Dynamics of Uninhibited and Covalently Inhibited Cysteine Protease on Non-physiological pH

  • Branko J. DrakulićEmail author
  • Marija Gavrović-Jankulović
Part of the Modeling and Optimization in Science and Technologies book series (MOST, volume 2)


Differences in activity and the structural stability under simulated gastric juice conditions of uninhibited and covalently inhibited cysteine protease, isolated from the fruit, were experimentally observed. We employed molecular dynamics simulations of proteins modeled from the similar ones with known 3D structure to explain experimental findings. Simulations were performed with NAMD, using CHARMM force field in explicit solvent model. Conformational changes observed in MD trajectories offer indication on differences in stability of inhibited vs. uninhibited protein on low pH values. Protonation states of the protein side chains, through the non-bonded interactions that stabilize 3D structures, likely, significantly contribute to difference in stability of uninhibited and covalently inhibited protein on low pH values.


Cysteine-protease Molecular dynamics Protonation states 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Chapman, H.A., Riese, R.J., Shi, G.P.: Emerging roles for cysteine proteases in human biology. Annu. Rev. Physiol. 59, 63–68 (1997)CrossRefGoogle Scholar
  2. 2.
    Sajid, M., McKerrow, J.H.: Cysteine proteases of parasitic organisms. Mol. Biochem. Parasitol. 120, 1–21 (2002)CrossRefGoogle Scholar
  3. 3.
    Santos, M.M.M., Moreira, R.: Michael acceptors as cysteine protease Inhibitors. Mini-Rev. Med. Chem. 7, 1040–1050 (2007)CrossRefGoogle Scholar
  4. 4.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucl. Acids Res. 28, 235–242 (2002), CrossRefGoogle Scholar
  5. 5.
    Bublin, M., Pfister, M., Radauer, C., Oberhuber, C., Bulley, S., Marknell-DeWitt, A., Lid-holm, J., Reese, G., Vieths, S., Breiteneder, H., Hoffmann-Sommergruber, K., Ballmer-Weber, B.K.: Component-resolved diagnosis of kiwifruit allergy with purified natural and recombinant kiwifruit allergens. J. Allergy Clin. Immunol. 125, 687–694 (2010)CrossRefGoogle Scholar
  6. 6.
    Grozdanovic, M.M., Aleksic, I., Burazer, L., Andjelkovic, U., Petersen, A., Gavrovic-Jankulovic, M.: Actinidin, a specific biomarker of kiwifruit allergy, exerts proteolytic activity upon treatment in the simulated gastrointestinal environment (2012) (submitted)Google Scholar
  7. 7.
    Varughese, K.I., Su, Y., Cromwell, D., Hasnain, S., Xuong, N.H.: Crystal structure of an actinidin-E-64 complex. Biochemistry 31, 5172–5176 (1992)CrossRefGoogle Scholar
  8. 8.
    Baker, E.N., Dodson, E.J.: Crystallographic refinement of the structure of actinidin at 1.7 angstroms resolution by fast Fourier least-squares methods. Acta Crystallogr., Sect. A 36, 559 (1980)CrossRefGoogle Scholar
  9. 9.
    Bas, D.C., Rogers, D.M., Jensen, J.H.: Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 73, 765–783 (2008), CrossRefGoogle Scholar
  10. 10.
    Eberini, I., Emerson, A., Sensi, C., Ragona, L., Ricchiuto, P., Pedretti, A., Gianazza, E., Tramontano, A.: Simulation of urea-induced protein unfolding: A lesson from bovine β-lactoglobulin. J. Mol. Graph. Mod. 30, 24–30 (2011)CrossRefGoogle Scholar
  11. 11.
    Grozdanović, M., Drakulić, B.J., Gavrović-Jankulović, M.: Conformational mobility of active and E-64-inhibited actinidin (submitted 2013)Google Scholar
  12. 12.
    Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G.: The Clus-talX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25, 4876–4882 (1997)CrossRefGoogle Scholar
  13. 13.
    Pedretti, A., Villa, L., Vistoli, G.: Vega - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J. Comp. Aided Mol. Des. 18, 167–173 (2004), CrossRefGoogle Scholar
  14. 14.
    Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kalé, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Compt. Chem. 26, 1781–1802 (2005), CrossRefGoogle Scholar
  15. 15.
    The PyMOL Molecular Graphics System, Version 0.99, Schrödinger, LLC,

Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Branko J. Drakulić
    • 1
    Email author
  • Marija Gavrović-Jankulović
    • 2
  1. 1.Department of Chemistry-IChTMUniversity of BelgradeBelgradeSerbia
  2. 2.Faculty of ChemistryUniversity of BelgradeBelgradeSerbia

Personalised recommendations