Computer aided subunit vaccine design against pathogenic Leptospira serovars

Interdisciplinary Sciences – Computational Life Sciences

Volumn 4, Issue 1, 2012, Pages 38-45

  Umamaheswari, Amineni ^a   Pradhan, Dibyabhaba ^a   Hemanthkumar, Marisetty ^b  

^a SRI VENKATESWARA INSTITUTE OF MEDICAL SCIENCES   (India)

^b AGRICULTURAL RESEARCH STATION   (India)

Author keywords

homology modeling; leptospirosis; MHC; ProPred; proteinprotein docking; subunit vaccine peptides; T cell epitope

Indexed keywords

LEPTOSPIRA;

BACTERIAL PROTEIN; EPITOPE; HLA ANTIGEN; MEMBRANE PROTEIN; PEPTIDE; SUBUNIT VACCINE;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGICAL MODEL; CD4+ T LYMPHOCYTE; CELLULAR IMMUNITY; CLASSIFICATION; COMPUTER AIDED DESIGN; DRUG DESIGN; EPITOPE MAPPING; HUMAN; IMMUNOLOGY; LEPTOSPIRA; LEPTOSPIROSIS; METABOLISM; MICROBIOLOGY; PROTEIN BINDING; SPECIES DIFFERENCE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CD4-POSITIVE T-LYMPHOCYTES; COMPUTER-AIDED DESIGN; DRUG DESIGN; EPITOPE MAPPING; EPITOPES, T-LYMPHOCYTE; HLA ANTIGENS; HUMANS; IMMUNITY, CELLULAR; LEPTOSPIRA; LEPTOSPIROSIS; MEMBRANE PROTEINS; MODELS, BIOLOGICAL; PEPTIDES; PROTEIN BINDING; SPECIES SPECIFICITY; VACCINES, SUBUNIT;

EID: 84864300010     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-012-0118-9     Document Type: Article

References (44)

1. Altschul, S. F., Thomas, L. M., Alejandro, A. S., Jinghui, Z., Zheng, Z., Webb, M., David J. L. 1997. Gapped BLAST and PSI BLAST: A new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
2. Barker, C. J., Beagley, K. W., Hafner, L. M., Timms, P. 2008. In silico identification and in vivo analysis of a novel T-cell antigen from Chlamydia, NrdB. Vaccine 26, 1285-1296.
3. Bharti, A. R., Nally, J. E., Ricaldi, J. N., Matthias, M. A., Diaz, M. M., Lovett, M. A., Levett, P. N., Gilman, R. H., Willig, M. R., Gotuzzo, E., Vinetz, J. M. 2003. Leptospirosis: A zoonotic disease of global importance. Lancet Infect Dis 3, 757-771.
4. Bryson, K., McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S., Jones, D. T. 2005. Protein structure prediction servers at University College London. Nucleic Acids Res 33, W36-38.
5. Bui, H. H., Sidney, J., Peters, B., Sathiamurthy, M., Sinichi, A., Purton, K. A., Mothé, B. R., Chisari, F. V., Watkins, D. I., Sette, A. 2005. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57, 304-314.
6. Bulach, D. M., Zuerner, R. L., Wilson, P., Seemann, T., McGrath, A., Cullen, P. A., Davis, J., Johnson, M., Kuczek, E., Alt, D. P., Peterson-Burch, B., Coppel, R. L., Rood, J. I., Davies, J. K., Adler, B. 2006. Genome reduction in Leptospira borgpetersenii reflects limited transmission potential. Proc Natl Acad Sci USA 103, 14560-14565.
7. Carver, T., Bleasby, A. 2003. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics 19, 1837-1843.
8. Castrignano, T., De, Meo, P. D., Cozzetto, D., Talamo, I. G., Tramontano, A. 2006. The PMDB Protein Model Database. Nucleic Acids Res 34, D306-D309.
9. de Groot, A. S., McMurry, J., Marcon, L., Franco, J., Rivera, D., Kutzler, M., Weiner, D., Martin, B. 2005. Developing an epitope-driven tuberculosis (TB) vaccine. Vaccine 23, 2121-2131.
10. Doolan, D. L., Southwood, S., Chesnut, R., Appella, E., Gomez, E., Richards, A., Higashimoto, Y. I., Maewal, A., Sidney, J., Gramzinski, R. A., Mason, C., Koech, D., Hoffman, S. L., Sette A. 2000. HLA-DRpromiscuous T cell epitopes from Plasmodium falciparum pre-erythrocytic-stage antigens restricted by multiple HLA class II alleles. J Immunol 165, 1123-1137.
11. Eswar, N., Eramian, D., Webb, B., Shen, M., Sali, A. 2008. Protein structure modeling with MODELLER. Methods Mol Biol 426, 145-159.
12. Eswar, N., Eramian, D., Webb, B., Shen, M. Y., Sali, A. 2006. The detection and characterization of pathogenic Leptospira and the use of OMPs as potential antigens and immunogens. Trop Biomed 23, 194-207.
13. Jenkins, M. K., Khoruts, A., Ingulli, E., Mueller, D. L., McSorley, S. J., Reinhardt, R. L., Itano, A., Pape, K. A. 2001. In vivo activation of antigen-specific CD4 T cells. Annu Rew Immunol 19, 23-45.
14. Laskowski, R. A., MacArthur, M. W., Moss, D. S., Thornton, J. M. 1993. PROCHECK: A program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
15. Lin, X., Sun, A., Ruan, P., Zhang, Z., Yan, J. 2011. Characterization of conserved combined T and B cell epitopes in Leptospira interrogans major outer membrane proteins OmpL1 and LipL41. BMC Microbiol 11, 21.
16. Méndez, R., Leplae, R., Lensink, M. F., Wodak, S. J. 2005. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60, 150-169.
17. Nascimento, A. L., Verjovski-Almeida, S., van Sluys, M. A., Monteiro-Vitorello, C. B., Camargo, L. E., Digiampietri, L. A., Harstkeerl, R. A., Ho, P. L., Marques, M. V., Oliveira, M. C., Setubal, J. C., Haake, D. A., Martins, E. A. 2004. Genome features of Leptospira interrogans serovar Copenhageni. Braz J Med Biol Res 37, 459-477.
18. Norel, R., Sheinerman, F., Petrey, D., Honig, B. 2001. Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis. Protein Sci 10, 2147-2161.
19. Panigada, M., Sturniolo, T., Besozzi, G., Boccieri, M. G., Sinigaglia, F., Grassi, G. G., Grassi, F. 2002. Identification of a promiscuous T-cell epitope in Mycobacterium tuberculosis Mce proteins. Infect Immun 70, 79-85.
20. Peters, B., Sette, A. 2007. Integrating epitope data into the emerging web of biomedical knowledge resources. Nat Rev Immunol 7, 485-490.
21. Rakesh, S., Pradhan, D., Umamaheswari, A. 2009. In silico approach for future development of subunit vaccines against Leptospira interrogans serovar Lai. Int J Bioinformatics Res 1, 85-92.
22. Rammensee, H., Bachmann, J., Emmerich, N. P., Bachor, O. A., Stevanovic, S. 1999. SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics 50, 213-219.
23. Ren, S. X., Fu, G., Jiang, X. G., Zeng, R., Miao, Y. G., Xu, H., Zhang, Y. X., Xiong, H., Lu, G., Lu, L. F., Jiang, H. Q., Jia, J., Tu, Y. F., Jiang, J. X., Gu, W. Y., Zhang, Y. Q., Cai, Z., Sheng, H. H., Yin, H. F., Zhang, Y., Zhu, G. F., Wan, M., Huang, H. L., Qian, Z., Wang, S. Y., Ma, W., Yao, Z. J., Shen, Y., Qiang, B. Q., Xia, Q. C., Guo, X. K., Danchin, A., Saint, Girons, I., Somerville, R. L., Wen, Y. M., Shi, M. H., Chen, Z., Xu, J. G., Zhao G. P. 2003. Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 422, 888-893.
24. Ritchie, D. W., Kozakov, D., Vajda, S. 2008. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions. Bioinformatics 24, 1865-1873.
25. Rudolph, M. G., Wilson, I. A. 2002. The specificity of TCR/pMHC interaction. Curr Opin Immunol 14, 52-65.
26. Serruto, D., Serino, L., Masignani, V., Pizza, M. 2009. Genome-based approaches to develop vaccines against bacterial pathogens. Vaccine 27, 3245-3250.
27. Singh, H., Raghava, G. P. 2001. ProPred: Prediction of HLA-DR binding sites. Bioinformatics 17, 1236-1237.
28. Singh, P., Suman, S., Chandna, S., Das, T. K. 2009. Possible role of amyloid-beta, adenine nucleotide translocase and cyclophilin-D interaction in mitochondrial dysfunction of Alzheimer's disease. Bioinformation 3, 440-445.
29. Smith, G. R., Sternberg, M. J. 2002. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 12, 28-35.
30. Southwood, S., Sidney, J., Kondo, A., de Guercio, M. F., Appella, E., Hoffman, S., Kubo, R. T., Chesnut, R. W., Grey, H. M., Sette, A. 1998. Several common HLA-DR types share largely overlapping peptide binding repertoires. J Immunol 160, 3363-3373.
31. Sylvester-Hvid, C., Kristensen, N., Blicher, T., Ferre, H., Lauemoller, S. L., Wolf, X. A., Lamberth, K., Nissen, M. H., Pedersen, L., Buus, S. 2002. Establishment of a quantitative ELISA capable of determining peptide - MHC class I interaction. Tissue Antigens 59, 251-258.
32. Texier, C., Pouvelle, S., Busson, M., Hervé, M., Charron, D., Ménez, A., Maillère, B. 2000. HLADR restricted peptide candidates for bee venom immunotherapy. J Immunol 164, 3177-3184.
33. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
34. Tuero, I., Vinetz, J. M., Klimpel, G. R. 2010. Lack of demonstrable memory T cell responses in humans who have spontaneously recovered from leptospirosis in the Peruvian Amazon. J Infect Dis 201, 420-427.
35. Turesson, C., Matteson, E. L. 2006. Genetics of rheumatoid arthritis. Mayo Clin Proc 81, 94-101.
36. Umamaheswari, A., Pradhan, D., Hemanthkumar M. 2010a. Identification of potential Leptospira phosphoheptose isomerase (GmhA) inhibitors through virtual high-throughput screening. Genomics Proteomics Bioinformatics 8, 246-255.
37. Umamaheswari, A., Pradhan, D., Hemanthkumar M. 2010b. In silico identification of common putative drug targets in Leptospira interrogans. J Chem Biol 4, 165-173.
38. Umamaheswari, A., Pradhan, D., Hemanthkumar M. 2010c. Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase. J Chem Biol 4, 175-187.
39. van der Merwe, P. A., Davis, S. J. 2003. Molecular interactions mediating T cell antigen recognition. Annu Rev Immunol 21, 659-684.
40. Wallner, B., Elofsson, A. 2003. Can correct protein models be identified. Protein Sci 12, 1073-1086.
41. Wang, P., Sidney, J., Dow, C., Mothé, B., Sette, A., Peters, B. 2008. A Systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 4, e1000048.
42. Wang. Z., Jin, L., Wegrzyn, A. 2007. Leptospirosis vaccines. Microb Cell Fact 6, 39.
43. Wiederstein, M., Sippl, M. J. 2007. ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35, W407-W410.
44. Zhang, G. L., Khan, A. M., Srinivasan, K. N., August, J. T., Brusic, V. 2005. MULTIPRED: A computational system for prediction of promiscuous HLA binding peptides. Nucleic Acids Res 33, W172-179.