Structural Bioinformatic Approach to Understand the Molecular Mechanism of the Interactions of Small Heat Shock Proteins IbpA and IbpB with Lon Protease

Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 340)


In order to survive under temperature stress conditions, bacterial cells come up with different biochemical mechanisms like production of chaperones; a class of proteins that maintain the proper folding of the other necessary proteins for survival. Chaperones mostly function as complexes. A member of such a family in E.coli is IbpAB protein complex. This protein complex is known to bind a protease called Lon. However, till date the modes of binding between these proteins are still obscure. In the present work, we employed molecular modeling and simulation techniques to analyze the pattern of interactions between these proteins. We observed that under cold and heat shock conditions, the interactions between IbpA and IbpB proteins increase whereas at physiological temperature the interactions decrease which allows Lon to promote better binding and degradation at physiological temperature. So far this is the first report to predict the interactions scheme between these proteins.


IbpA-IbpB interaction Lon protease Small heat-shock protein Heat stress 



The authors would like to thank the BIF center at the Department of Biochemistry and Biophysics and the DST Purse program, 2012–2015, for providing the infrastructural support. SB is thankful to DBT (Grant no: BT/PR6869/BID/7/714/2012) for financial support.


  1. 1.
    Kitagawa, M., Matsumura, Y., Tsuchido, T.: Small heat shock proteins, IbpA and IbpB, are involved in resistances to heat and superoxide stresses in Escherichia coli. FEMS Microbiol. Lett. 184, 165–171 (2000)CrossRefGoogle Scholar
  2. 2.
    Spiess, C., Beil, A., Ehrmann, M.: A temperature-dependent switch from chaperone to protease in a widely conserved heat shock protein. Cell 97(3), 339–347 (1999)CrossRefGoogle Scholar
  3. 3.
    Allen, S.P., Polazzi, J.O., Gierse, J.K., Easton, A.M.: Two novel heat shock genes encoding proteins produced in response to heterologous protein expression in Escherichia coli. J. Bacteriol. 174, 6938–6947 (1992)CrossRefGoogle Scholar
  4. 4.
    Goldberg, A.L., Moerschell, R.P., Chung, C.H., Maurizi, M.R.: ATP-dependent protease La (lon) from Escherichia coli. Methods Enzymol. 244, 350–375 (1994)CrossRefGoogle Scholar
  5. 5.
    Leinonen, R., Diez, F.G., Binns, D., Fleischmann, W., Lopez, R., Apweiler, R.: UniProt archive. Bioinformatics 20(17), 3236–3237 (2004) (PMID 15044231)Google Scholar
  6. 6.
    Berman, H.M.: The protein data bank: a historical perspective. Acta Crystallographica Sect. A: Found. Crystallogr. A64(1), 8895 (2008) (PMID 18156675)Google Scholar
  7. 7.
    Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T.L.: BLAST+: Architecture and applications. BMC Bioinform. 10, 421 (2009) (PMID 20003500)Google Scholar
  8. 8.
    Van Montfort, R.L.M., Basha, E., Friedrich, K.L., Slingsby, C., Vierling, E.: Crystal structure and assembly of a eukaryotic small heat shock protein. Nat. Struct. Biol. 8, 1025 (2001) (PMID:11702068)CrossRefGoogle Scholar
  9. 9.
    Peng, J., Jinbo, X.: RaptorX: exploiting structure information for protein alignment by statistical inference. Proteins 79, 161–71 (2011) (PMID 21987485)Google Scholar
  10. 10.
    Bennett-Lovsey, R.M., Herbert, A.D., Sternberg, M.J.E., Kelley, L.A.: Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins: Struct., Funct., Bioinf. 70(3), 611 (2007)CrossRefGoogle Scholar
  11. 11.
    Laskowski, R.A., MacArthur, M.W., Moss, D.S., Thornton, J.M.: PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993)CrossRefGoogle Scholar
  12. 12.
    Lüthy, R., Bowie, J.U., Eisenberg, D.: Assessment of protein models with three-dimensional profiles. Nature 356(6364), 83–85 (1992)CrossRefGoogle Scholar
  13. 13.
    Ramachandran, G.N., Ramakrishnan, C., Sasisekharan, V.: Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7, 95–99 (1963) (PMID 13990617)Google Scholar
  14. 14.
    Chen, R., Weng, Z.: ZDOCK: an initial-stage protein-docking algorithm. Proteins 52, 80–87 (2003)CrossRefGoogle Scholar
  15. 15.
    Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem. 4(2), 187–217 (1983)CrossRefGoogle Scholar
  16. 16.
    Lee, M.S., Salsbury, F.R., Olson, M.A.: An efficient hybrid explicit/implicit solvent method for biomolecular simulations. J. Comput. Chem. 25(16), 1967–1978 (2004)CrossRefGoogle Scholar
  17. 17.
    Hess, B., Kutzner, C., Van Der Spoel, D., Lindahl, E.: GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput. 4(2), 435–447 (2008)CrossRefGoogle Scholar
  18. 18.
    Botos, I., Melnikov, E.E., Cherry, S., Tropea, J.E., Khalatova, A.G., Rasulova, F., Dauter, Z., Maurizi, M.R., Rotanova, T.V., Wlodawer, A., Gustchina, A.: The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site. J. Biol. Chem. 279, 8140–8148 (2004) (PMID 14665623) CrossRefGoogle Scholar
  19. 19.
    Kuczynska-Winik, D., Kedzierska, S., Matuszewska, E., Lund, P., Taylor, A., Lipinska, B., Laskowska, E.: The Escherichia coli small heat shock proteins IbpA and IbpB prevent the aggregation of endogenous proteins denatured in vivo during extreme heat shock. Microbiology 148, 1757–1765 (2002)CrossRefGoogle Scholar
  20. 20.
    Eswar, N., Marti-Renom, M.A., Webb, B., Madhusudhan, M.S., Eramian, D., Shen, M., Pieper, U., Sali, A.: Comparative protein structure modeling with MODELLER. In: Current Protocols in Bioinformatics, vol. 5, pp. 5.6.1–5.6.30. Wiley, New York (2006)Google Scholar

Copyright information

© Springer India 2015

Authors and Affiliations

  1. 1.Department of Biochemistry and BiophysicsUniversity of KalyaniNadiaIndia

Personalised recommendations