Interdisciplinary Bio Central

Korean Society for Bioinformatics (한국생명정보학회)
권호 표지
DOI QR코드

DOI QR Code

Binding Mode Analysis of Bacillus subtilis Obg with Ribosomal Protein L13 through Computational Docking Study

  • Lee, Yu-No (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Bang, Woo-Young (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Kim, Song-Mi (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Lazar, Prettina (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Bahk, Jeong-Dong (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU)) ;
  • Lee, Keun-Woo (Division of Applied Life Science (BK21 Program), Environmental Biotechnology National Core Research Center (EB-NCRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University (GNU))
  • Published : 2009.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

Introduction: GTPases known as translation factor play a vital role as ribosomal subunit assembly chaperone. The bacterial Obg proteins ($Spo{\underline{0B}}$-associated ${\underline{G}}TP$-binding protein) belong to the subfamily of P-loop GTPase proteins and now it is considered as one of the new target for antibacterial drug. The majority of bacterial Obgs have been commonly found to be associated with ribosome, implying that these proteins may play a fundamental role in ribosome assembly or maturation. In addition, one of the experimental evidences suggested that Bacillus subtilis Obg (BsObg) protein binds to the L13 ribosomal protein (BsL13) which is known to be one of the early assembly proteins of the 50S ribosomal subunit in Escherichia coli. In order to investigate binding mode between the BsObg and the BsL13, protein-protein docking simulation was carried out after generating 3D structure of the BsL13 structure using homology modeling method. Materials and Methods: Homology model structure of BsL13 was generated using the EcL13 crystal structure as a template. Protein-protein docking of BsObg protein with ribosomal protein BsL13 was performed by DOT, a macro-molecular docking software, in order to predict a reasonable binding mode. The solvated energy minimization calculation of the docked conformation was carried out to refine the structure. Results and Discussion: The possible binding conformation of BsL13 along with activated Obg fold in BsObg was predicted by computational docking study. The final structure is obtained from the solvated energy minimization. From the analysis, three important H-bond interactions between the Obg fold and the L13 were detected: Obg:Tyr27-L13:Glu32, Obg:Asn76-L13:Glu139, and Obg:Ala136-L13:Glu142. The interaction between the BsObg and BsL13 structures were also analyzed by electrostatic potential calculations to examine the interface surfaces. From the results, the key residues for hydrogen bonding and hydrophobic interaction between the two proteins were predicted. Conclusion and Prospects: In this study, we have focused on the binding mode of the BsObg protein with the ribosomal BsL13 protein. The interaction between the activated Obg and target protein was investigated with protein-protein docking calculations. The binding pattern can be further used as a base for structure-based drug design to find a novel antibacterial drug.

Keywords

References

  1. Adesokan, A. A., Roberts, V. A., Lee, K. W., Lins, R. D. and Briggs, J. M. (2003). Prediction of HIV-1 Integrase/Viral DNA Interactions in the Catalytic Domain by Fast Molecular Docking. J. Med. Chem. 47, 821-828 https://doi.org/10.1021/jm0301890
  2. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. and McCammon, J. A. (2001). Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037–10041 https://doi.org/10.1073/pnas.181342398
  3. Berendsen, H. J. C., van der Spoel, D., van Drunen, R. (1995). GROMACS - a message-passing parallel molecular-dynamics implementation. Comput. Phys. Commun. 91, 43-56 https://doi.org/10.1016/0010-4655(95)00042-E
  4. Bourne, H. R., Sanders, D. A. and Mcrmick, F. (1991). The GTPase superfamily: conserved structure and molecular mechanism. Nature 349, 117-127 https://doi.org/10.1038/349117a0
  5. Bourne, H. R., Sanders, D. A. and Mcrmick, F. (1991). The GTPase superfamily: a conserved switch of diverse cell functions. Nature 348, 125-132 https://doi.org/10.1038/348125a0
  6. Buglino, J., Shen, V., Hakimian, P., Lima, C. D. (2002). Structural and biochemical analysis of the Obg GTP binding protein. Structure 10, 1581-1592 https://doi.org/10.1016/S0969-2126(02)00882-1
  7. Chan, Y. L., Olvera, J., Gluck, A., Wool, I. G. (1994). A leucine zipper-like motif and a basic region-leucine zipper-like element in rat ribosomal protein L13a. Identification of the tumtransplantation antigen P198. J. Biol. Chem. 269, 5589-5594
  8. Chandra Sanyal, S., Liljas, A. (2000). The end of the beginning: structural studies of ribosomal proteins. Curr. Opin. Struct. Biol. 10, 633-636 https://doi.org/10.1016/S0959-440X(00)00143-3
  9. Chao, Z., George, V., James, L. C., Charles, D. (1997). Determination of atomic desolvation energies from the structures of crystallized proteins. J. Mol. Biol. 267, 707-726 https://doi.org/10.1006/jmbi.1996.0859
  10. Comartin, D. J., Brown, E. D. (2006). Non-ribosomal factors in ribosome subunit assembly are emerging targets for new antibacterial drugs. Curr. Opin. Pharmacol. 6, 453-458 https://doi.org/10.1016/j.coph.2006.05.005
  11. Darden, T., York, D., Pedersen, L. (1993). Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089-10092 https://doi.org/10.1063/1.464397
  12. Datta, K., Skidmore, J. M., Pu, K. and Maddock, J. R. (2004). The Caulobacter crescentus GTPase CgtAC is required for progression through the cell cycle and for maintaining 50S ribosomal subunit levels. Mol. Microbiol. 54, 1379-1392 https://doi.org/10.1111/j.1365-2958.2004.04354.x
  13. Dutkiewicz, R., Słomińska, M., Wegrzyn, G. and Czyz, A. (2002). Overexpression of the cgtA (yhbZ, obgE) gene, coding for an essential GTP-binding protein, impairs the regulation of chromosomal functions in Escherichia coli. Curr. Microbiol. 45, 440-445 https://doi.org/10.1007/s00284-002-3713-x
  14. Jiang, M, Datta, K., Walker, A., Strahler, J., Bagamasbad, P., Andrews, P. C. and Maddock, J. R. (2006). The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly. J. Bacteriol. 188, 6757-6770 https://doi.org/10.1128/JB.00444-06
  15. Kobayashi, G., Moriya, S. and Wada, C. (2001). Deficiency of essential GTP-binding protein ObgE in Escherichia coli inhibits chromosome partition. Mol. Microbiol. 41, 1037-1051 https://doi.org/10.1046/j.1365-2958.2001.02574.x
  16. Kok, J., Trach, K. A. and Hoch, J. A. (1994). Effects on Bacillus subtilis of a conditional lethal mutation in the essential GTPbinding protein Obg. J. Bacteriol. 176, 7155-7160 https://doi.org/10.1128/jb.176.23.7155-7160.1994
  17. Kukimoto-Niino, M., Murayama, K., Inoue, M., Terada, T., Tame, J. R., Kuramitsu, S., Shirouzu, M., Yokoyama, S. (2004). Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8. J. Mol. Biol. 337, 761-770 https://doi.org/10.1016/j.jmb.2004.01.047
  18. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G. (2007). ClustalW and ClustalX version 2. Bioinformatics 23, 2947-2948 https://doi.org/10.1093/bioinformatics/btm404
  19. 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. Crystallogr. 26, 283–291 https://doi.org/10.1107/S0021889892009944
  20. Leipe, D. D., Wolf, Y. I., Koonin, E. V. and Aravind, L. (2002). Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317, 41-72 https://doi.org/10.1006/jmbi.2001.5378
  21. Lin, B., Thayer, D. A. and Maddock, J. R. (2004). The Caulobacter crescentus CgtAC protein cosediments with the free 50S ribosomal subunit. J. Bacteriol. 186, 481-489 https://doi.org/10.1128/JB.186.2.481-489.2004
  22. Maddock, J., Bhatt, A., Koch, M. and Skidmore, J. (1997). Identification of an essential Caulobacter crescentus gene encoding a member of the Obg family of GTP-binding proteins. J. Bacteriol. 179, 6426-6431 https://doi.org/10.1128/jb.179.20.6426-6431.1997
  23. Maguire, B. A., Zimmermann, R. A. (2001). The ribosome in focus. Cell 104, 813-816 https://doi.org/10.1016/S0092-8674(01)00278-1
  24. Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, E., Tsigelny, I. and Ten Eyck, L. F. (2001). Protein Docking Using Continuum Electrostatics and Geometric Fit. Prot. Eng. 14, 105-113 https://doi.org/10.1093/protein/14.2.105
  25. Okamoto, S., and Ochi, K. (1998). An essential GTP-binding protein functions as a regulator for differentiation in Streptomyces coelicolor. Mol. Microbiol. 30, 107-119 https://doi.org/10.1046/j.1365-2958.1998.01042.x
  26. Ramakrishnan, V., Moore, P. B. (2001). Atomic structures at last: the ribosome in 2000. Curr. Opin. Struct. Biol. 11, 144-154 https://doi.org/10.1016/S0959-440X(00)00184-6
  27. Sato, A., Kobayashi, G., Hayashi, H., Yoshida, H., Wada, A., Maeda, M., Hiraga, S., Takeyasu, K. and Wada, C. (2005). The GTP binding protein Obg homolog ObgE is involved in ribosome maturation. Genes Cells 10, 393-408 https://doi.org/10.1111/j.1365-2443.2005.00851.x
  28. Schuwirth, B. S., Day, J. M., Hau, C. W., Janssen, G. R., Dahlberg, A. E., Cate, J. H. D., Vila-Sanjurjo, A. (2006). Structural analysis of kasugamycin inhibition of translation. Nat. Struct. Mol. Biol. 13, 879-886 https://doi.org/10.1038/nsmb1150
  29. Scott, J. M., Ju, J., Mitchell, T., and Haldenwang, W. G. (2000). The Bacillus subtilis GTP binding protein Obg and regulators of the B stress response transcription factor cofractionate with ribosomes. J. Bacteriol. 182, 2771-2777 https://doi.org/10.1128/JB.182.10.2771-2777.2000
  30. Scott, J. M. and Haldenwang, W. G. (1999). Obg, an essential GTP binding protein of Bacillus subtilis, is necessary for stress activation of transcription factor B. J. Bacteriol. 181, 4653-4660
  31. Sikora, A. E., Zielke, R., Datta, K. and Maddock, J. R. (2006). The Vibrio harveyi GTPase CgtAV is essential and is associated with the 50S ribosomal subunit. J. Bacteriol. 188, 1205-1210 https://doi.org/10.1128/JB.188.3.1205-1210.2006
  32. Slominska, M., Konopa, G., Wegrzyn, G. and Czyz, A. (2002). Impaired chromosome partitioning and synchronization of DNA replication initiation in an insertional mutant in the Vibrio harveyi cgtA gene coding for a common GTP-binding protein. Biochem J. 362, 579-84 https://doi.org/10.1042/0264-6021:3620579
  33. Tan, J., Jakob, U. and Bardwell, J. C. A. (2002). Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase. J. Bacteriol. 184, 2692-2698 https://doi.org/10.1128/JB.184.10.2692-2698.2002
  34. Trach, K. and Hoch, J. A. (1989). The Bacillus subtilis spo0B stage sporulation operon encodes an essential GTP-binding protein. J. Bacteriol. 171, 1362-1371 https://doi.org/10.1128/jb.171.3.1362-1371.1989
  35. Van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A. R., Apol, E., Meulenhoff, P. J., et al. (2005). Gromacs User Manual version 3.3, http://www.gromacs.org/
  36. Vidwans, S. J., Ireton, K. and Grossman, A. D. (1995). Possible role for the essential GTP-binding protein Obg in regulating the initiation of sporulation in Bacillus subtilis. J. Bacteriol. 177, 3308-3311
  37. Wout, P., Pu, K., Sullivan, S. M., Reese, V., Zhou, S., Lin, B. and Maddock, J. R. (2004). The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. J. Bacteriol. 186, 5249-5257 https://doi.org/10.1128/JB.186.16.5249-5257.2004