Biocomputational analysis of phosphoenolpyruvate carboxykinase from Raillietina echinobothrida, a cestode parasite, and its interaction with possible modulators

Parasitology

Volumn 143, Issue 3, 2016, Pages 300-313

  Dutta, Asim Kumar ^a   Ramnath, ^a   Tandon, Veena ^a   Das, Bidyadhar ^a  

^a NORTH EASTERN HILL UNIVERSITY   (India)

Author keywords

Cestode; enzyme kinetics; molecular docking; PEPCK (GTP); THP

Indexed keywords

ASPARTIC ACID; COMPLEMENTARY DNA; CYSTEINE; DAIDZEIN; GENISTEIN; GLUTAMINE; LEUCINE; METHIONINE; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); SERINE; TETRAHYDROPALMATINE; BERBERINE DERIVATIVE; ENZYME INHIBITOR; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP);

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AMPLICON; ARTICLE; BINDING SITE; CESTODE; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME KINETICS; ENZYME PHOSPHORYLATION; GENE AMPLIFICATION; HYDROGEN BOND; HYDROPHOBICITY; IN VITRO STUDY; INHIBITION CONSTANT; MOLECULAR CLONING; MOLECULAR DOCKING; MOLECULAR WEIGHT; NONHUMAN; NUCLEOTIDE BINDING SITE; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RAILLIETINA ECHINOBOTHRIDA; SEQUENCE ALIGNMENT; SIMULATION; STOP CODON; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CHEMISTRY; DRUG EFFECTS; ENZYME ACTIVATION; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; MOLECULAR MODEL; PROTEIN TERTIARY STRUCTURE; REPRODUCIBILITY; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BERBERINE ALKALOIDS; CESTODA; COMPUTATIONAL BIOLOGY; ENZYME ACTIVATION; ENZYME INHIBITORS; KINETICS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PHOSPHOENOLPYRUVATE CARBOXYKINASE (ATP); PROTEIN STRUCTURE, TERTIARY; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS;

EID: 84960802380     PISSN: 00311820     EISSN: 14698161     Source Type: Journal    
DOI: 10.1017/S0031182015001742     Document Type: Article

References (45)

1. Ahmad, M. and Nizami, W. A. (1987). In vitro effects of mebendazole on the carbohydrate metabolism of Avitellina lahorea (Cestoda). Journal of Helminthology 61, 247-252.
2. Baker, D. and Sali, A. (2001). Protein structure prediction and structural genomics. Science 294, 93-96.
3. Bradford, M. M. (1976). A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein dye binding. Analytical Biochemistry 72, 248-254.
4. Carlson, G. M. and Holyoak, T. (2009). Structural insights into the mechanism of phosphoenolpyruvate carboxykinase catalysis. Journal of Biological Chemistry 284, 27037-27041.
5. Chan, J. D., Zarowiecki, M. and Marchant, J. S. (2013). Ca2+ channels and Praziquantel: A view from the free world. Parasitology International 62, 619-628.
6. Cheek, S., Zhang, H. and Grishin, N. V. (2002). Sequence and classification of kinases. Journal of Molecular Biology 320, 855-881.
7. Cheng, K. C. and Nowak, T. (1989). Arginine residues at the active site of avian liver phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 264, 3317-3324.
8. Cook, J. S., Weldon, S. L., Garcia-Ruiz, J. P., Hod, Y. and Hanson, R. W. (1986). Nucleotide sequence of the mRNA encoding the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) from the chicken. Proceedings of the National Academy of Sciences of USA 83, 7583-7587.
9. Das, B., Tandon, V. and Saha, N. (2004). Effects of phytochemicals of Flemingia vestita (Fabaceae) on glucose 6-phosphate dehydrogenase and enzymes of gluconeogenesis in a cestode (Raillietina echinobothrida). Comparative Biochemistry and Physiology-Part C 139, 141-146.
10. Das, B., Tandon, V., Saxena, J. K., Joshi, S. and Singh, A. R. (2013). Purification and characterization of phosphoenolpyruvate carboxykinase from Raillietina echinobothrida, a cestode parasite of the domestic fowl. Parasitology 140, 136-146.
11. Ghedin, E., Wang, S., Spiro, D., Caler, E., Zhao, Q., Crabtree, J., Allen, J. E., Delcher, A. L., Guiliano, D. B., Miranda-Saavedra, D., Angiuoli, S. V., Creasy, T., Amedeo, P., Haas, B., El-Sayed, N. M., Wortman, J. R., Feldblyum, T., Tallon, L., Schatz, M., Shumway, M., Koo, H., Salzberg, S. L., Schobel, S., Pertea, M., Pop, M., White, O., Barton, G. J., Carlow, C. K., Crawford, M. J., Daub, J., Dimmic, M. W., Estes, C. F., Foster, J. M., Ganatra, M., Gregory, W. F., Johnson, N. M., Jin, J., Komuniecki, R., Korf, I., Kumar, S., Laney, S., Li, B. W., Li, W., Lindblom, T. H., Lustigman, S., Ma, D., Maina, C. V., Martin, D. M., McCarter, J. P., McReynolds, L., Mitreva, M., Nutman, T. B., Parkinson, J., Peregrín-Alvarez, J. M., Poole, C., Ren, Q., Saunders, L., Sluder, A. E., Smith, K., Stanke, M., Unnasch, T. R., Ware, J., Wei, A. D., Weil, G., Williams, D. J., Zhang, Y., Williams, S. A., Fraser-Liggett, C., Slatko, B., Blaxter, M. L. and Scott, A. L. (2007). Draft genome of the filarial nematode parasite Brugia malayi. Science 317, 1756-1760.
12. Guruprasad, K., Reddy, B. V. B. and Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering 4, 155-161.
13. Hammes, G. G. (2002). Multiple conformational changes in enzyme catalysis. Biochemistry 41, 8221-8228.
14. Hanson, R. W. (2009). Thematic minireview series: A perspective on the biology of phosphoenolpyruvate carboxykinase 55 years after its discovery. Journal of Biological Chemistry 284, 27021-27023.
15. Hlavaty, J. J. and Nowak, T. (1997). Affinity cleavage at the metalbinding site of phosphoenolpyruvate carboxykinase. Biochemistry 36, 15514-15525.
16. Holyoak, T., Sullivan, S. M. and Nowak, T. (2006). Structural insights into the mechanism of PEPCK catalysis. Biochemistry 45, 8254-8263.
17. Huang, S. Y., Grinter, S. Z. and Zou, X. (2010). Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions. Physical Chemistry Chemical Physics 12, 12899-12908.
18. Jabalquinto, A. M., Laivenieks, M., González-Nilo, F. D., Yévenes, A., Encinas, M. V., Zeikus, J. G. and Cardemil, E. (2002). Evaluation by site-directed mutagenesis of active site amino acid residues of Anaerobiospirillum succiniciproducens phosphoenolpyruvate carboxykinase. Journal of Protein Chemistry 21, 393-400.
19. Jo, J. S., Ishihara, N. and Kikuchi, G. (1974). Occurrence and properties of four forms of phosphoenolpyruvate carboxykinase in the chicken liver. Archives of Biochemistry and Biophysics 160, 246-254.
20. Johnson, T. A. and Holyoak, T. (2012). The loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function. Biochemistry 51, 9547-9559.
21. Klein, R. D., Winterrowd, C. A., Hatzenbuhler, N. T., Shea, M. H., Favreau, M. A., Nulf, S. C. and Geary, T. G. (1992). Cloning of a cDNA encoding phosphoenolpyruvate carboxykinase from Haemonchus contortus. Molecular and Biochemical Parasitology 50, 285-294.
22. Knapp, J., Nakao, M., Yanagida, T., Okamoto, M., Saarma, U., Lavikainen, A. and Ito, A. (2011). Phylogenetic relationships within Echinococcus and Taenia tapeworms (Cestoda: Taeniidae): An inference from nuclear protein-coding genes. Molecular Phylogenetics and Evolution 61, 628-638.
23. Kyte, J. and Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology 157, 105-132.
24. Lewis, C. T., Haley, B. E. and Carlson, G. M. (1989). Formation of an intramolecular cystine disulfide during the reaction of 8-azidoguanosine 5'-triphosphate with cytosolic phosphoenolpyruvate carboxykinase (GTP) causes inactivation without photolabeling. Biochemistry 28, 9248-9255.
25. Lewis, C. T., Seyer, J. M., Cassell, R. G. and Carlson, G. M. (1993). Identification of vicinal thiols of phosphoenolpyruvate carboxykinase (GTP). Journal of Biological Chemistry 268, 1628-1636.
26. Lipinski, C. A., Lombardo, F., Dominy, B. W. and Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews 46, 3-26.
27. Liu, F., Lu, J., Hu, W., Wang, S. Y., Cui, S. J., Chi, M., Yan, Q., Wang, X. R., Song, H. D., Xu, X. N., Wang, J. J., Zhang, X. L., Zhang, X., Wang, Z. Q., Xue, C. L., Brindley, P. J., McManus, D. P., Yang, P. Y., Feng, Z., Chen, Z. and Han, Z. G. (2006). New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathogens 2, e29.
28. Makinen, A. L. and Nowak, T. (1989). A reactive cysteine in avian liver phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 264, 12148-12157.
29. Marhefka, C. A., Moore, B. M., Bishop, T. C., Kirkovsky, L., Mukherjee, A., Dalton, J. T. and Miller, D. D. (2001). Homology modeling using multiple molecular dynamics simulations and docking studies of the human androgen receptor ligand binding domain bound to testosterone and nonsteroidal ligands. Journal of Medicinal Chemistry 44, 1729-1740.
30. Matte, A., Tari, L. W., Goldie, H. and Delbaere, L. T. J. (1997). Structure and mechanism of phosphoenolpyruvate carboxykinase. Journal of Biological Chemistry 272, 8105-8108.
31. Mommsen, T. P., Patrick, J. W. and Moon, T. W. (1985). Gluconeogenesis in hepatocytes and kidney of Atlantic salmon. Molecular Physiology 8, 89-100.
32. Reynolds, C. H. (1980). Phosphoenolpyruvate carboxykinase from the rat and from the tapeworm, Hymenolepis diminuta. Comparative Biochemistry and Physiology 65, 481-487.
33. Ríos, S. E. and Nowak, T. (2002). Role of cysteine 306 in the catalytic mechanism of Ascaris suum phosphoenolpyruvate carboxykinase. Archives of Biochemistry and Biophysics 404, 25-37.
34. Rollinger, J. M., Stuppner, H. and Langer, T. (2008). Virtual screening for the discovery of bioactive natural products. Progress in Drug Research 65, 213-249.
35. Smith, A. A. and Caruso, A. (2013). In silico characterization and homology modeling of a cyanobacterial phosphoenolpyruvate carboxykinase enzyme. Structural Biology, Article ID 370820, 10.
36. Smyth, J. D. and McManus, D. P. (1989). The Physiology and Biochemistry of Cestodes. Cambridge University Press, Cambridge, UK.
37. Soulsby, E. J. L. (1982). Helminths, Arthropods and Protozoa of Domesticated Animals, 7th Edn, ELBS and Bailliere Tindall, London.
38. Swargiary, A., Verma, A. K. and Sarma, K. (2013). Homology modeling and docking studies of phosphoenolpyruvate carboxykinase in Schistosoma mansoni. Medicinal Chemistry Research 22, 2870-2878.
39. Tandon, V. and Das, B. (2007). In vitro testing of anthelmintic efficacy of Flemingia vestita (Fabaceae) on carbohydrate metabolism in Raillietina echinobothrida. Methods 42, 330-338.
40. Utter, M. F. and Kurahashi, K. (1954). Purification of oxalacetic carboxylase from chicken liver. Journal of Biological Chemistry 207, 787-802.
41. Verma, A. K., Swargiary, A., Prasad, S. B. and Arjun, J. (2012). Homology modeling of phosphoenolpyruvate carboxykinase of Ascaris suum. Journal of Pharmacy Research 5, 1248-1255.
42. Villarreal, J. M., Bueno, C., Arenas, F., Jabalquinto, A. M., González-Nilo, F. D., Encinas, M. V. and Cardemil, E. (2006). Nucleotide specificity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase kinetics, fluorescence spectroscopy, and molecular simulation studies. International Journal of Biochemistry and Cell Biology 38, 576-588.
43. Wang, X., Chen, W., Huang, Y., Sun, J., Men, J., Liu, H., Luo, F., Guo, L., Lv, X., Deng, C., Zhou, C., Fan, Y., Li, X., Huang, L., Hu, Y., Liang, C., Hu, X., Xu, J. and Yu, X. (2011). The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. Genome Biology 12, R107.
44. Weldon, S. L., Rando, A., Matathias, A. S., Hod, Y., Kalonick, P. A., Savon, S., Cook, J. S. and Hanson, R. W. (1990). Mitochondrial phosphoenolpyruvate carboxykinase from the chicken. Comparison of the cDNA and protein sequences with the cytosolic isozyme. Journal of Biological Chemistry 265, 7308-7317.
45. Yang, J., Kalhan, S. C. and Hanson, R. W. (2009). What is the metabolic role of phosphoenolpyruvate carboxykinase? Journal of Biological Chemistry 284, 27025-27029.