Skip to main content
Log in

A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant

  • Published:
Journal of Computer-Aided Molecular Design Aims and scope Submit manuscript

Abstract

Here we analyze in detail the possible catalytic role of the associative mechanism in the γ-phosphoryl transfer reaction in the catalytic subunit of the mammalian cyclic AMP-dependent protein kinase (PKA) enzyme and its D166A mutant. We have used a complete solvated model of the ATP-Mg2-Kemptide/PKA system and good levels of theory (B3LYP/MM and MP2/MM) to determine several potential energy paths from different MD snapshots, and we present a deep analysis of the interaction distances and energies between ligands, metals and enzyme residues. We have also tested the electrostatic stabilization of the transition state structures localized herein with the charge balance hypothesis. Overall, the results obtained in this work reopen the discussion about the plausibility of the associative reaction pathway and highlight the proposed role of the catalytic triad Asp166–Lys168–Thr201.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Cohen P (2002) Nat Rev Drug Discov 1:309–315

    Article  CAS  Google Scholar 

  2. Johnson L, Noble M, Owen D (1996) Cell 85:149–158

    Article  CAS  Google Scholar 

  3. Cohen P (2001) Eur J Biochem 268:5001–5010

    Article  CAS  Google Scholar 

  4. Adams JA (2001) Chem Rev 101:2271–2290

  5. Johnson DA, Akamine P, Radzio-Andzelm E, Madhusudan, Taylor SS (2001) Chem Rev 101:2243–2270

  6. Francis S, Corbin J (1994) Annu Rev Physiol 56:237–272

    Article  CAS  Google Scholar 

  7. Smith C, Radzio-Andzelm E, Madhusudan, Akamine P, Taylor SS (1999) Prog Biophys Mol Biol 71:313–341

  8. Taylor SS, Kornev A (2012) PKA: prototype for dynamic signaling in time and space. In: Wall ME (ed) Quantitative biology: from molecular to cellular systems. CRC Press, Boca Raton, Fl (USA), pp 267–298

  9. Zheng J, Trafny E, Knighton D, Xuong N-H, Taylor SS, Ten Eyck L, Sowadski J (1993) Acta Crystallogr D Biol Crystallogr D49:362–365

  10. Masterson L, Shi L, Metcalfe E, Gao J, Taylor SS, Veglia G (2011) Proc Natl Acad Sci USA 108:6969–6974

  11. Armstrong R, Kondo H, Granot J, Kaiser E, Mildvan A (1979) Biochemistry 18:1230–1238

    Article  CAS  Google Scholar 

  12. Shaffer J, Adams JA (1999) Biochemistry 38:12072–12079

  13. Adams JA, Taylor SS (1992) Biochemistry 31:8516–8522

  14. Bastidas A, Deal M, Steichen J, Guo Y, Wu J, Taylor SS (2013) J Am Chem Soc 135:4788–4798

  15. Jacobsen DM, Bao ZQ, O’Brien P, Brooks CL III, Young MA (2012) J Am Chem Soc 134:15357–15370

    Article  CAS  Google Scholar 

  16. Gerlits O, Waltman M, Taylor SS, Langan P, Kovalevsky A (2013) Biochemistry 52:3721–3727

  17. Gerlits O, Das A, Keshwani M, Taylor SS, Waltman M, Langan P, Heller W, Kovalevsky A (2014) Biochemistry 53:3179–3186

  18. Cheng Y, Zhang Y, McCammon J (2005) J Am Chem Soc 127:1553–1562

    Article  CAS  Google Scholar 

  19. Valiev M, Kawai R, Adams JA, Weare JH (2003) J Am Chem Soc 125:9926–9927

    Article  CAS  Google Scholar 

  20. Montenegro M, Garcia-Viloca M, Lluch JM, González-Lafont À (2011) Phys Chem Chem Phys 13:530–539

    Article  CAS  Google Scholar 

  21. Madhusudan, Akamine P, Xuong N-H, Taylor SS (2002) Nat Struct Biol 9:273–277

  22. Yang J, Ten Eyck LF, Xuong N-H, Taylor SS (2004) J Mol Biol 336:473–487

    Article  CAS  Google Scholar 

  23. Aimes R, Hemmer W, Taylor SS (2000) Biochemistry 39:8325–8332

  24. Gibbs C, Zoller M (1991) J Biol Chem 266:8923–8931

    CAS  Google Scholar 

  25. Madhusudan, Trafny E, Xuong N-H, Adams JA, Ten Eyck L, Taylor SS, Sowadski J (1994) Protein Sci 3:176–187

  26. Bossemeyer D, Engh R, Kinzel V, Ponstingl H, Huber R (1993) EMBO J 12:849–859

    CAS  Google Scholar 

  27. Skamnaki V, Owen D, Noble M, Lowe E, Lowe G, Oikonomakos N, Johnson L (1999) Biochemistry 38:14718–14730

    Article  CAS  Google Scholar 

  28. Hart JC, Sheppard DW, Hillier IH, Burton NA (1999) Chem Commun 1:79–80

  29. Sheppard DW, Burton NA, Hillier IH (2000) J Mol Struct (Theochem) 506:35–44

    Article  CAS  Google Scholar 

  30. Hutter MC, Helms V (2003) Int J Quantum Chem 95:479–486

    Article  CAS  Google Scholar 

  31. Valiev M, Yang J, Adams JA, Taylor SS, Weare J (2007) J Phys Chem B 111:13455–13464

  32. Díaz N, Field M (2004) J Am Chem Soc 126:529–542

    Article  Google Scholar 

  33. Cheng Y, Zhang Y, McCammon J (2006) Protein Sci 15:672–683

    Article  CAS  Google Scholar 

  34. Montenegro M, Garcia-Viloca M, González-Lafont À, Lluch JM (2007) J Comput Aided Mol Des 21:603–615

    Article  CAS  Google Scholar 

  35. Montenegro M, Masgrau L, González-Lafont À, Lluch JM, Garcia-Viloca M (2012) Biophys Chem 161:17–28

    Article  CAS  Google Scholar 

  36. Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H (2001) Biochemistry 40:10810–10818

    Article  CAS  Google Scholar 

  37. Thoden JB, Holden HM (2005) J Biol Chem 280:32784–32791

    Article  CAS  Google Scholar 

  38. Prasad B, Plotnikov N, Warshel A (2013) J Phys Chem B 117:153–163

    Article  CAS  Google Scholar 

  39. Lee J, Yang W (2006) Cell 127:1349–1360

    Article  CAS  Google Scholar 

  40. Jin Y, Cliff M, Baxter N, Dannatt H, Hounslow A, Bowler M, Blackburn G, Waltho J (2012) Angew Chem Int Ed 51:12242–12245

    Article  CAS  Google Scholar 

  41. Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow CRA, French SA, Sokol AA, Bromley ST, Thiel W, Turner AJ, Billeter S, Terstegen F, Thiel S, Kendrick J, Rogers SC, Casci J, Watson M, King F, Karlsen E, Sjøvoll M, Fahmi A, Schäfer A, Lennartz C (2003) J Mol Struct (Theochem) 632:1–28

  42. Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Chem Phys Lett 162:165–169

    Article  CAS  Google Scholar 

  43. Slater JC (1951) Phys Rev 81:385–390

    Article  CAS  Google Scholar 

  44. Vosko SH, Wilk L, Nusair M (1980) Can J Phys 58:1200–1211

    Article  CAS  Google Scholar 

  45. Becke AD (1988) Phys Rev A 38:3098–3100

    Article  CAS  Google Scholar 

  46. Becke AD (1993) J Chem Phys 98:5648–5652

    Article  CAS  Google Scholar 

  47. Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ (1994) J Phys Chem 98:11623–11627

    Article  CAS  Google Scholar 

  48. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785–789

    Article  CAS  Google Scholar 

  49. Smith W, Forester T (1996) J Mol Graph 14:136–141

    Article  CAS  Google Scholar 

  50. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  51. MacKerell AD, Feig M, Brooks CL (2004) J Am Chem Soc 126:698–699

    Article  CAS  Google Scholar 

  52. de Vries AH, Sherwood P, Collins SJ, Rigby AM, Rigutto M, Kramer G (1999) J Phys Chem B 103:6133–6141

    Article  Google Scholar 

  53. Sherwood P, de Vries AH, Collins SJ, Greatbanks SP, Burton NA, Vincent MA, Hillier IH (1997) Faraday Discuss Chem Soc 106:79–92

    Article  CAS  Google Scholar 

  54. Liu D, Nocedal J (1989) Math Prog 45:503–528

    Article  Google Scholar 

  55. Baker J (1986) J Comput Chem 7:385–395

    Article  CAS  Google Scholar 

  56. Billeter SR, Turner AJ, Thiel W (2000) Phys Chem Chem Phys 2:2177–2186

    Article  CAS  Google Scholar 

  57. Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys 83:735–746

    Article  CAS  Google Scholar 

  58. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14(33–38):27–38

    Google Scholar 

  59. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605–1612

    Article  CAS  Google Scholar 

  60. Khavrutskii I, Grant B, Taylor SS, McCammon J (2009) Biochemistry 48:11532–11545

  61. Grant B, Adams JA (1996) Biochemistry 35:2022–2029

    Article  CAS  Google Scholar 

  62. Szarek P, Dyguda-Kazimierowicz E, Tachibana A, Sokalski W (2008) J Phys Chem B 112:11819–11826

    Article  CAS  Google Scholar 

  63. Garcia-Viloca M, Truhlar D, Gao J (2003) Biochemistry 42:13558–13575

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the “Ministerio de Economía y Competitividad” through Project CTQ2011-24292 and by the “Generalitat de Catalunya” through Project 2009SGR409. Use of computational facilities at the “Centre de Serveis Científics i Acadèmics de Catalunya (CESCA)” is also gratefully acknowledged. Ayax Pérez-Gallegos acknowledges “Consejo Nacional de Ciencia y Tecnología (CONACYT)” Supporting Grant 213582.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Àngels González-Lafont.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Pérez-Gallegos, A., Garcia-Viloca, M., González-Lafont, À. et al. A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant. J Comput Aided Mol Des 28, 1077–1091 (2014). https://doi.org/10.1007/s10822-014-9786-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10822-014-9786-3

Keywords

Navigation