Selective pressure to increase charge in immunodominant epitopes of the H3 hemagglutinin influenza protein

Journal of Molecular Evolution

Volumn 72, Issue 1, 2011, Pages 90-103

  Pan, Keyao ^a   Long, Jinxue ^c   Sun, Haoxin ^d   Tobin, Gregory J ^c,e   Nara, Peter L ^c,e   Deem, Michael W ^a,b  

^a Rice University   (United States)

^b RICE UNIVERSITY   (United States)

^c Biological Mimetics Inc   (United States)

^d Johns Hopkins University   (United States)

^e IOWA STATE UNIVERSITY   (United States)

Author keywords

Influenza; Pepitope; Virus evolution

Indexed keywords

AMINO ACID; EPITOPE; INFLUENZA VIRUS HEMAGGLUTININ;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; DISEASE MODEL; GENETIC SELECTION; GENETICS; GUINEA PIG; HUMAN; IMMUNOLOGY; INFLUENZA; INFLUENZA VIRUS A H3N2; MOLECULAR EVOLUTION; MUTATION; ORTHOMYXOVIRUS INFECTION; PROBABILITY; PROTEIN BINDING; PROTEIN DOMAIN; STATIC ELECTRICITY; STATISTICAL MODEL; VIROLOGY;

AMINO ACIDS; ANIMALS; DISEASE MODELS, ANIMAL; EVOLUTION, MOLECULAR; GUINEA PIGS; HEMAGGLUTININ GLYCOPROTEINS, INFLUENZA VIRUS; HUMANS; IMMUNODOMINANT EPITOPES; INFLUENZA A VIRUS, H3N2 SUBTYPE; INFLUENZA, HUMAN; LIKELIHOOD FUNCTIONS; MARKOV CHAINS; MODELS, BIOLOGICAL; MUTATION; ORTHOMYXOVIRIDAE INFECTIONS; PROTEIN BINDING; PROTEIN INTERACTION DOMAINS AND MOTIFS; SELECTION, GENETIC; STATIC ELECTRICITY;

ANIMALIA; CAVIA; INFLUENZA A VIRUS; INFLUENZAVIRUS A; ORTHOMYXOVIRIDAE;

EID: 79951676141     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9405-4     Document Type: Article

References (28)

1. J Adachi M Hasegawa 1996 Model of amino acid substitution in proteins encoded by mitochondrial DNA J Mol Evol 42 459 468 1:CAS:528:DyaK28XivFKnurw%3D 10.1007/BF02498640 8642615 (Pubitemid 26154323)
2. T Clackson JA Wells 1995 A hot spot of binding energy in a hormone-receptor interface Science 267 383 386 1:CAS:528:DyaK2MXjt12nsbs%3D 10.1126/science.7529940 7529940
3. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Atlas of protein sequence and structure, vol 5, pp 345-352
4. Frank SA (2002) Immunology and evolution of infectious disease. Princeton University Press, Princeton, NJ
5. N Goldman S Whelan 2002 A novel use of equilibrium frequencies in models of sequence evolution Mol Biol Evol 19 1821 1831 1:CAS:528:DC%2BD38XovFOntLo%3D 12411592 (Pubitemid 35388106)
6. V Gupta DJ Earl MW Deem 2006 Quantifying influenza vaccine efficacy and antigenic distance Vaccine 24 3881 3888 1:CAS:528:DC%2BD28XksFaqurg%3D 10.1016/j.vaccine.2006.01.010 16460844 (Pubitemid 44308221)
7. S Henikoff JG Henikoff 1992 Amino-acid substitution matrices from protein blocks Proc Natl Acad Sci USA 89 10915 10919 1:CAS:528:DyaK3sXjsFCgsQ%3D%3D 10.1073/pnas.89.22.10915 1438297
8. NV Kaverin MN Matrosovich AS Gambaryan IA Rudneva AA Shilov NL Varich NV Makarova EA Kropotkina BV Sinitsin 2000 Intergenic HA-NA interactions in influenza A virus: postreassortment substitutions of charged amino acid in the hemagglutinin of different subtypes Virus Res 66 123 129 1:CAS:528: DC%2BD3cXhvV2lsL8%3D 10.1016/S0168-1702(99)00131-8 10725545 (Pubitemid 30139485)
9. C Kosiol N Goldman 2005 Different versions of the Dayhoff rate matrix Mol Biol Evol 22 193 199 1:CAS:528:DC%2BD2MXptFGitw%3D%3D 10.1093/molbev/msi005 15483331 (Pubitemid 40130187)
10. JA Leunissen HW van den Hooven WW de Jong 1990 Extreme differences in charge changes during protein evolution J Mol Evol 31 33 39 1:CAS:528: DyaK3cXltFWit74%3D 10.1007/BF02101790 2116529 (Pubitemid 20234487)
11. AC Lowen S Mubareka TM Tumpey A García-Sastre P Palese 2006 The Guinea pig as a transmission model for human influenza viruses Proc Natl Acad Sci USA 103 9988 9992 1:CAS:528:DC%2BD28XmvVajur8%3D 10.1073/pnas.0604157103 16785447 (Pubitemid 43993610)
12. Macken C, Lu H, Goodman J, Boykin L (2001) The value of a database in surveillance and vaccine selection. In: Osterhaus ADME, Cox N, Hampson AW (eds) Options for the control of influenza IV. Elsevier, Amsterdam, accession number ISDN38157. http://www.flu.lanl.gov/
13. JH McDonald 2006 Apparent trends of amino acid gain and loss in protein evolution due to nearly neutral variation Mol Biol Evol 23 240 244 1:CAS:528:DC%2BD28XntVamuw%3D%3D 10.1093/molbev/msj026 16195487 (Pubitemid 43100038)
14. VN Minin MA Suchard 2008 Counting labeled transitions in continuous-time markov models of evolution J Math Biol 56 391 412 10.1007/s00285-007-0120-8 17874105 (Pubitemid 350212025)
15. ET Muñoz MW Deem 2005 Epitope analysis for influenza vaccine design Vaccine 23 1144 1148 10.1016/j.vaccine.2004.08.028 15629357 (Pubitemid 40052010)
16. T Müller M Vingron 2000 Modeling amino acid replacement J Comput Biol 7 761 776 10.1089/10665270050514918 11382360 (Pubitemid 32692448)
17. T Müller R Spang M Vingron 2002 Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method Mol Biol Evol 19 8 13 11752185 (Pubitemid 34008042)
18. S Nakajima K Nakajima E Nobusawa J Zhao S Tanaka K Fukuzawa 2007 Comparison of epitope structures of H3HAs through protein modeling of influenza a virus hemagglutinin: mechanism for selection of antigenic variants in the presence of a monoclonal antibody Microbiol Immunol 51 1179 1187 1:CAS:528:DC%2BD1cXhtlWjtb0%3D 18094536
19. K Pan MW Deem 2009 Comment on Ndifon et al., "On the use of hemagglutination-inhibition for influenza surveillance: surveillance data are predictive of influenza vaccine effectiveness" Vaccine 27 5033 5034 10.1016/j.vaccine.2009.05.068 19524615
20. N Sinha S Mohan CA Lipschultz SJ Smith-Gill 2002 Differences in electrostatic properties at antibody-antigen binding sites: Implications for specificity and cross-reactivity Biophys J 83 2946 2968 1:CAS:528: DC%2BD3sXislShsw%3D%3D 10.1016/S0006-3495(02)75302-2 12496069 (Pubitemid 36041920)
21. DJ Smith S Forrest DH Ackley AS Perelson 1999 Variable efficacy of repeated annual influenza vaccination Proc Natl Acad Sci USA 96 14001 14006 1:CAS:528:DyaK1MXns1Oqurc%3D 10.1073/pnas.96.24.14001 10570188
22. DJ Smith AS Lapedes JC de Jong TM Bestebroer GF Rimmelzwaan ADME Osterhaus RAM Fouchier 2004 Mapping the antigenic and genetic evolution of influenza virus Science 305 371 376 1:CAS:528:DC%2BD2cXls1egtr4%3D 10.1126/science.1097211 15218094 (Pubitemid 38938148)
23. Sun J, Deem MW (2009) Statistical mechanics of the immune response to vaccines. In: Zaman MH (ed) Statistical mechanics of cellular systems and processes. Cambridge University Press, pp 177-213
24. J Sun DJ Earl MW Deem 2006 Localization and glassy dynamics in the immune system Mod Phys Lett B 20 63 95 1:CAS:528:DC%2BD28Xot1Wjug%3D%3D 10.1142/S0217984906010494 (Pubitemid 43244194)
25. JL Thorne 2000 Models of protein sequence evolution and their applications Curr Opin Genet Dev 10 602 605 1:CAS:528:DC%2BD3cXovFansr0%3D 10.1016/S0959-437X(00)00142-8 11088008
26. YY Tseng J Liang 2006 Estimation of amino acid residue substitution rates at local spatial regions and application in protein function inference: a Bayesian Monte Carlo approach Mol Biol Evol 23 421 436 1:CAS:528: DC%2BD28XntVaktQ%3D%3D 10.1093/molbev/msj048 16251508 (Pubitemid 43100056)
27. S Veerassamy A Smith ERM Tillier 2003 A transition probability model for amino acid substitutions from blocks J Comput Biol 10 997 1010 1:CAS:528:DC%2BD2cXhtVaqt7k%3D 10.1089/106652703322756195 14980022 (Pubitemid 38156410)
28. Zhou H, Pophale R, Deem MW (2009) Computer-assisted vaccine design. In: Wang Q, Tao YJ (eds) Influenza: molecular virology. Horizon Scientific Press, Norwich, UK