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Computational Approach to Explore Plasmodium falciparum 3D7 Seryl tRNA Synthetase Structure

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Author Affiliations

  • 1Department of Biotechnology, Acharya Nagarjuna University, Guntur, AP, INDIA

Int. Res. J. Biological Sci., Volume 3, Issue (6), Pages 29-40, June,10 (2014)

Abstract

Malaria remains the leading cause of deaths attributable to a communicable disease globally. The reemergence of drug-resistant to Plasmodium falciparum, which is the most fatal human cerebral malarial parasite, has focused attention on aminoacylation in protein translation. Seryl tRNA Synthetase is the enzyme involved in acylation of Serine amino acid to tRNA. The protein sequence of Seryl tRNA synthetase containing 539 residues was obtained from UniprotKB. The enzyme was characterized using computational tools. The secondary and tertiary (3D) structure of the enzyme was predicted using Seryl tRNA Synthetase from other species and validated by various structural quality validation tools. Results of the current study will provide a deep insight about the structure and function of Seryl tRNA synthetase and aid in drug docking, rational drug designing.

References

  1. World Malaria Report 2011 (Geneva: World Health Organization) WHO, (2011)
  2. White N.J., Determinants of relapse periodicity in Plasmodium vivax malaria, J. Malaria., (10), 297 (2011)
  3. Wells T.N., Alonso P.L. and Gutteridge W.E., New medicines to improve control and contribute to the eradication of malaria, Nat. Rev. Drug Discov., (8), 879–891 (2009)
  4. Bhatt T.K., Structural Characterization of Histone Deacetylase from Plasmodium falciparum, ISCA J. Biological Sci, (1), 65-68 (2012)
  5. Laurence Florens et al., A proteomic view of the Plasmodium falciparum life cycle, Nature, (419), 520–526 (2002)
  6. Cecile Crosnier, et al., Basigin is a receptor essential for erythrocyte invasion by Plasmodium falciparum,Nature.,(480), 534–538 (2011)
  7. Becker, S.A., Feist, A.M., Mo, M.L., Hannum, G., Palsson, B.O. and Herrgard, M.J., ‘Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox’, Nat. Protoc., (2),727–738(2007)
  8. Edwards J.S. and Palsson B.O., Metabolic flux balance analysis and the in silicoanalysis of Escherichia coli K-12 gene deletions, BMC Bioinf. (1:1), (2000)
  9. Kauffman K.J., Prakash P. and Edwards J.S., Advances in flux balance analysis, Curr. Opin. Biotechnol., (14), 491–496 (2003)
  10. Puntervoll P., Linding R., Gemünd C., Chabanis-Davidson S., Mattingsdal M., Cameron S., Martin D. M. A., Rahman S.A. and Schomburg D.‚ Observing local and global properties of metabolic pathway - load points and choke points in the metabolic networks, Bioinformatics,10(22), 1767–1774 (2006)
  11. Yeh I., Hanekamp T., Tsoka S., Karp P.D. and Altman R.B., Computational analysis of Plasmodium falciparummetabolism: organizing genomic information to facilitate drug discovery, Genome Res., (14), 917–924 (2004)
  12. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W. and Lipman D.J., Gapped BLAST and PSIBLAST: a new generation of protein database search programs, Nucleic Acids Res., (25), 3389-3402 (1997)
  13. Katrina C. Martinez, Franco G. Teves and Ma. Reina Suzette B. Madamba, Sequence Analysis of Putative luxS Gene Involved in Prodigiosin Biosynthesis from Philippine Local Strains of Serratia marcescens, ISCA J. Biological Sci, (2), 13-19 (2013)
  14. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F. and Higgins D.G., The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, (25), 4876-4882 (1997)
  15. Maithri S.K., Ramesh K.V., Dieudonné Mutangana and Deshmukh Sudha., Molecular Modeling and Docking Studies of PirB Fusion Protein from Photorhabdus Luminescens, ISCA J. Biological Sci, (1), 7-18 (2012)
  16. Ausiello G., Brannetti B., Costantini A., Ferrè F., Maselli V., Via A., Cesareni G., Diella F., Superti-Furga G., Wyrwicz L., Ramu C., McGuigan C., Gudavalli R., Letunic, I., Bork, P., Rychlewski, L., Küster, B., Helmer-Citterich, M., Hunter, W. N., Aasland, R. and Gibson, T. J., ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins, Nucleic Acids Res (31), 3625-3630 (2003)
  17. Combet C., Blanchet C., Geourjon C. and Deléage G.NPS: network protein sequence analysis. Trends Biochem Sci.,(25:3),147-150 (2000)
  18. Gasteiger E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D.and Bairoch, A., ‘Protein Identification and Analysis Tools on the ExPASy Server’, The Proteomics Protocols Handbook, 18,571-607 (2005)
  19. Kyte J. and Doolittle R.F., A simple method for displaying the hydropathic character of a protein, J. Mol. Biol, (157), 105-132 (1982)
  20. Garnier J., Osguthorpe DJ. and Robson B., Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins, J Mol Biol, (120), 97-120 (1978)
  21. Marti-Renom, M.A., Stuart, A., Fiser, A., Sanchez, R., Melo, F. and Sali, A., Comparative protein structure modeling of genes and genomes, Annu. Rev. Biophys. Biomol. Struct, 21(29),291-325(2000)
  22. Sali A. and Blundell T.L., Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol.,(234), 779-815(1993)
  23. Fiser, A., Do, R.K. and Sali, A., Modeling of loops in protein structures, Protein Science, (9),1753-1773(2000)
  24. Bhatt T.K., Structural Studies on Mitogen Activated Protein Kinase from Plasmodium falciparum, ISCA J. Biological Sci, (1), 42-46 (2012)
  25. Combet C., Jambon M., Deleage G. and Geourjon, C.‘Geno3D: automatic comparative molecular modelling of protein, Bioinformatics, (18), 213-214 (2002)
  26. Lambert, C., Leonard, N., De Bolle, X.and Depiereux, E., ‘ESyPred3D: Prediction of proteins 3D structures’, Bioinformatics, (18:9), 1250-1256 (2002)
  27. Bates, P.A., Kelley, L.A., MacCallum, R.M. and Sternberg, M.J.E.,‘Enhancement of Protein Modelling by Human Intervention in Applying the Automatic Programs 3D-JIGSAW and3D-PSSM’, Proteins: Structure, Function and Genetics, (5),39-46(2001)
  28. Bates, P.A. and Sternberg, M.J.E.,‘Model Building by Comparison at CASP3: Using Expert Knowledge and Computer Automation’, Proteins: Structure, Function and Genetics, (3),47-54(1999)
  29. Contreras-Moreira, B., Bates, P.A., ‘Domain Fishing: a first step in protein comparative modelling’, Bioinformatics, (18),1141-1142(2002)
  30. Arnold, K., Bordoli, L., Kopp, J. and Schwede, T.‘The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling”, Bioinformatics, (22),195-201(2006)
  31. Schwede, T., Kopp, J., Guex, N. and Peitsch, MC., ‘SWISS-MODEL: an automated protein homology-modeling server’, Nucleic Acids Research., (31),3381-3385(2003)
  32. Guex, N. and Peitsch, M. C., ‘SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling’., Electrophoresis., (18),2714-2723(1997)
  33. Nielsen, M., Lundegaard, C., Lund, O. and Petersen, TN., ‘Remote homology modeling using structure guided sequence profiles’, Nucleic Acids Research.,33(38),576-81(2010)
  34. Laskowski, R A., MacArthur, M W., Moss, D S. and Thornton, J M. (1993) , ‘PROCHECK - a program to check the stereochemical quality of protein structures’., J. App. Cryst., (26),283-291(1993)
  35. Laskowski, R A., Rullmannn, J A., MacArthur, M W., Kaptein, R. and Thornton, J M., ‘AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR’, J Biomol NMR, 35(8),477-486(1996)
  36. Sippl, M.J., Recognition of Errors in Three-Dimensional Structures of Proteins, Proteins (17),355-362(1993)