Structural Chemistry

, Volume 15, Issue 5, pp 405–414 | Cite as

MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations

  • Jolanta Zurek
  • Anna L. Bowman
  • W. Andrzej Sokalski
  • Adrian J. Mulholland


Aminoacyl-tRNA synthetases are centrally important enzymes in protein synthesis. We have investigated threonyl-tRNA synthetase from E. coli, complexed with reactants, using molecular mechanics and combined quantum mechanical/molecular mechanical (QM/MM) techniques. These modeling methods have the potential to provide molecular level understanding of enzyme catalytic processes. Modeling of this enzyme presents a number of challenges. The procedure of system preparation and testing is described in detail. For example, the number of metal ions at the active site, and their positions, were investigated. Molecular dynamics simulations suggest that the system is most stable when it contains only one magnesium ion, and the zinc ion is removed. Two different QM/MM methods were tested in models based on the findings of MM molecular dynamics simulations. AM1/CHARMM calculations resulted in unrealistic structures for the phosphates in this system. This is apparently due to an error of AM1. PM3/CHARMM calculations proved to be more suitable for this enzyme system. These results will provide a useful basis for future modeling investigations of the enzyme mechanism and dynamics.

QM/MM aminoacyl-tRNA synthetase AM1 PM3 CHARMM 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Berg, J. M.; Stryer, L.; Tymoczko, J. L. Biochemistry; Freeman: New York, 2001: pp.814–818.Google Scholar
  2. 2.
    Voet, D.; Voet, J. G.; Pratt, C. W. Fundamentals of Biochemistry; Wiley: New York, 1999: p.854.Google Scholar
  3. 3.
    Fersht, A. Structure and mechanism in protein science: A guide to enzyme catalysis and protein folding. Freeman: New York, 1999: pp. 422–435.Google Scholar
  4. 4.
    Lowe, G.; Tansley, G. Tetrahedron 1984, 40,113–117.Google Scholar
  5. 5.
    Cavarelli, J.; Eriani, G.; Rees, B.; Ruff, M.; Boeglin, M.; Mitschler, A.; Martin, F.; Gangloff, J.; Thierry, J. C.; Moras, D. EMBO J. 1994, 13,327–337.Google Scholar
  6. 6.
    Perona, J. J.; Rould, M. A.; Steitz, T. A. Biochemistry 1993, 32,8758–8771.Google Scholar
  7. 7.
    Belrhali, H.; Yaremchuk, A.; Tukalo, M.; Berthetcolominas, C.; Rasmussen, B.; Bosecke, P.; Diat, O.; Cusack, S. Structure 1995, 3,341–352.Google Scholar
  8. 8.
    Marahiel, M. A.; Stachelhaus, T.; Mootz, H. D. Chem. Rev. 1997, 97,2651–2673.Google Scholar
  9. 9.
    Arnez, J. G.; Moras, D. Trends Biochem. Sci. 1997, 22,211–216.Google Scholar
  10. 10.
    Mulholland, A. J. In Theoretical Biochemistry: Processes and Properties of Biological Systems; Eriksson, L. A., Ed.; Elsevier: Amsterdam, 2001.Google Scholar
  11. 11.
    Field, M. J.; Bash, P. A.; Karplus, M. J. Comput. Chem. 1990, 11,700–733.Google Scholar
  12. 12.
    Lyne, P. D.; Hodoscek, M.; Karplus, M. J. Phys. Chem. A 1999, 103,3462–3471.Google Scholar
  13. 13.
    Stanton, R. V.; Hartsough, D. S.; Merz, K. M. J. Comput. Chem. 1995, 16,113–128.Google Scholar
  14. 14.
    Ridder, L.; Rietjens, I.; Vervoort, J.; Mulholland, A. J. J. Am. Chem. Soc. 2002, 124,9926–9936.Google Scholar
  15. 15.
    Ridder, L.; Harvey, J. N.; Rietjens, I.; Vervoort, J.; Mulholland, A. J. J. Phys. Chem. B 2003, 107,2118–2126.Google Scholar
  16. 16.
    Topf, M.; Varnai, P.; Richards, W. G. J. Am. Chem. Soc. 2002, 124,14780–14788.Google Scholar
  17. 17.
    Ranaghan, K. E.; Ridder, L.; Szefczyk, B.; Sokalski, W. A.; Hermann, J. C.; Mulholland, A. J. Mol. Phys. 2003, 101,2695–2714.Google Scholar
  18. 18.
    Zhang, X. D.; Harrison, D. H. T.; Cui, Q. J. Am. Chem. Soc. 2002, 124,14871–14878.Google Scholar
  19. 19.
    Sankaranarayanan, R.; Dock-Bregeon, A. C.; Rees, B.; Bovee, M.; Caillet, J.; Romby, P.; Francklyn, C. S.; Moras, D. Nat. Struct. Biol. 2000, 7,461–465.Google Scholar
  20. 20.
    Schmitt, E.; Moulinier, L.; Fujiwara, S.; Imanaka, T.; Thierry, J. C.; Moras, D. EMBO J. 1998, 17,5227–5237.Google Scholar
  21. 21.
    Sankaranarayanan, R.; Dock-Bregeon, A. C.; Romby, P.; Caillet, J.; Springer, M.; Rees, B.; Ehresmann, C.; Ehresmann, B.; Moras, D. Cell 1999, 97,371–381.Google Scholar
  22. 22.
    Desogus, G.; Todone, F.; Brick, P.; Onesti, S. Biochemistry 2000, 39,8418–8425.Google Scholar
  23. 23.
    Torres-Larios, A.; Sankaranarayanan, R.; Rees, B.; Dock-Bregeon, A. C.; Moras, D. J. Mol. Biol. 2003, 331,201–211.Google Scholar
  24. 24.
    Airas, R. K. Eur. J. Biochem. 1996, 240,223–231.Google Scholar
  25. 25.
    Arnez, J. G.; Augustine, J. G.; Moras, D.; Francklyn, C. S. Proc. Natl. Acad. Sci. U.S.A. 1997, 94,7144–7149.Google Scholar
  26. 26.
    Guex, N.; Peitsch, M. C. Electrophoresis 1997, 18,2714–2723.Google Scholar
  27. 27.
    . Brunger, A. T.; Karplus, M. Proteins 1988, 4,148–156.Google Scholar
  28. 28.
    Cui, Q.; Karplus, M. J. Am. Chem. Soc. 2002, 124,3093–3124.Google Scholar
  29. 29.
    Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4,187–217.Google Scholar
  30. 30.
    Brooks, C. L.; Karplus, M. J. Mol. Biol. 1989, 208,159–181.Google Scholar
  31. 31.
    MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102,3586–3616.Google Scholar
  32. 32.
    Mackerell, A. D.; Wiorkiewicz-Kuczera, J.; Karplus, M. J. Am. Chem. Soc. 1995, 117,11946–11975.Google Scholar
  33. 33.
    Stote, R. H.; Karplus, M. Proteins:Struct., Funct., Genet. 1995, 23,12–31.Google Scholar
  34. 34.
    Brooks, C. L.; Karplus, M. J. Chem. Phys. 1983, 79,6312–6325.Google Scholar
  35. 35.
    Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107,3902–3909.Google Scholar
  36. 36.
    Dewar, M. J. S.; Jie, C. X. THEOCHEM-J. Mol. Struct. 1989, 56,1–13.Google Scholar
  37. 37.
    Stewart, J. J. P. J. Comput. Chem. 1989, 10,209–220.Google Scholar
  38. 38.
    Stewart, J. J. P. J. Comput. Chem. 1991, 12,320–341.Google Scholar
  39. 39.
    Hutter, M. C.; Reimers, J. R.; Hush, N. S. J. Phys. Chem. B 1998, 1 02 ,8080–8090.Google Scholar
  40. 40.
    Zhang, C. M.; Perona, J. J.; Hou, Y. M. Biochemistry 2003, 42,10931–10937.Google Scholar
  41. 41.
    Stewart, J. J. P. J. Comput.-Aided Mol. Des. 1990, 4 ,1–45.Google Scholar

Copyright information

© Plenum Publishing Corporation 2004

Authors and Affiliations

  • Jolanta Zurek
    • 1
    • 2
  • Anna L. Bowman
    • 1
  • W. Andrzej Sokalski
  • Adrian J. Mulholland
    • 1
  1. 1.Centre for Computational Chemistry, School of ChemistryUniversity of BristolBristolUnited Kingdom
  2. 2.Institute of Physical and Theoretical Chemistry I-30Wroclaw University of TechnologyWroclawPoland

Personalised recommendations