Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling

Theoretical Biology and Medical Modelling

Volumn 6, Issue 1, 2009, Pages

  Vlachakis, Dimitrios ^a  

^a INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

HELICASE; TRANSFER RNA; ADENOSINE TRIPHOSPHATE; RNA HELICASE;

ARTICLE; CELL PROLIFERATION; COMPUTER AIDED DESIGN; COMPUTER MODEL; COMPUTER SIMULATION; CRYSTAL STRUCTURE; ENZYME STRUCTURE; MOLECULAR DYNAMICS; MURRAY VALLEY ENCEPHALITIS VIRUS; NUCLEOTIDE SEQUENCE; THEORETICAL STUDY; THREE DIMENSIONAL IMAGING; VIRUS SURVIVAL; VIRUS TRANSMISSION; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; ENZYMOLOGY; FLAVIVIRUS; GENETICS; JAPANESE ENCEPHALITIS VIRUS; METABOLISM; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY; THERMODYNAMICS;

FLAVIVIRIDAE; MURRAY VALLEY ENCEPHALITIS VIRUS; USUTU VIRUS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; BINDING SITES; COMPUTER SIMULATION; ENCEPHALITIS VIRUS, MURRAY VALLEY; FLAVIVIRIDAE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RNA HELICASES; SEQUENCE HOMOLOGY, AMINO ACID; STATIC ELECTRICITY; STRUCTURAL HOMOLOGY, PROTEIN; THERMODYNAMICS;

EID: 68149150826     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-6-9     Document Type: Article

References (30)

1. Taxonomy of the virus family Flaviviridae. CH Calisher EA Gould, Adv Virus Res 2003 59 1 19 14696325
2. Characterization of an autonomous subgenomic pestivirus RNA replicon. S-E Behrens CW Grassmann H-J Thiel G Meyers N Tautz, Journal of Virology 1998 72 2364 2372 9499097
3. Subgenomic replicons of the flavivirus Kunjin: construction and applications. AA Khromykh EG Westaway, Journal of Virology 1997 71 1497 1505 8995675
4. Structure of the flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing. J Wu AK Bera RJ Kuhn JL Smith, J Virol 2005 79 10268 10277 16051820
5. Emergence of Usutu virus in Hungary. T Bakonyi K Erdélyi K Ursu E Ferenczi T Csörgo H Lussy S Chvala C Bukovsky T Meister H Weissenböck N Nowotny, J Clin Microbiol 2007 45 3870 3874 17913929
6. Complete genome analysis and molecular characterization of Usutu virus that emerged in Austria in 2001: comparison with the South African strain SAAR-1776 and other flaviviruses. T Bakonyi EA Gould J Kolodziejek H Weissenböck N Nowotny, Virology. 2004 328 2 301 310 15464850
7. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schäffer J Zhang Z Zhang W Miller, Nucleic Acids Res 1997 25 3389 3402 9254694
8. GenBank. DA Benson I Karsch-Mizrachi DJ Lipman J Ostell DL Wheeler, Nucleic Acids Res 2007 35 21 25 17148477
9. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 4673 4680 7984417
10. GeneSilico protein structure prediction meta-server. MA Kurowski JM Bujnicki, Nucleic Acids Res 2003 31 3305 3307 12824313
11. MOE, Chemical Computing Group, 1010 Sherbrooke St. West, Suite 910, Montreal, Canada, H3A 2R.
12. DeLano "The PyMOL Molecular Graphics System.". L Warren, DeLano Scientific LLC, San Carlos, CA, USA http://www.pymol.org
13. How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules. J Wang P Cieplak PA Kollman, J Comp Chem 2000 21 1049 1074
14. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. RA Laskowski JA Rullmannn MW MacArthur R Kaptein JM Thornton, J Biomol NMR 1996 8 477 486 9008363
15. VERIFY3D: assessment of protein models with three-dimensional profiles. D Eisenberg R Lüthy JU Bowie, Methods Enzymol 1997 277 396 404 9379925
16. Assessment of protein models with three-dimensional profiles. R Lüthy JU Bowie D Eisenberg, Nature 1992 356 83 85 1538787
17. Structure of the Murray Valley encephalitis virus RNA helicase at 1.9 Angstrom resolution. EJ Mancini R Assenberg A Verma TS Walter R Tuma JM Grimes RJ Owens DI Stuart, Protein Sci 2007 16 10 2294 300 17893366
18. Molecular targets for flavivirus drug discovery. A Sampath R Padmanabhan, Antiviral Res 2009 81 1 6 15 18796313
19. Generating and testing protein folds. SJ Wodak MJ Rooman, Current Opinion in Structural Biology 1993 3 247 259
20. Protein fold recognition. D Jones J Thornton, Journal of Computer Aided Molecular Design 1993 7 439 456 8229094
21. Inverted protein structure prediction. JU Bowie D Eisenberg, Current Opinion in Structural Biology 1993 3 437 444
22. Protein Structure Prediction By Threading Methods: Evaluation Of Current Techniques. C Lemer MJ Rooman SJ Wodak, Proteins. 1996 23 3 337 355
23. Fold-recognition detects an error in the Protein Data Bank. Janusz Bujnicki Leszek Rychlewski Daniel Fischer, Bioinformatics 2002 18 10 1391 1395 12376384
24. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. JL Kim KA Morgenstern JP Griffith MD Dwyer JA Thomson MA Murcko C Lin PR Caron, Structure 1998 6 89 100 9493270
25. The P-loop a common motif in ATP- and GTP-binding proteins. M Saraste PR Sibbald A Wittinghofer, Trends Biochem Sci 1990 15 430 434 2126155
26. Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). M Ruff S Krishnaswamy M Boeglin A Poterszman A Mitschler A Podjarny B Rees JC Thierry D Moras, Science 1991 252 1682 1689 2047877
27. Mechanisms of helicase-catalyzed DNA unwinding. TM Lohman KP Bjornson, Annu Rev Biochem 1996 65 169 214 8811178
28. Mutational analysis of a DEAD box RNA helicase: the mammalian translation initiation factor elF-4A. A Pause N Sonenberg, EMBO J 1992 11 2643 2654 1378397
29. The QRxGRxGRxxxG motif of the vaccinia virus DExH box RNA helicase NPH-II is required for ATP hydrolysis and RNA unwinding but not for RNA binding. CH Gross S Shuman, J Virol 1996 70 1706 1713 8627691
30. Insights Into RNA Unwinding and ATP Hydrolysis by the Flavivirus Ns3 Protein. D Luo T Xu RP Watson D Scherer-Becker A Sampath W Jahnke SS Yeong CH Wang SP Lim A Strongin SG Vasudevan J Lescar, EMBO J 2008 27 3209 3219 19008861