Skip to main content
NCBI home page
Springer Nature - PMC COVID-19 Collection logoLink to Springer Nature - PMC COVID-19 Collection
. 2009 Nov 14;1(4):272–279. doi: 10.1007/s12539-009-0053-6

Trends in global warming and evolution of matrix protein 2 family from influenza A virus

Shao-Min Yan 1, Guang Wu 2,✉
PMCID: PMC7091293  PMID: 20640805

Abstract

The global warming is an important factor affecting the biological evolution, and the influenza is an important disease that threatens humans with possible epidemics or pandemics. In this study, we attempted to analyze the trends in global warming and evolution of matrix protein 2 family from influenza A virus, because this protein is a target of anti-flu drug, and its mutation would have significant effect on the resistance to anti-flu drugs. The evolution of matrix protein 2 of influenza A virus from 1959 to 2008 was defined using the unpredictable portion of amino-acid pair predictability. Then the trend in this evolution was compared with the trend in the global temperature, the temperature in north and south hemispheres, and the temperature in influenza A virus sampling site, and species carrying influenza A virus. The results showed the similar trends in global warming and in evolution of M2 proteins although we could not correlate them at this stage of study. The study suggested the potential impact of global warming on the evolution of proteins from influenza A virus.

Key words: evolution, global warming, influenza A virus, matrix protein 2

References

  • [1].Althaus I.W., Chou J.J., Gonzales A.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. J Biol Chem. 1993;268:6119–6124. [PubMed] [Google Scholar]
  • [2].Althaus I.W., Chou J.J., Gonzales A.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry. 1993;32:6548–6554. doi: 10.1021/bi00077a008. [DOI] [PubMed] [Google Scholar]
  • [3].Althaus I.W., Gonzales A.J., Chou J.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J Biol Chem. 1993;268:14875–14880. [PubMed] [Google Scholar]
  • [4].Amino-acid pair predictability. 2009. http://www.dreamscitech.com/Service/rationale.htm.
  • [5].Andraos J. Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Can J Chem. 2008;86:342–357. doi: 10.1139/V08-020. [DOI] [Google Scholar]
  • [6].Basler C.F. Influenza viruses: basic biology and potential drug targets. Infect Disord Drug Targets. 2007;7:282–293. doi: 10.2174/187152607783018745. [DOI] [PubMed] [Google Scholar]
  • [7].Beigel J., Bray M. Current and future antiviral therapy of severe seasonal and avian influenza. Antiviral Res. 2008;78:91–102. doi: 10.1016/j.antiviral.2008.01.003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [8].Betakova T. M2 protein-a proton channel of influenza A virus. Current Pharm Des. 2007;13:3231–3235. doi: 10.2174/138161207782341295. [DOI] [PubMed] [Google Scholar]
  • [9].Chou K.C. Two new schematic rules for rate laws of enzyme-catalyzed reactions. J Theoret Biol. 1981;89:581–592. doi: 10.1016/0022-5193(81)90030-8. [DOI] [PubMed] [Google Scholar]
  • [10].Chou K.C. Low-frequency vibrations of helical structures in protein molecules. Biochem J. 1983;209:573–580. doi: 10.1042/bj2090573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [11].Chou K.C. Identification of low-frequency modes in protein molecules. Biochem J. 1983;215:465–469. doi: 10.1042/bj2150465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [12].Chou K.C. The biological functions of low-frequency phonons: 3. Helical structures and microenvironment. Biophys J. 1984;45:881–890. doi: 10.1016/S0006-3495(84)84234-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [13].Chou K.C. The biological functions of low-frequency phonons: 4. Resonance effects and allosteric transition. Biophys Chem. 1984;20:61–71. doi: 10.1016/0301-4622(84)80005-8. [DOI] [PubMed] [Google Scholar]
  • [14].Chou K.C. Low-frequency vibration of DNA molecules. Biochem J. 1984;221:27–31. doi: 10.1042/bj2210027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [15].Chou K.C. Low-frequency motions in protein molecules: beta-sheet and beta-barrel. Biophys J. 1985;48:289–297. doi: 10.1016/S0006-3495(85)83782-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [16].Chou K.C. The biological functions of low-frequency phonons: 6. A possible dynamic mechanism of allosteric transition in antibody molecules. Biopolymers. 1987;26:285–295. doi: 10.1002/bip.360260209. [DOI] [PubMed] [Google Scholar]
  • [17].Chou K.C. Review: Low-frequency collective motion in biomacromolecules and its biological functions. Biophys Chem. 1988;30:3–48. doi: 10.1016/0301-4622(88)85002-6. [DOI] [PubMed] [Google Scholar]
  • [18].Chou K.C. Graphical rules in steady and nonsteady enzyme kinetics. J Biol Chem. 1989;264:12074–12079. [PubMed] [Google Scholar]
  • [19].Chou K.C. Low-frequency resonance and cooperativity of hemoglobin. Trends Biochem Sci. 1989;14:212. doi: 10.1016/0968-0004(89)90026-1. [DOI] [PubMed] [Google Scholar]
  • [20].Chou K.C. Review: Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophys Chem. 1990;35:1–24. doi: 10.1016/0301-4622(90)80056-D. [DOI] [PubMed] [Google Scholar]
  • [21].Chou K.C. Energy-optimized structure of antifreeze protein and its binding mechanism. J Mol Biol. 1992;223:509–517. doi: 10.1016/0022-2836(92)90666-8. [DOI] [PubMed] [Google Scholar]
  • [22].Chou K.C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J Biol Chem. 1993;268:16938–16948. [PubMed] [Google Scholar]
  • [23].Chou K.C. Review: Prediction of HIV protease cleavage sites in proteins. Anal Biochem. 1996;233:1–14. doi: 10.1006/abio.1996.0001. [DOI] [PubMed] [Google Scholar]
  • [24].Chou K.C. Prediction of protein cellular attributes using pseudo amino acid composition. PROTEINS: Struct, Funct, Genet. 2001;43:246–255. doi: 10.1002/prot.1035. [DOI] [PubMed] [Google Scholar]
  • [25].Chou K.C. Review: Structural bioinformatics and its impact to biomedical science. Curr Med Chem. 2004;11:2105–2134. doi: 10.2174/0929867043364667. [DOI] [PubMed] [Google Scholar]
  • [26].Chou K.C. Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5. Biochem Biophys Res Commun. 2004;316:636–642. doi: 10.1016/j.bbrc.2004.02.098. [DOI] [PubMed] [Google Scholar]
  • [27].Chou K.C. Molecular therapeutic target for type-2 diabetes. J Proteome Res. 2004;3:1284–1288. doi: 10.1021/pr049849v. [DOI] [PubMed] [Google Scholar]
  • [28].Chou K.C. Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor. Biochem Biophys Res Commun. 2004;319:433–438. doi: 10.1016/j.bbrc.2004.05.016. [DOI] [PubMed] [Google Scholar]
  • [29].Chou K.C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J Proteome Res. 2005;4:1681–1686. doi: 10.1021/pr050145a. [DOI] [PubMed] [Google Scholar]
  • [30].Chou K.C. Prediction of G-protein-coupled receptor classes. J Proteome Res. 2005;4:1413–1418. doi: 10.1021/pr050087t. [DOI] [PubMed] [Google Scholar]
  • [31].Chou K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics. 2005;21:10–19. doi: 10.1093/bioinformatics/bth466. [DOI] [PubMed] [Google Scholar]
  • [32].Chou K.C., Chen N.Y. The biological functions of low-frequency phonons. Sci Sin. 1977;20:447–457. [Google Scholar]
  • [33].Chou K.C., Elrod D.W. Bioinformatical analysis of G-protein-coupled receptors. J Proteome Res. 2002;1:429–433. doi: 10.1021/pr025527k. [DOI] [PubMed] [Google Scholar]
  • [34].Chou K.C., Forsen S. Graphical rules for enzyme-catalyzed rate laws. Biochem J. 1980;187:829–835. doi: 10.1042/bj1870829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [35].Chou K.C., Jiang S.P. Studies on the rate of diffusion-controlled reactions of enzymes. Sci Sin. 1974;17:664–680. [PubMed] [Google Scholar]
  • [36].Chou K.C., Jiang S.P., Liu W.M., Fee C.H. Graph theory of enzyme kinetics: 1. Steady-state reaction system. Sci Sin. 1979;22:341–358. [Google Scholar]
  • [37].Chou K.C., Kezdy F.J., Reusser F. Review: Steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Anal Biochem. 1994;221:217–230. doi: 10.1006/abio.1994.1405. [DOI] [PubMed] [Google Scholar]
  • [38].Chou K.C., Liu W.M. Graphical rules for nonsteady state enzyme kinetics. J Theoret Biol. 1981;91:637–654. doi: 10.1016/0022-5193(81)90215-0. [DOI] [PubMed] [Google Scholar]
  • [39].Chou K.C., Maggiora G.M., Nemethy G., Scheraga H.A. Energetics of the structure of the four-alpha-helix bundle in proteins. Proceed Natl Acad Sci USA. 1988;85:4295–4299. doi: 10.1073/pnas.85.12.4295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [40].Chou K.C., Nemethy G., Scheraga H.A. Energetic approach to packing of a-helices: 2. General treatment of nonequivalent and nonregular helices. J Am Chem Soc. 1984;106:3161–3170. doi: 10.1021/ja00323a017. [DOI] [Google Scholar]
  • [41].Chou K.C., Shen H.B. Hum-PLoc: A novel ensemble classifier for predicting human protein subcellular localization. Biochem Biophys Res Commun. 2006;347:150–157. doi: 10.1016/j.bbrc.2006.06.059. [DOI] [PubMed] [Google Scholar]
  • [42].Chou K.C., Shen H.B. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem Biophys Res Commun. 2007;357:633–640. doi: 10.1016/j.bbrc.2007.03.162. [DOI] [PubMed] [Google Scholar]
  • [43].Chou K.C., Shen H.B. Review: Recent progresses in protein subcellular location prediction. Anal Biochem. 2007;370:1–16. doi: 10.1016/j.ab.2007.07.006. [DOI] [PubMed] [Google Scholar]
  • [44].Chou K.C., Shen H.B. Euk-mPLoc: a fusion classifier for large-scale eukaryotic protein subcellular location prediction by incorporating multiple sites. J Proteome Res. 2007;6:1728–1734. doi: 10.1021/pr060635i. [DOI] [PubMed] [Google Scholar]
  • [45].Chou K.C., Shen H.B. Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in various organisms. Nature Prot. 2008;3:153–162. doi: 10.1038/nprot.2007.494. [DOI] [PubMed] [Google Scholar]
  • [46].Chou K.C., Shen H.B. ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem Biophys Res Commun. 2008;376:321–325. doi: 10.1016/j.bbrc.2008.08.125. [DOI] [PubMed] [Google Scholar]
  • [47].Chou K.C., Wei D.Q., Du Q.S., Sirois S., Zhong W.Z. Review: Progress in computational approach to drug development against SARS. Curr Med Chem. 2006;13:3263–3270. doi: 10.2174/092986706778773077. [DOI] [PubMed] [Google Scholar]
  • [48].Chou K.C., Wei D.Q., Zhong W.Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. (Erratum: ibid., 2003, Vol.310, 675) Biochem Biophys Res Commun. 2003;308:148–151. doi: 10.1016/S0006-291X(03)01342-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [49].Chou K.C., Zhou G.P. Role of the protein outside active site on the diffusion-controlled reaction of enzyme. J Am Chem Soc. 1982;104:1409–1413. doi: 10.1021/ja00369a043. [DOI] [Google Scholar]
  • [50].Climatic Research Unit. 2009. http://www.cru.uea.ac.uk/cru/data/temperature/
  • [51].Dea-Ayuela M.A., Perez-Castillo Y., Meneses-Marcel A., Ubeira F.M., Bolas-Fernandez F., Chou K.C., Gonzalez-Diaz H. HP-Lattice QSAR for dynein proteins: Experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. Bioorg Med Chem. 2008;16:7770–7776. doi: 10.1016/j.bmc.2008.07.023. [DOI] [PubMed] [Google Scholar]
  • [52].Ding Y.S., Zhang T.L., Chou K.C. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein Pept Lett. 2007;14:811–815. doi: 10.2174/092986607781483778. [DOI] [PubMed] [Google Scholar]
  • [53].Du, Q.S., Huang, R.B., Wang, C.H., Li, X.M., Chou, K.C. 2009. Energetic analysis of the two controversial drug binding sites of the M2 proton channel in influenza A virus. J Theoret Biol doi:10.1016/j.jtbi.2009.1003.1003. [DOI] [PubMed]
  • [54].Du Q.S., Wang S.Q., Chou K.C. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Biochem Biophys Res Commun. 2007;362:525–531. doi: 10.1016/j.bbrc.2007.08.025. [DOI] [PubMed] [Google Scholar]
  • [55].Gao W.N., Wei D.Q., Li Y., Gao H., Xu W.R., Li A.X., Chou K.C. Agaritine and its derivatives are potential inhibitors against HIV proteases. Med Chem. 2007;3:221–226. doi: 10.2174/157340607780620644. [DOI] [PubMed] [Google Scholar]
  • [56].Garamszegi L.Z., Møller A.P. Prevalence of avian influenza and host ecology. Proc Biol Sci. 2007;274:2003–2012. doi: 10.1098/rspb.2007.0124. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [57].Get Lat Lon. 2009. http://www.getlatlon.com/.
  • [58].Gonzalez-Diaz H., Gonzalez-Diaz Y., Santana L., Ubeira F.M., Uriarte E. Proteomics, networks, and connectivity indices. Proteomics. 2008;8:750–778. doi: 10.1002/pmic.200700638. [DOI] [PubMed] [Google Scholar]
  • [59].Gong K., Li L., Wang J.F., Cheng F., Wei D.Q., Chou K.C. Binding mechanism of H5N1 influenza virus neuraminidase with ligands and its implication for drug design. Med Chem. 2009;5:242–249. doi: 10.2174/157340609788185936. [DOI] [PubMed] [Google Scholar]
  • [60].Gonzalez-Diaz H., Sanchez-Gonzalez A., Gonzalez-Diaz Y. 3D-QSAR study for DNA cleavage proteins with a potential anti-tumor ATCUN-like motif. J Inorg Biochem. 2006;100:1290–1297. doi: 10.1016/j.jinorgbio.2006.02.019. [DOI] [PubMed] [Google Scholar]
  • [61].Guo X.L., Li L., Wei D.Q., Zhu Y.S., Chou K.C. Cleavage mechanism of the H5N1 hemagglutinin by trypsin and furin. Amino Acids. 2008;35:375–382. doi: 10.1007/s00726-007-0611-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [62].Hayden F. Developing new antiviral agents for influenza treatment: what does the future hold? Clin Infect Dis. 2009;48(Suppl1):S3–S13. doi: 10.1086/591851. [DOI] [PubMed] [Google Scholar]
  • [63].Hayden F.G. Antivirals for influenza: historical perspectives and lessons learned. Antiviral Res. 2006;71:372–378. doi: 10.1016/j.antiviral.2006.05.016. [DOI] [PubMed] [Google Scholar]
  • [64].Hsieh H.P., Hsu J.T. Strategies of development of antiviral agents directed against influenza virus replication. Curr Pharm Des. 2007;13:3531–3542. doi: 10.2174/138161207782794248. [DOI] [PubMed] [Google Scholar]
  • [65].Huang R.B., Du Q.S., Wang C.H., Chou K.C. An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus. Biochem Biophys Res Commun. 2008;377:1243–1247. doi: 10.1016/j.bbrc.2008.10.148. [DOI] [PubMed] [Google Scholar]
  • [66].Influenza virus resources. 2009. http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/multiple.cgi
  • [67].Jahangir A., Watanabe Y., Chinen O., Yamazaki S., Sakai K., Okamura M., Nakamura M., Takehara K. Surveillance of avian influenza viruses in Northern pintails (Anas acuta) in Tohoku District, Japan. Avian Dis. 2008;52:49–53. doi: 10.1637/8035-062507-Reg. [DOI] [PubMed] [Google Scholar]
  • [68].Kelly M.L., Cook J.A., Brown-Augsburger P., Heinz B.A., Smith M.C., Pinto L.H. Demonstrating the intrinsic ion channel activity of virally encoded proteins. FEBS Lett. 2003;552:61–67. doi: 10.1016/S0014-5793(03)00851-2. [DOI] [PubMed] [Google Scholar]
  • [69].Krauss S., Walker D., Pryor S.P., Niles L., Chenghong L., Hinshaw V.S., Webster R.G. Influenza A viruses of migrating wild aquatic birds in North America. Vector Borne Zoonotic Dis. 2004;4:177–189. doi: 10.1089/vbz.2004.4.177. [DOI] [PubMed] [Google Scholar]
  • [70].Kuzmic P., Ng K.Y., Heath T.D. Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation. Anal Biochem. 1992;200:68–73. doi: 10.1016/0003-2697(92)90278-F. [DOI] [PubMed] [Google Scholar]
  • [71].Li T.T., Chou K.C. The quantitative relations between diffusion-controlled reaction rate and characteristic parameters in enzyme-substrate reaction system: 1. Neutral substrate. Sci Sin. 1976;19:117–136. [PubMed] [Google Scholar]
  • [72].Myers D., Palmer G. Microcomputer tools for steady-state enzyme kinetics. Bioinformatics. 1985;1:105–110. doi: 10.1093/bioinformatics/1.2.105. [DOI] [PubMed] [Google Scholar]
  • [73].New M., Hulme M., Jones P. Representing twentieth-century space-time climate variability. Part II: Development of 1901–96 monthly grids of terrestrial surface climate. J Clim. 2000;13:2217–2238. doi: 10.1175/1520-0442(2000)013<2217:RTCSTC>2.0.CO;2. [DOI] [Google Scholar]
  • [74].Pielak R.M., Jason R., Schnell J.R., Chou J.J. Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proceed Natl Acad Sci, USA. 2009;106:7379–7384. doi: 10.1073/pnas.0902548106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [75].Pinto L.H., Lamb R.A. Controlling influenza virus replication by inhibiting its proton channel. Mol Biosyst. 2007;3:18–23. doi: 10.1039/b611613m. [DOI] [PubMed] [Google Scholar]
  • [76].Prado-Prado F.J., Gonzalez-Diaz H., de la Vega O.M., Ubeira F.M., Chou K.C. Unified QSAR approach to antimicrobials. Part 3: First multi-tasking QSAR model for Input-Coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. Bioorg Med Chem. 2008;16:5871–5880. doi: 10.1016/j.bmc.2008.04.068. [DOI] [PubMed] [Google Scholar]
  • [77].Rayner N.A., Brohan P., Parker D.E., Folland C.K., Kennedy J.J., Vanicek M., Ansell T., Tett S.F.B. Improved analyses of changes and uncertainties in marine temperature measured in situ since the mid nineteenth century: The HadSST2 dataset. J Clim. 2006;19:446–469. doi: 10.1175/JCLI3637.1. [DOI] [Google Scholar]
  • [78].Schnell J.R., Chou J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature. 2008;451:591–595. doi: 10.1038/nature06531. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [79].Schotsaert M., De Filette M., Fiers W., Saelens X. Universal M2 ectodomain-based influenza A vaccines: preclinical and clinical developments. Exp Rev Vaccines. 2009;8:499–508. doi: 10.1586/erv.09.6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [80].Shen H.B., Chou K.C. Signal-3L: a 3-layer approach for predicting signal peptide. Biochem Biophys Res Commun. 2007;363:297–303. doi: 10.1016/j.bbrc.2007.08.140. [DOI] [PubMed] [Google Scholar]
  • [81].Shen H.B., Chou K.C. HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins. Anal Biochem. 2008;375:388–390. doi: 10.1016/j.ab.2008.01.012. [DOI] [PubMed] [Google Scholar]
  • [82].Shen H.B., Chou K.C. Identification of proteases and their types. Anal Biochem. 2009;385:153–160. doi: 10.1016/j.ab.2008.10.020. [DOI] [PubMed] [Google Scholar]
  • [83].Sirois S., Wei D.Q., Du Q.S., Chou K.C. Virtual Screening for SARS-CoV Protease Based on KZ7088 Pharmacophore Points. J Chem Inf Comput Sci. 2004;44:1111–1122. doi: 10.1021/ci034270n. [DOI] [PubMed] [Google Scholar]
  • [84].Thomas C.D., Cameron A., Green R.E., Bakkenes M., Beaumont L.J., Collingham Y.C., Erasmus B.F., De Siqueira M.F., Grainger A., Hannah L., Hughes L., Huntley B., Van Jaarsveld A.S., Midgley G.F., Miles L., Ortega-Huerta M.A., Peterson A.T., Phillips O.L., Williams S.E. Extinction risk from climate change. Nature. 2004;427:145–148. doi: 10.1038/nature02121. [DOI] [PubMed] [Google Scholar]
  • [85].Wang J.F., Yan J.Y., Wei D.Q., Chou K.C. Binding of CYP2C9 with diverse drugs and its implications for metabolic mechanism. Med Chem. 2009;5:263–270. doi: 10.2174/157340609788185954. [DOI] [PubMed] [Google Scholar]
  • [86].Wang S.Q., Du Q.S., Chou K.C. Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Biochem Biophys Res Commun. 2007;354:634–640. doi: 10.1016/j.bbrc.2006.12.235. [DOI] [PubMed] [Google Scholar]
  • [87].Weber T.P., Stilianakis N.I. Ecologic immunology of avian influenza (H5N1) in migratory birds. Emerg Infect Dis. 2007;13:1139–1143. doi: 10.3201/eid1308.070319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [88].Wei D.Q., Du Q.S., Sun H., Chou K.C. Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Biochem Biophys Res Commun. 2006;344:1048–1055. doi: 10.1016/j.bbrc.2006.03.210. [DOI] [PubMed] [Google Scholar]
  • [89].Wu G. Application of the queueing theory with Monte Carlo simulation to inhalation toxicology. Arch Toxicol. 1998;72:330–335. doi: 10.1007/s002040050510. [DOI] [PubMed] [Google Scholar]
  • [90].Wu G. Application of queueing theory with Monte Carlo simulation to the study of the intake and adverse effects of ethanol. Alcohol Alcohol. 1998;33:519–527. doi: 10.1093/alcalc/33.5.519. [DOI] [PubMed] [Google Scholar]
  • [91].Wu G., Yan S. Estimation of the rate of arrivals of ions at a single-channel. J Biochem Mol Biol Biophys. 2001;5:505–511. [Google Scholar]
  • [92].Wu G., Yan S. Randomness in the primary structure of protein: methods and implications. Mol Biol Today. 2002;3:55–69. [Google Scholar]
  • [93].Wu G., Yan S. Fate of influenza A virus proteins. Protein Pept Lett. 2006;13:399–406. doi: 10.2174/092986606775974474. [DOI] [PubMed] [Google Scholar]
  • [94].Wu G., Yan S. Mutation trend of hemagglutinin of influenza a virus: A review from computational mutation viewpoint. Acta Pharmacol Sin. 2006;27:513–526. doi: 10.1111/j.1745-7254.2006.00329.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [95].Wu G., Yan S. Lecture notes on computational mutation. New York: Nova Science Publishers; 2008. [Google Scholar]
  • [96].Wu G., Yan S. Prediction of mutations engineered by randomness in H5N1 neuraminidases from influenza a virus. Amino Acids. 2008;34:81–90. doi: 10.1007/s00726-007-0579-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [97].Wu G., Yan S. Prediction of mutations initiated by internal power in H3N2 hemagglutinins of influenza a virus from North America. Int J Pept Res Ther. 2008;14:41–51. doi: 10.1007/s10989-007-9104-1. [DOI] [PubMed] [Google Scholar]
  • [98].Wu G., Yan S. Prediction of mutations engineered by randomness in H5N1 hemagglutinins of influenza a virus. Amino Acid. 2008;35:365–373. doi: 10.1007/s00726-007-0602-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [99].Xiao X., Chou K.C. Digital coding of amino acids based on hydrophobic index. Protein Pept Lett. 2007;14:871–875. doi: 10.2174/092986607782110293. [DOI] [PubMed] [Google Scholar]
  • [100].Xiao X., Lin W.Z., Chou K.C. Using grey dynamic modeling and pseudo amino acid composition to predict protein structural classes. J Comput Chem. 2008;29:2018–2024. doi: 10.1002/jcc.20955. [DOI] [PubMed] [Google Scholar]
  • [101].Xiao X., Shao S., Ding Y., Huang Z., Huang Y., Chou K.C. Using complexity measure factor to predict protein subcellular location. Amino Acids. 2005;28:57–61. doi: 10.1007/s00726-004-0148-7. [DOI] [PubMed] [Google Scholar]
  • [102].Xiao X., Shao S.H., Huang Z.D., Chou K.C. Using pseudo amino acid composition to predict protein structural classes: approached with complexity measure factor. J Comput Chem. 2006;27:478–482. doi: 10.1002/jcc.20354. [DOI] [PubMed] [Google Scholar]
  • [103].Xiao X., Wang P., Chou K.C. Predicting protein structural classes with pseudo amino acid composition: an approach using geometric moments of cellular automaton image. J Theoret Biol. 2008;254:691–696. doi: 10.1016/j.jtbi.2008.06.016. [DOI] [PubMed] [Google Scholar]
  • [104].Xiao X., Wang P., Chou K.C. GPCR-CA: A cellular automaton image approach for predicting Gprotein-coupled receptor functional classes. J Comput Chem. 2009;30:1414–1423. doi: 10.1002/jcc.21163. [DOI] [PubMed] [Google Scholar]
  • [105].Xiao X., Wang P., Chou K.C. Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition. J Appl Crystallogr. 2009;42:169–173. doi: 10.1107/S0021889809002751. [DOI] [Google Scholar]
  • [106].Zhang R., Wei D.Q., Du Q.S., Chou K.C. Molecular modeling studies of peptide drug candidates against SARS. Med Chem. 2006;2:309–314. doi: 10.2174/157340606776930736. [DOI] [PubMed] [Google Scholar]
  • [107].Zhang T.L., Ding Y.S., Chou K.C. Prediction protein structural classes with pseudo amino acid composition: approximate entropy and hydrophobicity pattern. J Theoret Biol. 2008;250:186–193. doi: 10.1016/j.jtbi.2007.09.014. [DOI] [PubMed] [Google Scholar]
  • [108].Zhou G.P. Biological functions of soliton and extra electron motion in DNA structure. Phys Scrip. 1989;40:698–701. doi: 10.1088/0031-8949/40/5/021. [DOI] [Google Scholar]
  • [109].Zhou G.P., Cai Y.D. Predicting protease types by hybridizing gene ontology and pseudo amino acid composition. PROTEINS: Struct, Funct, Bioinformat. 2006;63:681–684. doi: 10.1002/prot.20898. [DOI] [PubMed] [Google Scholar]
  • [110].Zhou G.P., Deng M.H. An extension of Chou’s graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochem J. 1984;222:169–176. doi: 10.1042/bj2220169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • [111].Zhou G.P., Doctor K. Subcellular location prediction of apoptosis proteins. PROTEINS: Struct, Funct, Genet. 2002;50:44–48. doi: 10.1002/prot.10251. [DOI] [PubMed] [Google Scholar]
  • [112].Zhou G.P., Surks H.K., Schnell J.R., Chou J.J., Michael E., Mendelsohn M.E., Rigby A.C. The Three-Dimensional Structure of the cGMP-Dependent Protein Kinase I-α Leucine Zipper Domain and Its Interaction with the Myosin Binding Subunit. Blood. 2004;104:963a. doi: 10.1182/blood-2004-01-0145. [DOI] [Google Scholar]
  • [113].Zhou G.P., Troy F.A. Characterization by NMR and molecular modeling of the binding of polyisoprenols (PI) and polyisoprenyl recognition sequence (PIRS) peptides: three-dimensional structure of the complexes reveals sites of specific interactions. Glycobiology. 2003;13:51–71. doi: 10.1093/glycob/cwg008. [DOI] [PubMed] [Google Scholar]
  • [114].Zhou G.P., Troy F.A. Invited Review: NMR studies on how the binding complex of polyisoprenol recognition sequence peptides and polyisoprenols can modulate membrane structure. Curr Protein Pept. 2005;6:399–411. doi: 10.2174/138920305774329377. [DOI] [PubMed] [Google Scholar]
  • [115].Zhou G.P., Troy F. A. NMR study of the preferred membrane orientation of polyisoprenols (dolichol) and the impact of their complex with polyisoprenyl recognition sequence peptides on membrane structure. Glycobiology. 2005;15:347–359. doi: 10.1093/glycob/cwi016. [DOI] [PubMed] [Google Scholar]

Articles from Interdisciplinary Sciences, Computational Life Sciences are provided here courtesy of Nature Publishing Group

RESOURCES