Homology modelling and protein structure based functional analysis of five cucumovirus coat proteins

Journal of Molecular Graphics and Modelling

Volumn 24, Issue 5, 2006, Pages 319-327

  Gellért, Ákos ^a,b   Salánki, Katalin ^a   Náray Szabó, Gábor ^b   Balázs, Ervin ^a,c  

^a SZENT ISTVÁN UNIVERSITY   (Hungary)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^c INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Electrostatic potential analysis; Homology modelling; Phosphorylation; Sequence analysis; Virology

Indexed keywords

COMPUTER SOFTWARE; ELECTRIC POTENTIAL; MOLECULAR STRUCTURE; STRAIN; VIRUSES;

ELECTROSTATIC POTENTIAL ANALYSIS; HOMOLOGY MODELING; SEQUENCE ANALYSIS; VIROLOGY;

PROTEINS;

COAT PROTEIN;

ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; ELECTRICITY; IMMUNE RESPONSE; MOLECULAR MODEL; MOSAIC VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; VIRUS INFECTIVITY; VIRUS MUTATION; VIRUS STRAIN; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CAPSID PROTEINS; CUCUMOVIRUS; ELECTROSTATICS; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL PROTEINS;

CUCUMBER MOSAIC VIRUS; CUCUMOVIRUS; PEANUT STUNT VIRUS; TOMATO ASPERMY VIRUS;

EID: 33644610860     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.09.015     Document Type: Article

References (25)

1. T.J. Smith, E. Chase, T. Schmidt, and K.L. Perry The structure of Cucumber mosaic virus and comparison to Cowpea chlorotic mottle virus J. Virol. 74 2000 7578 7586
2. P. Palukaitis, and F. García-Arenal Cucumoviruses Adv. Virus Res. 62 2004 241 323
3. M. Suzuki, S. Kuwata, J. Kataoka, C. Masuta, N. Nitta, and Y. Takanami Functional analysis of deletion mutants of cucumber mosaic virus RNA3 using an in vitro transcription system Virology 183 1991 106 113
4. I.B. Kaplan, L. Zhang, and P. Palukaitis Characterization of cucumber mosaic virus. V. Cell-to-cell movement requires capsid protein but not virions Virology 246 1998 221 231
5. H. Nagano, K. Mise, I. Furusawa, and T. Okuno Conversion in the requirement of coat protein in cell-to-cell movement mediated by the cucumber mosaic virus movement protein J. Virol. 75 2001 8045 8053
6. K. Salánki, Á. Gellért, E. Huppert, G. Náray-Szabó, and E. Balázs Compatibility of the movement protein and the coat protein of cucumoviruses is required for cell-to-cell movement J. Gen. Virol. 85 2004 1039 1048
7. L. Terradot, M. Souchet, and D.G. Ducray-Bourdin Analysis of three-dimensional structure of Potato leafroll virus coat protein obtained by homology modelling Virology 286 2001 72 82
8. G. Náray-Szabó Analysis of molecular recognition: steric electrostatic and hydrophobic complementarity J. Mol. Recog. 6 1993 205 210
9. S.B. Needleman, and C.D.A. Wunsch general method applicable to the search for similarities in the amino acid sequence of two proteins J. Mol. Biol. 48 1970 443 453
10. GCG, Wisconsin Package, version 10.0, Accelrys Inc, San Diego, CA, 1999.
11. J. Felsenstein, PHYLIP, version 3.5, University of Washington, Seattle, WA, 1998.
12. A. Sali Modeling mutations and homologous proteins Curr. Opin. Biotechnol. 6 1995 437 451
13. S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner A new force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 106 1984 765 784
14. M.K. Gilson, K.A. Sharp, and B. Honig Calculating electrostatic interactions in biomolecules: method and error assessment J. Comp. Chem. 9 1987 327 335
15. A. Nicholls, K. Sharp, and B. Honig Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons Proteins Struct. Funct. Genet. 11 1991 281 296
16. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling Electrophoresis 18 1997 2714 2723
17. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
18. C.J. Sigrist, L. Cerutti, N. Hulo, A. Gattiker, L. Falquet, M. Pagni, A. Bairoch, P. Bucher, PROSITE: a documented database using patterns and profiles as motif descriptors, Brief Bioinf. 3 (2002) 265-274, http://us.expasy.org/ prosite.
19. D. Szilassy, K. Salánki, and E. Balázs Stunting induced by Cucumber mosaic cucumovirus-infected Nicotiana glutinosa is determined by a single amino acid residue in the coat protein MPMI 12 1999 1105 1113
20. S.M. Wong, S.S.C. Thio, M.H. Shintaku, and P. Palukaitis The rate of cell-to-cell movement in squash of cucumber mosaic virus is affected by sequences of the capsid protein MPMI 12 1999 629 632
21. K.H. Ryu, C.H. Kim, and P. Palukaitis The coat protein of cucumber mosaic virus is a host range determinant for infection of maize MPMI 11 1998 351 357
22. S. Liu, X. He, G. Park, C. Josefsson, and K.L. Perry A conserved capsid protein surface domain of cucumber mosaic virus is essential for efficient aphid vector transmission J. Virol. 76 2002 9756 9762
23. K.L. Perry, L. Zhang, M.H. Shintaku, and P. Palukaitis Mapping determinants in Cucumber mosaic virus for transmission by Aphis gossypii Virology 205 1994 591 595
24. R.W. Lucas, S.B. Larson, M.A. Canady, and A. McPherson The structure of tomato aspermy virus by X-ray crystallography J. Struct. Biol. 139 2002 90 102
25. PyMol, version 0.97, DeLano Scientific, San Carlos, CA, 2002.