Genetic analysis and homology modeling of capsid protein of norovirus GII.14

Journal of Medical Virology

Volumn 86, Issue 2, 2014, Pages 329-334

  Chan It, Wisoot ^a   Thongprachum, Aksara ^a,b   Okitsu, Shoko ^a,b   Mizuguchi, Masashi ^a   Ushijima, Hiroshi ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b NIHON UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

Genetic diversity; Homology modeling; Norovirus GII.14; P2 domain

Indexed keywords

CAPSID PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CHINA; GENETIC ANALYSIS; JAPAN; NONHUMAN; NOROVIRUS; PROTEIN DOMAIN; SEQUENCE HOMOLOGY; VIRAL GENETICS; VIRUS CAPSID; VIRUS STRAIN;

MIRIDAE; NOROVIRUS;

GENETIC DIVERSITY; HOMOLOGY MODELING; NOROVIRUS GII.14; P2 DOMAIN;

AMINO ACID SEQUENCE; CAPSID PROTEINS; CHILD; CHILD, PRESCHOOL; CHINA; CLUSTER ANALYSIS; CONSERVED SEQUENCE; GENOTYPE; HUMANS; JAPAN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; MUTATION, MISSENSE; NOROVIRUS; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 84890240878     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.23720     Document Type: Article

References (30)

1. Allen DJ, Gray JJ, Gallimore CI, Xerry J, Iturriza-Gomara M. 2008. Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes. PloS ONE 3:e1485.
2. Bok K, Abente EJ, Realpe-Quintero M, Mitra T, Sosnovtsev SV, Kapikian AZ, Green KY. 2009. Evolutionary dynamics of GII.4 noroviruses over a 34-year period. J Virol 83:11890-11901.
3. Boon D, Mahar JE, Abente EJ, Kirkwood CD, Purcell RH, Kapikian AZ, Green KY, Bok K. 2011. Comparative evolution of GII.3 and GII.4 norovirus over a 31-year period. J Virol 85:8656-8666.
4. Bu W, Mamedova A, Tan M, Xia M, Jiang X, Hegde RS. 2008. Structural basis for the receptor binding specificity of Norwalk virus. J Virol 82:5340-5347.
5. Cannon JL, Lindesmith LC, Donaldson EF, Saxe L, Baric RS, Vinje J. 2009. Herd immunity to GII.4 noroviruses is supported by outbreak patient sera. J Virol 83:5363-5374.
6. Cao S, Lou Z, Tan M, Chen Y, Liu Y, Zhang Z, Zhang XC, Jiang X, Li X, Rao Z. 2007. Structural basis for the recognition of blood group trisaccharides by norovirus. J Virol 81:5949-5957.
7. Chan-It W, Thongprachum A, Okitsu S, Nishimura S, Kikuta H, Baba T, Yamamoto A, Sugita K, Hashira S, Tajima T, Mizuguchi M, Ushijima H. 2011. Detection and genetic characterization of norovirus infections in children with acute gastroenteritis in Japan, 2007-2009. Clin Lab 57:213-220.
8. Chan-It W, Thongprachum A, Khamrin P, Kobayashi M, Okitsu S, Mizuguchi M, Ushijima H. 2012. Emergence of a new norovirus GII. 6 variant in Japan, 2008-2009. J Med Virol 84:1089-1096.
9. Choi JM, Hutson AM, Estes MK, Prasad BV. 2008. Atomic resolution structural characterization of recognition of histo-blood group antigens by Norwalk virus. Proc Natl Acad Sci 105:9175-9180.
10. Donaldson EF, Lindesmith LC, Lobue AD, Baric RS. 2010. Viral shape-shifting: Norovirus evasion of the human immune system. Nat Rev Microbiol 8:231-241.
11. Eswar N, Ramakrishnan C. 2000. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Eng 13:227-238.
12. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. 2006. Comparative protein structure modeling using Modeller. Curr Protoc Bioinform Chapter 5:Unit 5.6.
13. Fang H, Tan M, Xia M, Wang L, Jiang X. 2013. Norovirus p particle efficiently elicits innate, humoral and cellular immunity. PloS ONE 8:e63269.
14. Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714-2723.
15. Hansman GS, Biertumpfel C, Georgiev I, McLellan JS, Chen L, Zhou T, Katayama K, Kwong PD. 2011. Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. J Virol 85:6687-6701.
16. Iritani N, Vennema H, Siebenga JJ, Siezen RJ, Renckens B, Seto Y, Kaida A, Koopmans M. 2008. Genetic analysis of the capsid gene of genotype GII.2 noroviruses. J Virol 82:7336-7345.
17. Iritani N, Kaida A, Abe N, Sekiguchi J, Kubo H, Takakura K, Goto K, Ogura H, Seto Y. 2012. Increase of GII.2 norovirus infections during the 2009-2010 season in Osaka City, Japan. J Med Virol 84:517-525.
18. Jiang X, Wang M, Graham DY, Estes MK. 1992. Expression, self-assembly, and antigenicity of the Norwalk virus capsid protein. J Virol 66:6527-6532.
19. Jin M, Xie HP, Duan ZJ, Liu N, Zhang Q, Wu BS, Li HY, Cheng WX, Yang SH, Yu JM, Xu ZQ, Cui SX, Zhu L, Tan M, Jiang X, Fang ZY. 2008. Emergence of the GII4/2006b variant and recombinant noroviruses in China. J Med Virol 80:1997-2004.
20. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM. 2006. MUSTANG: A multiple structural alignment algorithm. Proteins 64:559-574.
21. Krieger E, Koraimann G, Vriend G. 2002. Increasing the precision of comparative models with YASARA NOVA-A self-parameterizing force field. Proteins 47:393-402.
22. Kumar S, Ochoa W, Kobayashi S, Reddy VS. 2007. Presence of a surface-exposed loop facilitates trypsinization of particles of Sinsiro virus, a genogroup II.3 norovirus. J Virol 81:1119-1128.
23. Kuntal BK, Aparoy P, Reddanna P. 2010. EasyModeller: A graphical interface to MODELLER. BMC Res Notes 3:226.
24. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. 2000. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291-325.
25. Richardson C, Bargatze RF, Goodwin R, Mendelman PM. 2013. Norovirus virus-like particle vaccines for the prevention of acute gastroenteritis. Expert Rev Vaccines 12:155-167.
26. Shirato H, Ogawa S, Ito H, Sato T, Kameyama A, Narimatsu H, Xiaofan Z, Miyamura T, Wakita T, Ishii K, Takeda N. 2008. Noroviruses distinguish between type 1 and type 2 histo-blood group antigens for binding. J Virol 82:10756-10767.
27. Siebenga JJ, Vennema H, Renckens B, de Bruin E, van der Veer B, Siezen RJ, Koopmans M. 2007. Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J Virol 81:9932-9941.
28. Tan M, Jiang X. 2010. Norovirus gastroenteritis, carbohydrate receptors, and animal models. PLoS Pathog 6:e1000983.
29. Tan M, Huang P, Meller J, Zhong W, Farkas T, Jiang X. 2003. Mutations within the P2 domain of norovirus capsid affect binding to human histo-blood group antigens: Evidence for a binding pocket. J Virol 77:12562-12571.
30. Xia M, Farkas T, Jiang X. 2007. Norovirus capsid protein expressed in yeast forms virus-like particles and stimulates systemic and mucosal immunity in mice following an oral administration of raw yeast extracts. J Virol 79:74-83.