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Mechanisms of enzymatic hydrolysis of nucleoside triphosphates by quantum and molecular mechanics

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Abstract

Results of simulation of the mechanism of hydrolysis of adenosine triphosphate and guanosine triphosphate in protein matrices, as well as of deprotonated methyl triphosphate in water clusters by quantum and molecular mechanics with separation of the reaction system into conformationally flexible effective fragments are discussed.

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References

  1. Minkin, V.I., Simkin, B.Ya., and Minyaev R.M., Teoriya stroeniya molekul (Theory of Molecular Structure), Rostov-on-Don: Feniks, 1997.

    Google Scholar 

  2. Molecular Mechanics, Burkert, U. and Allinger, N.L., Eds., Washington, DC: ACS, 1982.

    Google Scholar 

  3. Warshel, A. and Levitt, M., J. Mol. Biol., 1976, vol. 103, p. 227.

    Article  CAS  Google Scholar 

  4. Nemukhin, A.V., Grigorenko, B.L., Epifanovskii, E.M., and Moskovskii A.A., Ross. Khim. Zh., 2006, vol. 50, p. 45.

    CAS  Google Scholar 

  5. Grigorenko, B.L., Nemukhin, A.V., Topol, I.A., and Burt, S.K., J. Phys. Chem. A, 2002, vol. 106, p. 1066.

    Article  CAS  Google Scholar 

  6. Nemukhin, A.V., Grigorenko, B.L., Topol, I.A., and Burt, S.K., J. Comp. Chem., 2003, vol. 24, p. 1410.

    Article  CAS  Google Scholar 

  7. Nemukhin, A.V., Grigorenko, B.L., Bochenkova, A.V., et al., Struct. Chem., 2004, vol. 15, p. 3.

    Article  CAS  Google Scholar 

  8. Nemukhin, A.V., Grigorenko, B.L., and Knyazeva, M.A., Zh. Fiz. Khim., 2004, vol. 78, p. 1028.

    CAS  Google Scholar 

  9. Nemukhin, A.V, Grigorenko, B.L., Rogov, A.V., et al., Theor. Chem. Acc., 2004, vol. 111, p. 36.

    CAS  Google Scholar 

  10. Schmidt M.W., Baldridge K.K., Boatz J.A., et al., J. Comput. Chem., 1993, vol. 14, p. 1347.

    Article  CAS  Google Scholar 

  11. Nemukhin, A.V., Grigorenko, B.L., and Granovskii, A.A., Vestn. Mosk. Univ., Ser. 2: Khim., 2004, vol. 45, p. 75.

    Google Scholar 

  12. Trentham, D.R., Eccleston, J.F., and Bagshaw, C.R., Quart. Rev. Biophys., 1976, vol. 9, p. 217.

    CAS  Google Scholar 

  13. Okimoto, N., Yamanaka, K., Ueno, J., et al., Biophys. J., 2001, vol. 81, p. 2786.

    CAS  Google Scholar 

  14. Li, G. and Cui, Q., J. Phys. Chem. B, 2004, vol. 108, p 3342.

    Article  CAS  Google Scholar 

  15. Schwarzl, S., Smith, J.C., and Fisher, S., Biochemistry, 2006, vol. 45, p. 5830.

    Article  CAS  Google Scholar 

  16. Grigorenko, B.L., Rogov A.V., Topol I.A., et al., Proc. Natl. Acad. Sci. USA, 2007, vol. 104, p. 7057.

    Article  CAS  Google Scholar 

  17. Onishi, H., Mochizuki, N., and Morales, M.F., Biochemistry, 2004, vol. 43, p. 3757.

    Article  CAS  Google Scholar 

  18. Smith, C.A. and Rayment, I., Ibid., 1996, vol. 35, p. 5405.

    Google Scholar 

  19. Hay, P.J. and Wadt, W.R., J. Chem. Phys., 1985, vol. 82, p. 270.

    Article  CAS  Google Scholar 

  20. Cornell, W.D., Cieplak, P., Bayly, C.I., et al., J. Am. Chem. Soc., 1995, vol. 117, p. 5179.

    Article  CAS  Google Scholar 

  21. Nemukhin, A.V., Topol, I.A., Grigorenko, B.L., and Burt, S.K., J. Phys. Chem. B., 2003, vol. 107, p. 2958.

    Article  CAS  Google Scholar 

  22. Langen, R., Schweins, T., and Warshel, A., Biochemistry, 1992, vol. 31, p. 869.

    Article  Google Scholar 

  23. Schweins, T., Langen, R., and Warshel, A., Nature Struct. Biol., 1994, vol. 1, p. 476.

    Article  CAS  Google Scholar 

  24. Schweins, T. and Warshel, A., Biochemistry, 1996, vol. 35, p. 14232.

    Article  CAS  Google Scholar 

  25. Futatsugi, N., Hata, M., Hoshino, T., and Tsuda, M., Biophys. J., 1999, vol. 77, p. 3287.

    CAS  Google Scholar 

  26. Futatsugi, N. and Tsuda, M., Ibid., 2001, vol. 81, p. 3483.

    Article  CAS  Google Scholar 

  27. Cavalli, A. and Carloni, P., J. Am. Chem. Soc., 2002, vol. 124, p. 3763.

    Article  CAS  Google Scholar 

  28. Grigorenko, B.L., Shadrina, M.S., Topol, I.A., et al., Proteins: Struct. Funct. Bioinf., 2007, vol. 66, p. 456.

    Article  CAS  Google Scholar 

  29. Scheidig, A.J., Burmester, C., and Goody, R.S., Structure, 1999, vol. 7, p. 1311.

    Article  CAS  Google Scholar 

  30. Shadrina, M.S., Rogov, A.V., Bravaya, K.B., and Nemukhin, A.V., Vestn. Mosk. Univ., Ser. 2: Khim., 2005, vol. 46, p. 363.

    CAS  Google Scholar 

  31. Vetter, I.R. and Wittinghofer, A., Science, 2001, vol. 294, p. 1299.

    Article  CAS  Google Scholar 

  32. Kosloff, M. and Selinger, Z., Trends Biochem. Sci., 2001, vol. 26, p. 257.

    Article  Google Scholar 

  33. Li, G. and Zhang, X.C., J. Mol. Biol., 2004, vol. 340, p. 921.

    Article  CAS  Google Scholar 

  34. Wittinghofer, A., Trends Biochem. Sci., 2006, vol. 31, p. 20.

    Article  CAS  Google Scholar 

  35. Glennon, T.M., Villa, J., and Warshel, A., Biochemistry, 2000, vol. 39, p. 9641.

    Article  CAS  Google Scholar 

  36. Shurki, A. and Warshel, A., Proteins, 2004, vol. 55, p. 1.

    Article  CAS  Google Scholar 

  37. Topol, I.A., Cachau, R.E., Nemukhin, A.V., et al., Biochem. Biophys. Acta, 2004, vol. 1700, p. 125.

    CAS  Google Scholar 

  38. Grigorenko, B.L., Nemukhin, A.V., Topol, I.A., et al., Proteins: Struct. Funct. Bioinf., 2005, vol. 60, p. 495.

    Article  CAS  Google Scholar 

  39. Grigorenko, B.L., Rogov, A.V., Knyazeva, M.A., Isaeva, E.V., and Nemukhin, A.V., Vestn. Mosk. Univ., Ser. 2: Khim., 2005, vol. 46, p. 19.

    CAS  Google Scholar 

  40. Scheffzek, K., Ahmadian, M.R., Kabsch, W., et al., Science, 1997, vol. 277, p. 333.

    Article  CAS  Google Scholar 

  41. Grigorenko, B.L., Nemukhin, A.V., Cachau, R.E., et al., J. Mol. Simulation, 2005, vol. 11, p. 503.

    CAS  Google Scholar 

  42. Sondek, J., Lambright, D.G., Noel, J.P., et al., Nature, 1994, vol. 372, p. 276.

    Article  CAS  Google Scholar 

  43. Bunton, C.A., Llewellyn, D.R., Oldham, K.G., and Vernon, C.A., J. Chem. Soc., 1958, p. 3574.

  44. Hu, C.H. and Brinck, T.J., J. Phys. Chem. A, 1999, vol. 103, p. 5379.

    Article  CAS  Google Scholar 

  45. Akola, J. and Jones, R.O., J. Phys. Chem. B, 2003, vol. 107, p. 11774.

    Article  CAS  Google Scholar 

  46. Grigorenko, B. L., Rogov, A. V., and Nemukhin, A. V., Ibid., 2006, vol. 110, p. 4407.

    Article  CAS  Google Scholar 

  47. Rogov, A.V., Grigorenko, B.L., Bochenkova, A.V., et al., Vestn. Mosk. Univ., Ser. 2: Khim., 2007, vol. 48, p. 152.

    CAS  Google Scholar 

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Authors and Affiliations

  1. Chemical Department, Lomonosov Moscow State University, Leninskie Goty 1/3, Moscow, 119992, Russia

    A. V. Nemukhin, B. L. Grigorenko & M. S. Shadrina

  2. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, ul. Kosygina 4, Moscow, 119334, Russia

    A. V. Nemukhin

Authors
  1. A. V. Nemukhin
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  2. B. L. Grigorenko
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  3. M. S. Shadrina
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Correspondence to A. V. Nemukhin.

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Original Russian Text © A.V. Nemukhin, B.L. Grigorenko, M.S. Shadrina, 2007, published in Rossiiskii Khimicheskii Zhurnal, 2007, Vol. 51, No. 5, pp. 27–33.

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Nemukhin, A.V., Grigorenko, B.L. & Shadrina, M.S. Mechanisms of enzymatic hydrolysis of nucleoside triphosphates by quantum and molecular mechanics. Russ J Gen Chem 78, 696–703 (2008). https://doi.org/10.1134/S1070363208040312

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  • DOI: https://doi.org/10.1134/S1070363208040312

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