In Silico Analysis of Conformational Changes Induced by Normal and Mutation of Macrophage Infectivity Potentiator Catalytic Residues and its Interactions with Rapamycin

  • Ramachandran Vijayan
  • Naidu Subbarao
  • Natesan ManoharanEmail author
Original Research Article


The Legionella pneumophila (Lp), human pathogen, causes severe and often fatal Legionnaires’ disease, produces a major virulence factor, termed ‘macrophage infectivity potentiator protein’ (Mip), that is necessary for optimal multiplication of the bacteria within human alveolar macrophages. Mip exhibits peptidyl prolyl cis–trans isomerase (PPIase) activity, which can be inhibited by rapamycin and FK506. It was previously shown that substitutions at the catalytic residues, aspartate-142 position replaced to leucine-142 and tyrosine-185 position replaced to alanine-185 strongly reduces the PPIase activity of Mip proteins. Therefore, we aim to develop an in silico mutagenesis model for both important catalytic residues, validated the stability of the mutated model. Further, we have docked the known inhibitor rapamycin with Lp Mip (native) and mutants (D142L and Y185A) to analyze the conformational and binding mode. Electrostatic contributions and van der Waals interactions are the major driving forces for rapamycin binding and largely responsible for the binding differences between the Lp Mip (native and mutated) proteins.


Legionella Mip In silico mutagenesis Rapamycin Molecular docking 


  1. 1.
    McDade JE, Shepard CC, Fraser DW, Tsai TR, Redus MA, Dowdle WR (1997) Legionnaires’ disease. Isolation of the bacterium and demonstration of its role in other respiratory disease. N Engl J Med 297:1197–1203CrossRefGoogle Scholar
  2. 2.
    Winn WC (1988) Legionnaires’ disease: historical perspective. Clin Microbiol Rev 1:60–81CrossRefGoogle Scholar
  3. 3.
    Rowbotham TJ (1980) Preliminary report on the pathogenicity of Legionella pneumophila for freshwater and soil amoebae. J Clin Pathol 33:1179–1183CrossRefGoogle Scholar
  4. 4.
    Rowbotham TJ (1986) Current views on the relationship between amoebae, Legionellae and man. Isr J Med Sci 22:678–689PubMedGoogle Scholar
  5. 5.
    Steinert M, Ott M, Luök PC, Hacker J (1994) Studies on the uptake and intracellular replication of Legionella pneumophila in protozoa and in macrophage-like cells. FEMS Microbiol Ecol 15:299–308CrossRefGoogle Scholar
  6. 6.
    Cianciotto NP, Stamos JV, Kamp DW (1995) Infectivity of Legionella pneumophila MIP mutant for alveolar epithelial cells. Curr Microbiol 30:247–250CrossRefGoogle Scholar
  7. 7.
    Wintermeyer E, Ludwig B, Steinert M, Schmidt B, Fischer G, Hacker J (1995) Influence of site specifically altered MIP proteins on intracellular survival of Legionella pneumophila in eucaryotic cells. Infect Immun 63:4576–4583PubMedPubMedCentralGoogle Scholar
  8. 8.
    Juli C, Sippel M, Jager J, Thiele A, Weiwad M, Schweimer K, Rosch P, Steinert M, Sotriffer CA, Holzgrabe U (2011) Pipecolic acid derivatives as small-molecule inhibitors of the Legionella MIP protein. J Med Chem 54:277–283CrossRefGoogle Scholar
  9. 9.
    Riboldi-Tunnicliffe A, Konig B, Jessen S, Weiss MS, Rahfeld J, Hacker J, Fischer G, Hilgenfeld R (2001) Crystal structure of MIP, a prolylisomerase from Legionella pneumophila. Nat Struct Biol 8:779–783CrossRefGoogle Scholar
  10. 10.
    Fischer G, Bang H, Ludwig B, Mann K, Hacker J (1992) Mip protein of Legionella pneumophila exhibits peptidyl-prolyl cis/trans isomerase (PPIase) activity. Mol Microbiol 6:1375–1383CrossRefGoogle Scholar
  11. 11.
    Guba M, Breitenbuch VP, Steinbauer M, Koehl G, Flegel S, Hornung M, Bruns CJ, Zuelke C, Farkas S, Anthuber M, Jauch KW, Geissler EK (2002) Rapamycin inhibits primary and metastatic tumor growth by antiangiogenesis: involvement of vascular endothelial growth factor. Nat Med 8:128–135CrossRefGoogle Scholar
  12. 12.
    Huai Q, Kim HY, Liu Y, Zhao Y, Mondragon A, Liu JO, Ke H (2002) Crystal structure of calcineurin–cyclophilin–cyclosporin shows common but distinct recognition of immunophilin–drug complexes. Proc Natl Acad Sci USA 99:12037–12042CrossRefGoogle Scholar
  13. 13.
    Ke H, Huai Q (2003) Structures of calcineurin and its complexes with immunophilins–immunosuppressants. Biochem Biophys Res Commun 311:1095–1102CrossRefGoogle Scholar
  14. 14.
    Sharma VK, Li B, Khanna A, Sehajpal PK, Suthanthiran M (1994) Which way for drug-mediated immunosuppression. Curr Opin Immunol 6:784–790CrossRefGoogle Scholar
  15. 15.
    Vijayan R, Subbarao N, Mallick BN (2007) In silico modeling of \(\alpha\)-1A adrenoceptor: interactions of its normal and mutated active sites with noradrenaline as well as its agonist and antagonist. Am J Biochem Biotechnol 3:216–224CrossRefGoogle Scholar
  16. 16.
    Shanmugam A, Natarajan J (2014) Combination of site directed mutagenesis and secondary structure analysis predicts the amino acids essential for stability of M. leprae MurE. Interdiscip Sci Comput Life Sci 6:40–47CrossRefGoogle Scholar
  17. 17.
    Ludwig B, Rahfeld J, Schmidt B, Mann K, Wintermeyer E, Fischer G, Hacker J (1994) Characterization of Mip proteins of Legionella pneumophila. FEMS Microbiol Lett 118:23–30CrossRefGoogle Scholar
  18. 18.
    Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A (2009) Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29:291–325CrossRefGoogle Scholar
  19. 19.
    Adzhubei I, Jordan DM, Sunyaev SR (2013) Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet 7:7–20Google Scholar
  20. 20.
    Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucl Acids Res 33:W306–W310CrossRefGoogle Scholar
  21. 21.
    Cheng J, Randall A, Baldi P (2006) Prediction of protein stability changes for single-site mutations using support vector machines. Proteins Struct Funct Bioinform 62:1125–1132CrossRefGoogle Scholar
  22. 22.
    The PyMOL molecular graphics system, version Schrödinger, LLCGoogle Scholar
  23. 23.
    Huang B, Schroeder M (2006) LIGSITE csc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct Biol 6:19CrossRefGoogle Scholar
  24. 24.
    Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34:116–118CrossRefGoogle Scholar
  25. 25.
    Boyle NMO, James BM, Morley CA, Vandermeersch T, Hutchison GR (2011) Open Babel: an open chemical toolbox. J Cheminform 3:33CrossRefGoogle Scholar
  26. 26.
    Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727–748CrossRefGoogle Scholar
  27. 27.
    Accelrys Software Inc. (2013) Discovery studio modeling environment, release 4.0. Accelrys Software Inc., San DiegoGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Ramachandran Vijayan
    • 1
    • 2
  • Naidu Subbarao
    • 2
  • Natesan Manoharan
    • 1
    Email author
  1. 1.Department of Marine ScienceBharathidasan UniversityTiruchirapalliIndia
  2. 2.Centre for Computational Biology and Bioinformatics, School of Computational and Integrative SciencesJawaharlal Nehru UniversityNew DelhiIndia

Personalised recommendations