Journal of Molecular Modeling

, 14:777 | Cite as

Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme

  • Peter Kyomuhendo
  • Inge W. Nilsen
  • Bjørn Olav Brandsdal
  • Arne O. SmalåsEmail author
Original Paper


It is known that bacteria contain inhibitors of lysozyme activity. The recently discovered Escherichia coli inhibitor of vertebrate lysozyme (Ivy) and its potential interactions with several goose-type (g-type) lysozymes from fish were studied using functional enzyme assays, comparative homology modelling, protein–protein docking, and molecular dynamics simulations. Enzyme assays carried out on salmon g-type lysozyme revealed a lack of inhibition by Ivy. Detailed analysis of the complexes formed between Ivy and both hen egg white lysozyme (HEWL) and goose egg white lysozyme (GEWL) suggests that electrostatic interactions make a dominant contribution to inhibition. Comparison of three dimensional models of aquatic g-type lysozymes revealed important insertions in the β domain, and specific sequence substitutions yielding altered electrostatic surface properties and surface curvature at the protein–protein interface. Thus, based on structural homology models, we propose that Ivy is not effective against any of the known fish g-type lysozymes. Docking studies suggest a weaker binding mode between Ivy and GEWL compared to that with HEWL, and our models explain the mechanistic necessity for conservation of a set of residues in g-type lysozymes as a prerequisite for inhibition by Ivy.


Lysozyme Goose-type Inhibitor Vertebrate Homology modelling Protein docking 



This work was supported by the Norwegian Research Council (NFR), the Norwegian Institute of Fisheries and Aquaculture Research, Tromsø (Fiskeriforskning) and the Norwegian Structural Biology Centre (NorStruct) at the University of Tromsø. Recombinant Ivy was a kind gift from Professor Chris Michiels at the Catholic University of Leuven, Belgium.


  1. 1.
    Flemming A (1922) Proc R Soc London, Ser B 39:306–317Google Scholar
  2. 2.
    Jolles P, Jolles J (1984) Mol Cell Biochem 63:165–189CrossRefGoogle Scholar
  3. 3.
    Jollès P (1996) Lysozymes: Model enzymes in biochemistry and biology. Birkhäuser, BaselGoogle Scholar
  4. 4.
    Wild P, Gabrieli A, Schraner EM, Pellegrini A, Thomas U, Frederik PM, Stuart MCA, VonFellenberg R (1997) Microsc Res Tech 39:297–304CrossRefGoogle Scholar
  5. 5.
    Canfield RE, McMurry S (1967) Biochem Biophys Res Commun 26:38–42CrossRefGoogle Scholar
  6. 6.
    Hikima J, Minagawa S, Hirono I, Aoki T (2001) Biochim Biophys Acta 1520:35–44Google Scholar
  7. 7.
    Irwin DM, Gong Z (2003) J Mol Evol 56:234–242CrossRefGoogle Scholar
  8. 8.
    Nilsen IW, Myrnes B, Edvardsen RB, Chourrout D (2003) Cell Mol Life Sci 60:2210–2218CrossRefGoogle Scholar
  9. 9.
    Jolles J, Jolles P (1975) Eur J Biochem 54:19–23CrossRefGoogle Scholar
  10. 10.
    Nilsen IW, Overbo K, Sandsdalen E, Sandaker E, Sletten K, Myrnes B (1999) FEBS Lett 464:153–158CrossRefGoogle Scholar
  11. 11.
    Nilsen IW, Myrnes B (2001) Gene 269:27–32CrossRefGoogle Scholar
  12. 12.
    Bachali S, Jager M, Hassanin A, Schoentgen F, Jolles P, Fiala-Medioni A, Deutsch JS (2002) J Mol Evol 54:652–664CrossRefGoogle Scholar
  13. 13.
    Weaver LH, Grutter MG, Remington SJ, Gray TM, Isaacs NW, Matthews BW (1984) J Mol Evol 21:97–111CrossRefGoogle Scholar
  14. 14.
    Grinde B (1989) FEMS Microbiol Lett 60:179–182CrossRefGoogle Scholar
  15. 15.
    Monchois V, Abergel C, Sturgis J, Jeudy S, Claverie JM (2001) J Biol Chem 276:18437–18441CrossRefGoogle Scholar
  16. 16.
    Fernie-King BA, Seilly DJ, Davies A, Lachmann PJ (2002) Infect Immun 70:4908–4916CrossRefGoogle Scholar
  17. 17.
    Callewaert L, Aertsen A, Deckers D, Michiels CW (2006) Commun Appl Biol Sci 71:87–90Google Scholar
  18. 18.
    Abergel C, Monchois V, Byrne D, Chenivesse S, Lembo F, Lazzaroni JC, Claverie JM (2007) Proc Natl Acad Sci USA 104:6394–6399CrossRefGoogle Scholar
  19. 19.
    Deckers D, Masschalck B, Aertsen A, Callewaert L, Van Tiggelen CG, Atanassova M, Michiels CW (2004) Cell Mol Life Sci 61:1229–1237CrossRefGoogle Scholar
  20. 20.
    Lukomski S, Hoe NP, Abdi I, Rurangirwa J, Kordari P, Liu MY, Dou SJ, Adams GG, Musser JM (2000) Infect Immun 68:535–542CrossRefGoogle Scholar
  21. 21.
    Fernie-King BA, Seilly DJ, Lachmann PJ (2004) Immunol 111:444–452CrossRefGoogle Scholar
  22. 22.
    Callewaert L, Masschalck B, Deckers D, Nakimbugwe D, Atanassova M, Aertsen A, Michiels CW (2005) Enzyme Microb Technol 37:205–211CrossRefGoogle Scholar
  23. 23.
    Callewaert L, Masschalck B, Aertsen A, Michiels CW (2005) Commun Appl Biol Sci 70:73–87Google Scholar
  24. 24.
    Kyomuhendo P, Myrnes B, Nilsen IW (2007) Cell Mol Life Sci 64:2841–2847CrossRefGoogle Scholar
  25. 25.
    Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O’Donovan C, Redaschi N, Yeh LS (2005) Nucleic Acids Res 33:D154–159CrossRefGoogle Scholar
  26. 26.
    Notredame C, Higgins DG, Heringa J (2000) J Mol Biol 302:205–217CrossRefGoogle Scholar
  27. 27.
    Boguski MS, Lowe TM, Tolstoshev CM (1993) Nat Genet 4:332–333CrossRefGoogle Scholar
  28. 28.
    Hall T (1999) Nucleic Acids Symp Ser 41:95–98Google Scholar
  29. 29.
    Saitou N, Nei M (1987) Mol Biol Evol 4:406–425Google Scholar
  30. 30.
    Felsenstein J (1989) Cladistics 5:164–166Google Scholar
  31. 31.
    Felsenstein J (1985) Evolution 39:783–791CrossRefGoogle Scholar
  32. 32.
    Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28:235–242CrossRefGoogle Scholar
  33. 33.
    Abagyan R, Totrov M, Kuznetsov D (1994) J Comput Chem 15:488–506CrossRefGoogle Scholar
  34. 34.
    Jaroszewski L, Pawlowski K, Godzik A (1998) J Mol Model 4:294–309CrossRefGoogle Scholar
  35. 35.
    Luthy R, Bowie JU, Eisenberg D (1992) Nature 356:83–85CrossRefGoogle Scholar
  36. 36.
    Colovos C, Yeates TO (1993) Protein Sci 2:1511–1519CrossRefGoogle Scholar
  37. 37.
    Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283–291CrossRefGoogle Scholar
  38. 38.
    Hooft RWW, Vriend G, Sander C, Abola EE (1996) Nature 381:272–272CrossRefGoogle Scholar
  39. 39.
    Schneidman-Duhovny D, Inbar Y, Polak V, Shatsky M, Halperin I, Benyamini H, Barzilai A, Dror O, Haspel N, Nussinov R, Wolfson HJ (2003) Proteins Struct Funct Genet 52:107–112CrossRefGoogle Scholar
  40. 40.
    Guex N, Peitsch MC (1997) Electrophoresis 18:2714–2723CrossRefGoogle Scholar
  41. 41.
    Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman P (1995) Comput Phys Commun 91:1–41CrossRefGoogle Scholar
  42. 42.
    Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR (1984) J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  43. 43.
    Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089–10092CrossRefGoogle Scholar
  44. 44.
    Ryckaert JP, Ciccotti G, Berendsen HJC (1977) J Comput Phys 23:327–341CrossRefGoogle Scholar
  45. 45.
    Weaver LH, Grutter MG, Matthews BW (1995) J Mol Biol 245:54–68CrossRefGoogle Scholar
  46. 46.
    Grütter MG, Weaver LH, Matthews BW (1983) Nature 303:828–831CrossRefGoogle Scholar
  47. 47.
    Drozdov-Tikhomirov LN, Linde DM, Poroikov VV, Alexandrov AA, Skurida GI (2001) J Biomol Struct Dyn 19:279–284Google Scholar
  48. 48.
    Honig B, Nicholls A (1995) Science 268:1144–1149CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Peter Kyomuhendo
    • 1
    • 2
  • Inge W. Nilsen
    • 1
  • Bjørn Olav Brandsdal
    • 2
  • Arne O. Smalås
    • 2
    Email author
  1. 1.Marine Biotechnology and Fish HealthNorwegian Institute of Fisheries and AquacultureTromsøNorway
  2. 2.The Norwegian Structural Biology Centre, Department of ChemistryUniversity of TromsøTromsøNorway

Personalised recommendations