Transition state structure invariance to model system size and calculation levels: A QM/MM study of the carboxylation step catalyzed by Rubisco

Theoretical Chemistry Accounts

Volumn 101, Issue 1-3, 1999, Pages 228-233

  Moliner, V ^a   Andres J ^a   Oliva, M ^a   Safont, V S ^a   Tapia, O ^b  

^a UNIVERSITAT JAUME I   (Spain)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

Carboxylation step; Hybrid theoretical calculations; QM MM; Rubisco; Transition state structure

Indexed keywords

EID: 0033470016     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002140050434     Document Type: Article

References (87)

1. Houk KN, Gustafson SM, Black KA (1992) J Am Chem Soc 114: 8565
2. Williams IH (1993) Chem Soc Rev 277
3. Tapia O, Paulino M, Stamato FMLG (1994) Mol Eng 3: 377
4. Houk KN, González J, Li Y (1995) Acc Chem Res 28: 81
5. Wigner E (1938) Trans Faraday Soc 34: 29
6. Neumark DM (1993) Acc Chem Res 26: 33
7. Tapia O, Andres J, Stamato FMG (1996) In: Solvent effects and chemical reactivity. Kluwer, Dordrecht, pp CF18: 283-361
8. Lerner RL, Tramontano A (1987) Trends Biochem Sci 12: 427
9. Tramontano A, Janda KD, Lerner RA (1988) Science 234: 1566
10. Pollack SJ, Schultz PG (1987) Cold Spring Harbor Symp Quant Biol LII: 97
11. Schultz PG, Lerner RA (1993) Acc Chem Res 26: 391
12. Reymond JL, Jahangiri GK, Stoudt C, Lerner RA (1993) J Am Chem Soc 115: 3909
13. Gouverneur VE, Houk KN, Pascual-Teresa B, Beno B, Janda KD, Lerner RA (1993) Science 262: 204
14. Polanyi JC, Zewail AH (1995) Acc Chem Res 28: 119
15. Neumark DM (1996) Science 272: 1446
16. Wenthold PG, Hrovat DA, Borden WT, Lineberger WC (1996) Science 272: 1456
17. Wolfenden R, Radzicka A (1991) Curr Opin Struct Biol 1: 780
18. Schröer J, Sanner M, Reymond J-L, Lerner RA (1997) J Org Chem 62: 3220
19. Houk KN, Rondan NG, von Rague Schleyer P, Kaufmann E, Clark T (1985) J Am Chem Soc 107: 2821
20. Wu Y-D, Houk KN (1987) J Am Chem Soc 109: 2226
21. Wu Y-D, Houk KN (1987) J Am Chem Soc 109: 906
22. Tapia O, Cárdenas R, Andrés J, Colonna-Cesari F (1988) J Am Chem Soc 110: 4046
23. Mezey PG (1987) Potential energy hypersurfaces. Elsevier, Amsterdam
24. Mezey PG (1980) Theoret Chim Acta 54: 95
25. Mezey PG (1981) In: Computational theoretical organic chemistry. Reidel, Dordrecht, pp 101-128
26. Tapia O, Cárdenas R, Andrés J, Krechl J, Campillo M, Colonna-Cesari F (1991) Int J Quantum Chem 39: 767
27. Tapia O, Jacob O, Colonna F (1992) Theor Chim Acta 82: 217
28. Tapia O, Andrés J, Cárdenas R (1992) Chem Phys Lett 189: 395
29. Tapia O, Jacob O, Colonna F (1993) Theor Chim Acta 85: 217
30. Andres J, Moliner V, Krechl J, Silla E (1994) J Phys Chem 98: 3664
31. Tapia O, Andrés J, Safont VS (1994) J Chem Soc Faraday Trans 90: 2365
32. Andrés J, Moliner V, Safont VS (1995) J Chem Soc Faraday Trans 90: 1703
33. Tapia O, Andres J (1995) J Mol Struct (Theochem) 335: 267
34. Tapia O, Andrés J, Safont VS (1995) J Mol Struct (Theochem) 342: 131
35. Andres J, Moliner V, Krechl J, Domingo JL, Picher MT (1995) J Am Chem Soc 117: 8807
36. Tapia O, Poulain E, Sussman F (1975) Chem Phys Lett 33: 65
37. Warshel A, Levin H (1976) J Mol Biol 103: 227
38. Tapia O, Johannin G (1981) J Chem Phys 75: 3624
39. Singh UC, Kollman PA (1986) J Comput Chem 7: 718
40. Tapia O, Colonna F, Angyan JG (1990) J Chim Phys 87: 875
41. Tapia O (1992) J Math Chem 10: 139
42. Tomasi J, Persico M (1994) Chem Rev 94: 2027
43. Sehgal A, Shao L, Gao J (1995) J Am Chem Soc 117: 11337
44. Barnes JA, Williams IH (1996) J Chem Soc Chem Commun 193
45. Bash PA, Field MJ, Karplus M ( 1987) J Am Chem Soc 109: 8092
46. Field MJ, Bash PA, Karplus M (1990) J Comput Chem 11: 700
47. Bash PA, Field MJ, Davenport GA, Petsko D, Karplus M (1991) Biochemistry 30: 5826
48. Waszkowycz B, Hillier IH, Gensmantel N, Payling DW (1991) J Chem Soc, Perkin Trans 2: 225
49. Aqvist J, Warshel A (1993) Chem Rev 93: 2523
50. Lyne P, Mulholland AJ, Richards WG (1995) J Am Chem Soc 117: 11345
51. Barnes JA, Williams IH (1996) Biochem Soc Trans 24: 263
52. Moliner V, Turner AJ, Williams IH (1997) J Chem Soc Chem Commun 1271
53. Turner AJ (1997) University of Bath, Thesis
54. Lorimer GH, Gutteridge S, Madden MW (1987) In: Plant molecular biology. Plenum, New York, pp 21-31
55. Andrews TJ, Lorimer GH (1987) In: The biochemistry of plants. Academic, New York, pp 131-218
56. Hartman FC, Harpel MR (1994) Annu Rev Biochem 63: 197
57. Hartman FC (1992) In: Plant protein engineering. Cambridge University Press, Cambridge, pp 61-92
58. Saver BG, Knowles JR (1982) Biochemistry 21: 5398
59. Sue JM, Knowles JR (1982) Biochemistry 21: 5404
60. Hartman FC, Soper TS, Niyogi SK, Mural RJ, Foote RS, Mitra S, Lee EH, Machanoff R, Larimer WF (1987) J Biol Chem 262: 3496
61. Lorimer GH, Hartman FC (1988) J Biol Chem 263: 6468
62. Smith HB, Larimer FW, Hartman FC (1988) Biochem Biophys Res Commun 152: 579
63. Schloss JV (1990) In: Enzymatic and model carboxylation and reduction reactions for carbon dioxide utilization. Kluwer, Dordrecht, pp 321-345
64. Newman J, Gutteridge S (1993) J Biol Chem 268: 25876
65. Andersson I (1996) J Mol Biol 259: 160
66. Safont VS, Oliva M, Andres J, Tapia O (1997) Chem Phys Lett 278: 291
67. Tapia O, Andres J (1992) Mol Eng 2: 37
68. Andrés J, Safont VS, Tapia O (1992) Chem Phys Lett 198: 515
69. Andrés J, Safont VS, Queralt J, Tapia O (1993) J Phys Chem 97: 7888
70. Tapia O, Andrés J, Safont VS (1994) J Phys Chem 98: 4821
71. Tapia O, Andres J, Safont VS (1996) J Phys Chem 100: 8543
72. (a)Knight S, Andersson I, Bränden C (1990) J Mol Biol 215: 113;
73. (b)Andersson I (1996) J Mol Biol 259: 160
74. Taylor TC, Andersson I (1996) Nat Struct Biol 3: 95
75. Taylor TC, Fothergill D, Andersson I (1996) J Biol Chem 271: 32894
76. Taylor TC, Andersson I (1997) Biochemistry 36: 4041
77. Taylor TC, Andersson I (1997) J Mol Biol 265: 432
78. Schlegel HB (1982) J Comput Chem 3: 214
79. Schlegel HB (1982) J Chem Phys 77: 3676
80. Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Johnson BG, Robb MA, Cheeseman JR, Keith T, Peterson GA, Montgomery JA, Raghavachari K, Al-Laham MA, Zakrzewski VG, Ortiz JV, Foresman JB, Cioslowski J, Stefanov BB, Nanayakkara A, Challacombe M, Peng CY, Ayala PY, Chen W, Wong MW, Andres JL, Replogle ES, Gomperts R, Martin RL, Fox DJ, Binkley JS, Defrees DJ, Baker J, Stewart JP, Head-Gordon M, Gonzalez C, Pople JA (1995) GAUSSIAN94, Revision B. 1 Gaussian, Inc., Pittsburgh, Pa
81. Nakagawa S, Yu HA, Karplus M, Umeyama H (1993) Proteins 16: 172
82. Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107: 3902
83. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) J Comput Chem 4: 187
84. Tapia O, Andres J (1984) Chem Phys Lett 109: 471
85. Cleland WW, Andrews TJ, Gutteridge S, Hartman FC, Lorimer GH (1998) Chem Rev 98: 549
86. Pauling L (1948) Nature 161: 707
87. Fukui K (1970) J Phys Chem 74: 4161