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

Journal of Computer-Aided Molecular Design

Volumn 28, Issue 11, 2014, Pages 1077-1091

  Pérez Gallegos, Ayax ^a   Garcia Viloca, Mireia ^a   González Lafont, Àngels ^a   Lluch, José M ^a  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Enzyme catalysis; Enzyme models; Protein kinase; QM MM calculations; Reaction mechanisms

Indexed keywords

CATALYSIS; ENZYMES; MAMMALS; MOLECULAR MODELING;

ASSOCIATIVE MECHANISMS; CATALYTIC ROLE; ENZYME CATALYSIS; ENZYME MODELS; PHOSPHORYLATION REACTIONS; PROTEIN KINASE; PROTEIN KINASE A; QM/MM CALCULATIONS; REACTION CATALYZED; REACTION MECHANISM;

POTENTIAL ENERGY;

CYCLIC AMP DEPENDENT PROTEIN KINASE; KEMPTIDE; OLIGOPEPTIDE;

ANIMAL; CATALYSIS; CHEMISTRY; ENERGY METABOLISM; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; GENETICS; MUTATION; PHOSPHORYLATION; QUANTUM THEORY; THEORETICAL MODEL;

ANIMALS; CATALYSIS; CATALYTIC DOMAIN; CYCLIC AMP-DEPENDENT PROTEIN KINASES; ENERGY METABOLISM; MODELS, THEORETICAL; MUTATION; OLIGOPEPTIDES; PHOSPHORYLATION; QUANTUM THEORY; SUBSTRATE SPECIFICITY;

EID: 84921626832     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9786-3     Document Type: Article

References (63)

1. Cohen P (2002) Nat Rev Drug Discov 1:309-315
2. Johnson L, Noble M, Owen D (1996) Cell 85:149-158
3. Cohen P (2001) Eur J Biochem 268:5001-5010
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
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
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
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
19. Valiev M, Kawai R, Adams JA, Weare JH (2003) J Am Chem Soc 125:9926-9927
20. Montenegro M, Garcia-Viloca M, Lluch JM, González-Lafont À (2011) Phys Chem Chem Phys 13:530-539
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
23. Aimes R, Hemmer W, Taylor SS (2000) Biochemistry 39:8325-8332
24. Gibbs C, Zoller M (1991) J Biol Chem 266:8923-8931
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
27. Skamnaki V, Owen D, Noble M, Lowe E, Lowe G, Oikonomakos N, Johnson L (1999) Biochemistry 38:14718-14730
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
30. Hutter MC, Helms V (2003) Int J Quantum Chem 95:479-486
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
33. Cheng Y, Zhang Y, McCammon J (2006) Protein Sci 15:672-683
34. Montenegro M, Garcia-Viloca M, González-Lafont À, Lluch JM (2007) J Comput Aided Mol Des 21:603-615
35. Montenegro M, Masgrau L, González-Lafont À, Lluch JM, Garcia-Viloca M (2012) Biophys Chem 161:17-28
36. Krishna SS, Zhou T, Daugherty M, Osterman A, Zhang H (2001) Biochemistry 40:10810-10818
37. Thoden JB, Holden HM (2005) J Biol Chem 280:32784-32791
38. Prasad B, Plotnikov N, Warshel A (2013) J Phys Chem B 117:153-163
39. Lee J, Yang W (2006) Cell 127:1349-1360
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
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
43. Slater JC (1951) Phys Rev 81:385-390
44. Vosko SH, Wilk L, Nusair M (1980) Can J Phys 58:1200-1211
45. Becke AD (1988) Phys Rev A 38:3098-3100
46. Becke AD (1993) J Chem Phys 98:5648-5652
47. Stephens PJ, Devlin FJ, Chabalowski CF, Frisch MJ (1994) J Phys Chem 98:11623-11627
48. Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785-789
49. Smith W, Forester T (1996) J Mol Graph 14:136-141
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
51. MacKerell AD, Feig M, Brooks CL (2004) J Am Chem Soc 126:698-699
52. de Vries AH, Sherwood P, Collins SJ, Rigby AM, Rigutto M, Kramer G (1999) J Phys Chem B 103:6133-6141
53. Sherwood P, de Vries AH, Collins SJ, Greatbanks SP, Burton NA, Vincent MA, Hillier IH (1997) Faraday Discuss Chem Soc 106:79-92
54. Liu D, Nocedal J (1989) Math Prog 45:503-528
55. Baker J (1986) J Comput Chem 7:385-395
56. Billeter SR, Turner AJ, Thiel W (2000) Phys Chem Chem Phys 2:2177-2186
57. Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys 83:735-746
58. Humphrey W, Dalke A, Schulten K (1996) J Mol Graph 14(33-38):27-38
59. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) J Comput Chem 25:1605-1612
60. Khavrutskii I, Grant B, Taylor SS, McCammon J (2009) Biochemistry 48:11532-11545
61. Grant B, Adams JA (1996) Biochemistry 35:2022-2029
62. Szarek P, Dyguda-Kazimierowicz E, Tachibana A, Sokalski W (2008) J Phys Chem B 112:11819-11826
63. Garcia-Viloca M, Truhlar D, Gao J (2003) Biochemistry 42:13558-13575