Biochemistry (Moscow)

, Volume 75, Issue 2, pp 233–241 | Cite as

Thermodynamic analysis of protein kinase A Iα activation

  • O. N. RogachevaEmail author
  • A. V. Popov
  • E. V. Savvateeva-Popova
  • V. E. Stefanov
  • B. F. Shchegolev


Thermodynamic analysis of protein kinase A (PKA) Iα activation was performed using Quantum 3.3.0 docking software and a Gaussian 03W quantum mechanical computational package. Expected stacking interactions between adenine of 3′:5′-AMP and aromatic moieties of amino acids were taken into account by means of MP2/6-31G(d) IPCM (iso-density polarizable continuum model) computations (ɛ = 4.0). It is demonstrated that thermodynamically favorable agonist-induced PKA Iα activation is mediated by two processes. First, 3′:5′-AMP binding is accompanied by structural changes leading to a thermodynamically favorable regulatory subunit conformation, which is hardly realized in the absence of the ligand (ΔG R o = −23.9 ± 8.2 kJ/mol). Second, 3′:5′-AMP affinity to the regulatory subunit conformation observed after agonist-induced PKA Iα activation is higher than that to inactive holoenzyme complex (ΔG 3′:5′−AMP o = −28.1 ± 9.7 kJ/mol). ATP is capable of docking into the 3′:5′-AMP-binding site B of the regulatory subunit complexed with the catalytic one, resulting in inhibition of kinase activation. True constants of 3′:5′-AMP binding to PKA Iα holoenzyme were found to be 60 and 57 μM for the regulatory subunit domains A and B, respectively. These constants, unlike the binding equilibrium constant determined using established experimental techniques and ranging from 15 nM to 2.9 μM, are proved to be direct measures of 3′:5′-AMP-PKA Iα binding affinity. Their values are in a reasonable agreement with the changes in 3′:5′-AMP concentration in the cell (2-55 μM) and account for PKA Iα activation in response to adequate stimuli.

Key words

protein kinase A Iα activation 3′:5′-AMP (cyclic adenosine-3′,5′-monophosphate) ATP standard Gibbs free energy change (ΔGostacking interaction 



Isodensity Polarizable Continuum Model


second-order Meller-Plesset perturbation theory


protein kinase A Iα


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Li, Y., Yin, W., Wang, X., Zhu, W., Huang, Y., and Yan, G. (2007) Proc. Natl. Acad. Sci. USA, 104, 13438–13443.CrossRefPubMedGoogle Scholar
  2. 2.
    Fetalvero, K. M., Shyu, M., Nomikos, A. T., Chiu, Y.-F., Wagner, R. J., Powell, R. J., Hwa, J., and Martin, K. A. (2006) Am. J. Physiol. Heart Circ. Physiol., 290, 1337–1346.CrossRefGoogle Scholar
  3. 3.
    Masai, I., Yamaguchi, M., Tonou-Fujimori, N., Komori, A., and Okamoto, H. (2005) Development, 132, 1539–1553.CrossRefPubMedGoogle Scholar
  4. 4.
    Aandahl, E. M., Aukrust, P., Skalhegg, B. S., Muller, F., Froland, S. S., Hansson, V., and Tasken, K. (1998) FASEB J., 12, 855–862.PubMedGoogle Scholar
  5. 5.
    Skalhegg, B. S., and Tasken, K. (1997) Front. Biosci., 2, 331–342.Google Scholar
  6. 6.
    Kim, C., Xuong, N.-H., and Taylor, S. S. (2005) Science, 307, 690–696.CrossRefPubMedGoogle Scholar
  7. 7.
    Kim, C., Cheng, C. Y., Saldanha, A. S., and Taylor, S. S. (2007) Cell, 130, 1032–1043.CrossRefPubMedGoogle Scholar
  8. 8.
    Su, Y., Dostmann, W. R., Herberg, F. W., Durick, K., Xuong, N.-H., Ten Eyck, L. F., Taylor, S. S., and Varughese, K. I. (1995) Science, 269, 807–813.CrossRefPubMedGoogle Scholar
  9. 9.
    Wu, J., Jones, J. M., Xuong, N.-H., Ten Eyck, L. F., and Taylor, S. S. (2004) Biochemistry, 43, 6620–6629.CrossRefPubMedGoogle Scholar
  10. 10.
    Ogreid, D., Ekanger, R., Suva, R. H., Miller, J. P., and Doskeland, S. O. (1989) Eur. J. Biochem., 181, 19–31.CrossRefPubMedGoogle Scholar
  11. 11.
    Doskeland, S. O., and Ogreid, D. (1981) Int. J. Biochem., 13, 1–19.CrossRefPubMedGoogle Scholar
  12. 12.
    Doskeland, S. O., and Ogreid, D. (1984) J. Biol. Chem., 259, 2291–2301.PubMedGoogle Scholar
  13. 13.
    Steinberg, R. A., Gorman, K. B., Ogreid, D., Doskeland, S. O., and Weber, I. T. (1991) J. Biol. Chem., 266, 3547–3553.PubMedGoogle Scholar
  14. 14.
    Bubis, J., Saraswat, L. D., and Taylor, S. S. (1988) Biochemistry, 27, 1570–1576.CrossRefPubMedGoogle Scholar
  15. 15.
    Johnson, D. A., Akamine, P., Radzio-Andzelm, E., Madhusudan, and Taylor, S. S. (2001) Chem. Rev., 101, 2243–2270.CrossRefPubMedGoogle Scholar
  16. 16.
    Huang, L. J., and Taylor, S. S. (1998) J. Biol. Chem., 273, 26739–26746.CrossRefPubMedGoogle Scholar
  17. 17.
    Durgerian, S., and Taylor, S. S. (1989) J. Biol. Chem., 264, 9807–9813.PubMedGoogle Scholar
  18. 18.
    Dao, K. K., Teigen, K., Kopperud, R., Hodneland, E., Schwede, F., Christensen, A. E., Martinez, A., and Doskeland, S. O. (2006) J. Biol. Chem., 281, 21500–21511.CrossRefPubMedGoogle Scholar
  19. 19.
    Iancu, R. V., Jones, S. W., and Harvey, R. D. (2007) Biophys. J., 92, 3317–3331.CrossRefPubMedGoogle Scholar
  20. 20.
    Rich, T. C., Fagan, K. A., Nakata, H., Schaack, J., Cooper, D. M. F., and Karpen, J. W. (2000) J. Gen. Physiol., 116, 147–161.CrossRefPubMedGoogle Scholar
  21. 21.
    Ringheim, G. E., and Taylor, S. S. (1990) J. Biol. Chem., 265, 4800–4808.PubMedGoogle Scholar
  22. 22.
    Neitzel, J. J., Dostmann, W. R., and Taylor, S. S. (1991) Biochemistry, 30, 733–739.CrossRefPubMedGoogle Scholar
  23. 23.
    Doskeland, S. O., and Ogreid, D. (1984) J. Biol. Chem., 259, 2291–2301.PubMedGoogle Scholar
  24. 24.
    Moll, D., Schweinsberg, S., Hammann, C., and Herberg, F. W. (2007) Biol. Chem., 388, 163–172.CrossRefPubMedGoogle Scholar
  25. 25.
    Schweinsberg, S., Moll, D., Burghardt, N. C. G., Hahnefeld, C., Schwede, F., Zimmermann, B., Drewianka, S., Werner, L., Kleinjung, F., Genieser, H.-G., Schuchhardt, J., and Herberg, F. W. (2008) Proteomics, 8, 1212–1220.CrossRefPubMedGoogle Scholar
  26. 26.
    Zhang, L., Duan, C. J., Binkley, C., Li, G., Uhler, M. D., Logsdon, C. D., and Simeone, D. M. (2004) Mol. Cell Biol., 24, 2169–2180.CrossRefPubMedGoogle Scholar
  27. 27.
    Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph., 14, 33–38.CrossRefPubMedGoogle Scholar
  28. 28.
    Guex, N., and Peitsch, M. C. (1997) Electrophoresis, 18, 2714–2723.CrossRefPubMedGoogle Scholar
  29. 29.
    Lindahl, E., Hess, B., and van der Spoel, D. (2001) J. Mol. Mod., 7, 306–317.Google Scholar
  30. 30.
    Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. (1995) Comp. Phys. Comm., 91, 43–56.CrossRefGoogle Scholar
  31. 31.
    Quantum, 3.3.0 (2007) Quantum Pharmaceuticals, Moscow.Google Scholar
  32. 32.
    Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Vreven, Jr. T., Kudin, K. N., Burant, J. C., Millam, J. M., Iyengar, S. S., et al. (2003) Gaussian 03, Revision B.05, Gaussian, Inc., Pittsburgh PA.Google Scholar
  33. 33.
    Pople, J. A., Binkley, J. S., and Seeger, R. (1976) Int. J. Quantum Chem., S10, 1–19.Google Scholar
  34. 34.
    Ditchfield, R., Hehre, W. J., and Pople, J. A. (1971) J. Chem. Phys., 54, 724–728.CrossRefGoogle Scholar
  35. 35.
    Hehre, W. J., Ditchfield, R., and Pople, J. A. (1972) J. Chem. Phys., 56, 2257–2261.CrossRefGoogle Scholar
  36. 36.
    Hariharan, P. C., and Pople, J. A. (1973) Theoret. Chim. Acta, 28, 213–222.CrossRefGoogle Scholar
  37. 37.
    Foresman, J. B., Keith, T. A., Wiberg, K. B., Snoonian, J., and Frish, M. J. (1996) J. Phys. Chem., 100, 16098–16104.CrossRefGoogle Scholar
  38. 38.
    Canaves, J. M., and Taylor, S. S. (2002) J. Mol. Evol., 54, 17–29.CrossRefPubMedGoogle Scholar
  39. 39.
    Berman, H. M., Ten Eyck, L. F., Goodsell, D. S., Haste, N. M., Kornev, A., and Taylor, S. S. (2005) Proc. Natl. Acad. Sci. USA, 102, 45–50.CrossRefPubMedGoogle Scholar
  40. 40.
    Herberg, F. W., Taylor, S. S., and Dostmann, W. R. G. (1996) Biochemistry, 35, 2934–2942.CrossRefPubMedGoogle Scholar
  41. 41.
    Wu, J., Brown, S., Xuong, N.-H., and Taylor, S. S. (2004) Structure, 12, 1057–1065.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2010

Authors and Affiliations

  • O. N. Rogacheva
    • 1
    Email author
  • A. V. Popov
    • 1
  • E. V. Savvateeva-Popova
    • 2
  • V. E. Stefanov
    • 3
  • B. F. Shchegolev
    • 2
  1. 1.Sechenov Institute of Evolutionary Physiology and BiochemistryRussian Academy of SciencesSt. PetersburgRussia
  2. 2.Pavlov Institute of PhysiologyRussian Academy of SciencesSt. PetersburgRussia
  3. 3.St. Petersburg State UniversitySt. PetersburgRussia

Personalised recommendations