1887

Abstract

Viral structural genomic projects aim at unveiling the function of unknown viral proteins by employing high-throughput approaches to determine their 3D structure and to identify their function through fold-homology studies. The ‘irl enme dule calization’ (VaZyMolO) tool has been developed, which aims at defining viral protein modules that might be expressed in a soluble and functionally active form, thereby identifying candidates for crystallization studies. VaZyMolO includes 114 complete viral genome sequences of both negative- and positive-sense, single-stranded RNA viruses available from NCBI. In VaZyMolO, a module is defined as a structural and/or functional unit. Modules were first identified by homology search and then validated by the convergence of results from sequence composition analysis, motif search, transmembrane region search and domain definitions, as found in the literature. The public interface of VaZyMolO, which is accessible from http://www.vazymolo.org, allows comparison of a query sequence to all VaZyMolO modules of known function.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.80590-0
2005-03-01
2019-11-15
Loading full text...

Full text loading...

/deliver/fulltext/jgv/86/3/vir860743.html?itemId=/content/journal/jgv/10.1099/vir.0.80590-0&mimeType=html&fmt=ahah

References

  1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  2. Bateman, A., Birney, E., Durbin, R., Eddy, S. R., Howe, K. L. & Sonnhammer, E. L. ( 2000; ). The Pfam protein families database. Nucleic Acids Res 28, 263–266.[CrossRef]
    [Google Scholar]
  3. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., Rapp, B. A. & Wheeler, D. L. ( 2002; ). GenBank. Nucleic Acids Res 30, 17–20.[CrossRef]
    [Google Scholar]
  4. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. ( 2000; ). The Protein Data Bank. Nucleic Acids Res 28, 235–242.[CrossRef]
    [Google Scholar]
  5. Callebaut, I., Labesse, G., Durand, P., Poupon, A., Canard, L., Chomilier, J., Henrissat, B. & Mornon, J. P. ( 1997; ). Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell Mol Life Sci 53, 621–645.[CrossRef]
    [Google Scholar]
  6. Corpet, F. ( 1988; ). Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16, 10881–10890.[CrossRef]
    [Google Scholar]
  7. Couthino, P. & Henrissat, B. ( 1999a; ). Carbohydrate-active enzyme: an integrated approach. In Recent Advances in Carbohydrate Bioengineereing, pp. 3–12. Edited by H. Gilbert, G. Davies, B. Henrissat & B. Svensson. Cambridge: The Royal Society of Chemistry.
  8. Couthino, P. & Henrissat, B. ( 1999b; ). The modular structure of cellulases and other carbohydrate-active enzymes: an integrated database approach. In Genetics, Biochemistry and Ecology of Cellulose Degradation, pp. 15–23. Edited by K. Ohmiya, K. Hayashi, K. Sakka, Y. Kobayashi, S. Karita & T. Kimura. Tokyo: Uni Publishers.
  9. Egloff, M. P., Benarroch, D., Selisko, B., Romette, J. L. & Canard, B. ( 2002; ). An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. EMBO J 21, 2757–2768.[CrossRef]
    [Google Scholar]
  10. Egloff, M. P., Ferron, F., Campanacci, V. & 7 other authors ( 2004; ). The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world. Proc Natl Acad Sci U S A 101, 3792–3796.[CrossRef]
    [Google Scholar]
  11. Ferron, F., Longhi, S., Henrissat, B. & Canard, B. ( 2002; ). Viral RNA-polymerases – a predicted 2′-O-ribose methyltransferase domain shared by all Mononegavirales. Trends Biochem Sci 27, 222–224.[CrossRef]
    [Google Scholar]
  12. Fischer, D. ( 2000; ). Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput, 119–130.
    [Google Scholar]
  13. Iakoucheva, L. M., Kimzey, A. L., Masselon, C. D., Bruce, J. E., Garner, E. C., Brown, C. J., Dunker, A. K., Smith, R. D. & Ackerman, E. J. ( 2001; ). Identification of intrinsic order and disorder in the DNA repair protein XPA. Protein Sci 10, 560–571.[CrossRef]
    [Google Scholar]
  14. Johansson, K., Bourhis, J. M., Campanacci, V., Cambillau, C., Canard, B. & Longhi, S. ( 2003; ). Crystal structure of the measles virus phosphoprotein domain responsible for the induced folding of the C-terminal domain of the nucleoprotein. J Biol Chem 278, 44567–44573.[CrossRef]
    [Google Scholar]
  15. Jones, D. T. ( 1999; ). GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287, 797–815.[CrossRef]
    [Google Scholar]
  16. Karlin, D., Ferron, F., Canard, B. & Longhi, S. ( 2003; ). Structural disorder and modular organization in Paramyxovirinae N and P. J Gen Virol 84, 3239–3252.[CrossRef]
    [Google Scholar]
  17. Kelley, L. A., MacCallum, R. M. & Sternberg, M. J. ( 2000; ). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J Mol Biol 299, 499–520.
    [Google Scholar]
  18. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. ( 2001; ). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305, 567–580.[CrossRef]
    [Google Scholar]
  19. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J. & Russell, R. B. ( 2003a; ). Protein disorder prediction: implications for structural proteomics. Structure (Camb) 11, 1453–1459.[CrossRef]
    [Google Scholar]
  20. Linding, R., Russell, R. B., Neduva, V. & Gibson, T. J. ( 2003b; ). GlobPlot: exploring protein sequences for globularity and disorder. Nucleic Acids Res 31, 3701–3708.[CrossRef]
    [Google Scholar]
  21. Pruitt, K. D., Tatusova, T. & Maglott, D. R. ( 2003; ). NCBI reference sequence project: update and current status. Nucleic Acids Res 31, 34–37.[CrossRef]
    [Google Scholar]
  22. Rost, B. ( 1996; ). PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol 266, 525–539.
    [Google Scholar]
  23. Tarbouriech, N., Curran, J., Ruigrok, R. W. & Burmeister, W. P. ( 2000; ). Tetrameric coiled coil domain of Sendai virus phosphoprotein. Nat Struct Biol 7, 777–781.[CrossRef]
    [Google Scholar]
  24. Uversky, V. N., Gillespie, J. R. & Fink, A. L. ( 2000; ). Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins 41, 415–427.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.80590-0
Loading
/content/journal/jgv/10.1099/vir.0.80590-0
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error