysis of amino-acid sequence of human tumor necrosis factor. Cancer Lett 153:145-150
65. Wu G (2000c) Frequency and Markov chain analysis of amino-acid sequences of mouse p53. Hum Exp Toxicol 19:535-539
66. Wu G (2000d) Frequency and Markov chain analysis of the amino acid sequence of human alcohol dehydrogenase α-chain. Alcohol Alcohol 35:302-306
67. Wu G (2000e) Frequency and Markov chain analysis of the amino-acid sequence of sheep p53 protein. J Biochem Mol Biol Biophys 4:179-185
68. Wu G (2000f) The first, second and third order Markov chain analysis on amino acids sequence of human tyrosine aminotransferase and its variant causing tyrosinemia type II. Pediatr Relat Top 39:37-47
69. Wu G (2000g) The first, second, third and fourth order Markov chain analysis on amino acids sequence of human dopamine β-hydroxylase. Mol Psychiatry 5:448-451
70. Wu G, Yan S (2000a) Frequency and Markov chain analysis of amino-acids sequence of human platelet-activating factor acetylhydrolase α-subunit and its variant causing the lissencephaly syndrome. Pediatr Relat Top 39:513-526
71. Wu G, Yan S (2000b) Prediction of two- and three-amino acid sequence of human acute myeloid leukemia 1 protein from its amino acid composition. Comp Haematol Int 10:85-89
72. Wu G, Yan S (2000c) Prediction of two- and three-amino-acid sequences of Citrobacter Freundii β-lactamase from its amino acid composition. J Mol Microbiol Biotechnol 2:277-281
73. Wu G, Yan S (2000d) Prediction of distributions of amino acids and amino acid pairs in human haemoglobin α-chain and its seven variants causing α-thalassemia from their occurrences according to the random mechanism. Comp Haematol Int 10:80-84
74. Wu G, Yan S (2001a) Frequency and Markov chain analysis of amino-acid sequences of human connective tissue growth factor. J Mol Model 5:120-124
75. Wu G, Yan S (2001b) Prediction of presence and absence of two- and three-amino-acid sequence of human monoamine oxidase B from its amino acid composition according to the random mechanism. Biomol Eng 18:23-27
76. Wu G, Yan S (2001c) Prediction of presence and absence of two- and three-amino-acid sequence of human tyrosinase from their amino acid composition and related changes in human tyrosinase variant causing oculocutaneous albinism. Pediatr Relat Top 40:153-166
77. Wu G, Yan S (2001d) Analysis of distributions of amino acids, 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
78. Wu G, Yan S (2001e) 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
79. Wu G, Yan S (2002a) Determination of amino acid pairs sensitive to variants in human low-density lipoprotein receptor precursor by means of a random approach. J Biochem Mol Biol Biophys 6:401-406
80. Wu G, Yan S (2002b) Estimation of amino acid pairs sensitive to variants in human phenylalanine hydroxylase protein by means of a random approach. Peptides 23:2085-2090
81. Wu G, Yan S (2002c) Random analysis of presence and absence 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
82. Wu G, Yan S (2002d) Analysis of distributions of amino acids in the primary structure of apoptosis regulator Bcl-2 family according to the random mechanism. J Biochem Mol Biol Biophys 6:407-414
83. Wu G, Yan S (2002e) Analysis of distributions of amino acids in the primary structure of tumor suppressor p53 family according to the random mechanism. J Mol Model 8:191-198
84. Wu G, Yan S (2002f) Randomness in the primary structure of protein: methods and implications. Mol Biol Today 3:55-69
85. Wu G, Yan S (2003a) Analysis of amino acid pairs sensitive to variants in human collagen α5(IV) chain precursor by means of a random approach. Peptides 24:347-352
86. Wu G, Yan S (2003b) Determination of amino acid pairs in human haemoglobulin α-chain sensitive to variants by means of a random approach. Comp Clin Pathol 12:21-25
87. Wu G, Yan S (2003c) Determination of amino acid pairs in human p53 protein sensitive to mutations/variants by means of a random approach. J Mol Model 9:337-341
88. Wu G, Yan S (2003d) Determination of amino acid pairs in Von Hippel-Lindau disease tumour suppressor (G7 protein) sensitive to variants by means of a random approach J. Appl Res 3:512-520
89. Wu G, Yan S (2003e) Determination of amino acid pairs sensitive to variants in human β-glucocerebrosidase by means of a random approach. Protein Eng 16:195-199
90. Wu G, Yan S (2003f) Determination of amino acid pairs sensitive to variants in human Bruton's tyrosine kinase by means of a random approach. Mol Simul 29:249-254
91. Wu G, Yan S (2003g) Determination of amino acid pairs sensitive to variants in human coagulation factor IX precursor by means of a random approach. J Biomed Sci 10:451-454
92. Wu G, Yan S (2003h) Prediction of amino acid pairs sensitive to mutations in the spike protein from SARS related coronavirus. Peptides 24:1837-1845
93. Wu G, Yan S (2004a) Amino acid pairs sensitive to variants in human collagen α1(I) chain precursor. EXCLI J 3:10-19
94. Wu G, Yan S (2004b) Susceptible amino acid pairs in variants of human collagen α1(III) chain precursor. EXCLI J 3:20-28
95. Wu G, Yan S (2004c) Determination of amino acid pairs sensitive to variants in human copper-transporting ATPase 2. Biochem Biophys Res Commun 319:27-31
96. Wu G, Yan S (2004d) Fate of 130 hemagglutinins from different influenza A viruses. Biochem Biophys Res Commun 317:917-924
97. Wu G, Yan S (2004e) Potential targets for anti-SARS drugs in the structural proteins from SARS related coronavirus. Peptides 25:901-908
98. Wu G, Yan S (2004f) Determination of sensitive positions to mutations in human p53 protein. Biochem Biophys Res Commun 321:313-319
99. Wu G, Yan S (2005a) Amino acid pairs susceptible to variants in human protein C precursor. Protein Pept Lett 10:491-494
100. Wu G, Yan S (2005b) Mutation features of 215 polymerase proteins from different influenza A viruses. Med Sci Monit 11:BR367-BR372
101. Wu G, Yan S (2005c) Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species. J Mol Model 11:8-16
102. Wu G, Yan S (2005d) Searching of main cause leading to severe influenza A virus mutations and consequently to influenza pandemics/epidemics. Am J Infect Dis 1:116-123
103. Wu G, Yan S (2005e) Prediction of mutation trend in hemagglutinins and neuraminidases from influenza A viruses by means of cross-impact analysis. Biochem Biophys Res Commun 326:475-482
104. Wu G, Yan S (2005f) Timing of mutation in hemagglutinins from influenza A virus by means of unpredictable portion of amino-acid pair and fast Fourier transform. Biochem Biophys Res Commun 333:70-78
105. Wu G, Yan S (2005g) Determination of mutation trend in proteins by means of translation probability between RNA codes and mutated amino acids Biochem. Biophys Res Commun 337:692-700
106. Wu G, Yan S (2006a) Determination of mutation trend in hemagglutinins by means of translation probability between RNA codons and mutated amino acids. Protein Pept Lett 13:601-609
107. Wu G, Yan S (2006b) Fate of influenza A virus proteins. Protein Pept Lett 13:377-384
108. Wu G, Yan S (2006c) Timing of mutation in hemagglutinins from influenza A virus by means of amino-acid distribution rank and fast Fourier transform. Protein Pept Lett 13:143-148
109. Wu G, Yan S (2006d) Mutation trend of hemagglutinin of influenza A virus: a review from computational mutation viewpoint. Acta Pharmacol Sin 27:513-526
110. Wu G, Yan S (2006e) Prediction of possible mutations in H5N1 hemagglutinins of influenza A virus by means of logistic regression. Comp Clin Pathol 15:255-261
111. Wu G, Yan S (2006f) Prediction of mutations in H5N1 hemagglutinins from influenza A virus. Protein Pept Lett 13:971-976
112. Wu G, Yan S (2007a) Improvement of model for prediction of hemagglutinin mutations in H5N1 influenza viruses with distinguishing of arginine, leucine and serine. Protein Pept Lett 14:191-196
113. Wu G, Yan S (2007b) Translation probability between RNA codons and translated amino acids, and its applications to protein mutations. In: Ostrovskiy MH (ed) Leading-edge messenger RNA research communications. Nova Science Publishers, New York
114. Wu G, Yan S (2007c) Improvement of prediction of mutation positions in H5N1 hemagglutinins of influenza A virus using neural network with distinguishing of arginine, leucine and serine. Protein Pept Lett 14:465-470