Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase

Journal of Chemical Physics

Volumn 128, Issue 2, 2008, Pages

  Mata, Ricardo A ^a   Werner, Hans Joachim ^a   Thiel, Stephan ^b   Thiel, Walter ^b  

^a UNIVERSITY OF STUTTGART   (Germany)

^b MAX PLANCK INSTITUT FÜR KOHLENFORSCHUNG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; FUNCTIONAL GROUPS; MOLECULAR DYNAMICS; OPTIMIZATION; PARAMETER ESTIMATION; REACTION KINETICS;

COMPUTATIONAL PARAMETERS; HYDROXYBENZOATE HYDROXYLASE; OPTIMIZED GEOMETRIES;

ENZYME ACTIVITY;

4 HYDROXYBENZOATE 3 MONOOXYGENASE;

ARTICLE; CATALYSIS; COMPUTER SIMULATION; ENZYME SPECIFICITY; METABOLISM; QUANTUM THEORY;

4-HYDROXYBENZOATE-3-MONOOXYGENASE; CATALYSIS; COMPUTER SIMULATION; QUANTUM THEORY; SUBSTRATE SPECIFICITY;

EID: 38349061612     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.2823055     Document Type: Article

References (50)

1. H. M. Senn and W. Thiel, Top. Curr. Chem. TPCCAQ 0340-1022 268, 173 (2007).
2. B. Entsch and W. J. H. van Berkel, FASEB J. FAJOEC 0892-6638 9, 476 (1995).
3. H. M. Senn, S. Thiel, and W. Thiel, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct049844p 1, 494 (2005).
4. W. J. H. van Berkel and F. Müller, Eur. J. Biochem. EJBCAI 0014-2956 10.1111/j.1432-1033.1989.tb14556.x 179, 307 (1989).
5. M. Husain, B. Entsch, D. P. Ballou, V. Massey, and P. J. Chapman, J. Biol. Chem. JBCHA3 0021-9258 255, 4189 (1980).
6. B. Entsch, B. A. Palfey, D. P. Ballou, and V. Massey, J. Biol. Chem. JBCHA3 0021-9258 266, 17431 (1991).
7. M. Ortiz-Maldonado, L. J. Cole, S. M. Dumas, B. Entsch, and D. P. Ballou, Biochemistry BICHAW 0006-2960 10.1021/bi030193d 43, 1569 (2004).
8. L. Ridder, A. J. Mulholland, J. Vervoort, and I. M. C. M. Rietjens, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja980639r 120, 7641 (1998).
9. L. Ridder, A. J. Mulholland, I. M. C. M. Rietjens, and J. Vervoort, J. Mol. Graphics Modell. JMGMFI 1093-3263 10.1016/S1093-3263(99)00027-3 17, 163 (1999).
10. L. Ridder, B. A. Palfeyl, I. M. C. M. Rietjens, J. Vervoort, and A. J. Mulholland, FEBS Lett. FEBLAL 0014-5793 10.1016/S0014-5793(00)01844-5 478, 197 (2000).
11. L. Ridder, J. N. Harvey, I. M. C. M. Rietjens, J. Vervoort, and A. J. Mulholland, J. Phys. Chem. B JPCBFK 1089-5647 10.1021/jp026213n 107, 2118 (2003).
12. S. R. Billeter, A. J. Turner, and W. Thiel, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/a909486e 2, 2177 (2000); S. R. Billeter, C. F. W. Hanser, T. Z. Mordasini, M. Scholten, W. Thiel, and W. F. van Gunsteren, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b009011p 3, 688 (2001).
13. J. Kästner, H. M. Senn, S. Thiel, N. Otte, and W. Thiel, J. Chem. Theory Comput. JCTCCE 1549-9618 10.1021/ct050252w 2, 452 (2006).
14. J. Kästner and W. Thiel, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2052648 123, 144104 (2005).
15. M. J. S. Dewar, E. G. Zoebisch, E. F. Healy, and J. J. P. Stewart, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00299a024 107, 3902 (1985).
16. L. Ridder, A. J. Mulholland, I. M. C. M. Rietjens, and J. Vervoort, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja0007814 122, 8728 (2000).
17. A. D. Becke, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.464913 98, 5648 (1993).
18. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The GROMOS96 Manual and User Guide (Biomos b. v., Zürich and Groningen / VdF Hochschulverlag, ETH Zürich, Zürich, 1996).
19. F. Claeyssens, J. N. Harvey, F. R. Manby, R. A. Mata, A. J. Mulholland, K. E. Ranaghan, M. Schütz, S. Thiel, W. Thiel, and H.-J. Werner, Angew. Chem., Int. Ed. ACIEF5 1433-7851 10.1002/anie.200602711 45, 6856 (2006).
20. S. R. Billeter, A. J. Turner, and W. Thiel, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/a909486e 2, 2177 (2000).
21. P. Sherwood, A. H. de Vries, M. F. Guest, G. Schreckenbach, C. R. A. Catlow, S. A. French, A. A. Sokol, S. T. Bromley, W. Thiel, A. J. Turner, S. R. Billeter, F. Terstegen, S. Thiel, J. Kendrick, S. C. Rogers, J. Casci, M. Watson, F. King, E. Karlsen, M. Sjøvoll, A. Fahmi, A. Schäfer, and C. Lennartz, J. Mol. Struct.: THEOCHEM THEODJ 0166-1280 10.1016/s0166-1280(03) 00285-9 632, 1 (2003).
22. A. Schäfer, C. Huber, and R. Ahlrichs, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.467146 100, 5829 (1994).
23. H.-J. Werner, P. J. Knowles, R. Lindh, F. R. Manby, M. Schütz, MOLPRO, Version 2006.1, a package of ab initio programs, see http://www.molpro.net (http://molpro.net/).
24. C. Hampel and H.-J. Werner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.471289 104, 6286 (1996).
25. G. Hetzer, P. Pulay, and H.-J. Werner, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(98)00491-6 290, 143 (1998).
26. M. Schütz, G. Hetzer, and H.-J. Werner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.479957 111, 5691 (1999).
27. G. Hetzer, M. Schütz, H. Stoll, and H.-J. Werner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1321295 113, 9443 (2000).
28. M. Schütz and H.-J. Werner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1330207 114, 661 (2001).
29. M. Schütz and H.-J. Werner, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/S0009-2614(00)00066-X 318, 370 (2000).
30. M. Schütz, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1323265 113, 9986 (2000).
31. M. Schütz, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1470497 116, 8772 (2002).
32. P. Pulay, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(83)80703-9 100, 151 (1983).
33. S. Saebø and P. Pulay, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/0009-2614(85)85003-X 113, 13 (1985).
34. F. R. Manby, H.-J. Werner, T. B. Adler, and A. J. May, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2173247 124, 094103 (2006).
35. H.-J. Werner, T. B. Ader, and F. R. Manby, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2712434 126, 16410 (2007).
36. D. P. Tew, W. Klopper, C. Neiss, and C. Hättig, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b617230j 9, 1921 (2007).
37. H.-J. Werner and F. R. Manby, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2150817 124, 054114 (2006).
38. H.-J. Werner, F. R. Manby, and P. Knowles, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1564816 118, 8149 (2003).
39. R. Polly, H.-J. Werner, F. R. Manby, and P. J. Knowles, Mol. Phys. MOPHAM 0026-8976 10.1080/0026897042000274801 102, 2311 (2004).
40. M. Schütz and F. R. Manby, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b304550a 5, 3349 (2003).
41. H.-J. Werner and M. Schütz (unpublished).
42. T. H. Dunning, Jr., J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.456153 90, 1007 (1989).
43. R. A. Kendall, T. H. Dunning, and R. J. Harrison, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.462569 96, 6796 (1992).
44. F. Weigend, Phys. Chem. Chem. Phys. PPCPFQ 1463-9076 10.1039/b204199p 4, 4285 (2002).
45. F. Weigend, A. Köhn, and C. Hättig, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1445115 116, 3175 (2002).
46. J. W. Boughton and P. Pulay, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.540140615 14, 736 (1993).
47. M. Schütz, H.-J. Werner, R. Lindh, and F. R. Manby, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1760747 121, 737 (2004).
48. M. Schütz, G. Rauhut, and H.-J. Werner, J. Phys. Chem. A JPCAFH 1089-5639 10.1021/jp981168y 102, 5997 (1998).
49. R. A. Mata and H.-J. Werner, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2364487 125, 184110 (2006).
50. S. Grimme, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1569242 118, 9095 (2003).