Active site structure of class I ribonucleotide reductase intermediate X: A density functional theory analysis of structure, energetics, and spectroscopy

Journal of the American Chemical Society

Volumn 127, Issue 45, 2005, Pages 15778-15790

  Han, Wen Ge ^a   Liu, Tiqing ^a,b   Lovell, Timothy ^a,c   Noodleman, Louis ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^c ASTRAZENECA R AND D   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN BONDS; IRON; MOLECULAR STRUCTURE; PROBABILITY DENSITY FUNCTION;

ACTIVE SITE STRUCTURES; BIDENTATE CARBOXYLATES; CONDUCTOR-LIKE SCREENING; ENERGETICS;

ENZYMES;

ASPARTIC ACID; BRIDGED COMPOUND; CARBOXYLIC ACID; GLUTAMIC ACID; HYDROGEN; IRON 57; OXYGEN 17; RIBONUCLEOTIDE REDUCTASE;

ARTICLE; COMPARATIVE STUDY; DENSITY FUNCTIONAL THEORY; ENERGY TRANSFER; ENZYME ACTIVE SITE; ENZYME STRUCTURE; HYDROGEN BOND; MODEL; MOSSBAUER SPECTROSCOPY; SOLVATION; SPECTROSCOPY;

ASPARTIC ACID; BINDING SITES; ELECTRON SPIN RESONANCE SPECTROSCOPY; GLUTAMIC ACID; HYDROGEN BONDING; IRON; MODELS, MOLECULAR; MOLECULAR STRUCTURE; RIBONUCLEOSIDE DIPHOSPHATE REDUCTASE; WATER;

EID: 27844488367     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja050904q     Document Type: Article

References (90)

1. Wallar, B. J.; Lipscomb, J. D. Chem. Rev. 1996, 96, 2625-2657.
2. Sjöberg, B. M. Struct. Bonding 1997, 88, 139-173.
3. Fontecave, M.; Nordlund, P.; Eklund, H.; Reichard, P. Adv. Enzymol. Relat. Areas Mol. Biol. 1992, 65, 147-183.
4. (a) Sturgeon, B. E.; Burdi, D.; Chen, S.; Huynh, B. H.; Edmondson, D. E.; Stubbe, J.; Hoffman, B. M. J. Am. Chem. Soc. 1996, 118, 7551-7557.
5. (b) Stubbe, J.; van der Donk, W. A. Chem. Biol. 1995, 2, 793-801.
6. (a) Henriksen, M. A.; Cooperman, B. S.; Salem, J. S.; Li, L. S.; Rubin, H. J. Am. Chem. Soc. 1994, 116, 9773-9774.
7. (b) Högbom, M.; Stenmark, P.; Voevodskaya, N.; McClarty, G.; Gräslund, A.; Nordlund, P. Science 2004, 305, 245-248.
8. (c) Larsson, A.; Sjöberg, B. M. EMBO J. 1986, 5, 2037-2040.
9. (d) Putsch, S.; Lendzian, F.; Ingemarson, R.; Hornberg, A.; Thelander, L.; Lubitz, W.; Lassmann, G.; Graslund, A. J. Biol. Chem. 1999, 274, 17696-17704.
10. (a) Nordlund, P.; Sjöberg, B. M.; Eklund, H. Nature 1990, 345, 593-598.
11. (b) Nordlund, P.; Eklund, H. J. Mol. Biol. 1993, 232, 123-164.
12. (c) Nordlund, P.; Eklund, H. Curr. Opin. Struct. Biol. 1995, 5, 758-766.
13. Logan, D. T.; Su, X. D.; Åberg, A.; Regnström, K.; Hajdu, J.; Eklund, H.; Nordlund, P. Structure 1996, 4, 1053-1064.
14. (a) Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5251-5266.
15. (b) Lovell, T.; Li, J.; Noodleman, L. J. Biol. Inorg. Chem. 2002, 7, 799-809.
16. (c) Lovell, T.; Himo, F.; Han, W.-G.; Noodleman, L. Coord. Chem. Rev. 2003, 238-239, 211-232.
17. (d) Noodleman, L.; Lovell, T.; Han, W.-G.; Liu, T.; Torres, R. A.; Himo, F. In Comprehensive Coordination Chemistry II: From Biology to Nanotechnology; Lever, A. B. P., Ed.; Elsevier: Philadelphia, 2003; Vol. 2, pp 491-510.
18. (a) Mitic, N.; Saleh, L.; Schenk, G.; Bollinger, J. M., Jr.; Solomon, E. I. J. Am. Chem. Soc. 2003, 125, 11200-11201.
19. (b) Skulan, A. J.; Brunold, T. C.; Baldwin, J.; Saleh, L.; Bollinger, J. M., Jr.; Solomon, E. I. J. Am. Chem. Soc. 2004, 126, 8842-8855.
20. (a) Bollinger, J. M., Jr.; Edmondson, D. E.; Huynh, B. H.; Filley, J.; Norton, J. R.; Stubbe, J. Science 1991, 253, 292-298.
21. (b) Bollinger, J. M., Jr.; Stubbe, J.; Huynh, B. H.; Edmondson, D. E. J. Am. Chem. Soc. 1991, 113, 6289-6291.
22. (c) Bollinger, J. M., Jr.; Tong, W. H.; Ravi, N.; Huynh, B. H.; Edmondson, D. E.; Stubbe, J. J. Am. Chem. Soc. 1994, 116, 8015-8023; 8024-8032.
23. (d) Baldwin, J.; Krebs, C.; Ley, B. A.; Edmondson, D. E.; Huynh, B. H.; Bollinger, J. M., Jr. J. Am. Chem. Soc. 2000, 122, 12195-12206.
24. (e) Krebs, C.; Chen, S.; Baldwin, J.; Ley, B. A.; Patel, U.; Edmondson, D. E.; Huynh, B. H.; Bollinger, J. M., Jr. J. Am. Chem. Soc. 2000, 122, 12207-12219.
25. Ravi, N.; Bollinger, J. M., Jr.; Huynh, B. H.; Edmondson, D. E.; Stubbe, J. J. Am. Chem. Soc. 1994, 116, 8007-8014.
26. Burdi, D.; Sturgeon, B. E.; Tong, W. H.; Stubbe, J.; Hoffman, B. M. J. Am. Chem. Soc. 1996, 118, 281-282.
27. Veselov, A.; Scholes, C. P. Inorg. Chem. 1996, 35, 3702-3705.
28. Willems, J. P.; Lee, H. I.; Burdi, D.; Doan, P. E.; Stubbe, J.; Hoffman, B. M. J. Am. Chem. Soc. 1997, 119, 9816-9824.
29. Riggs-Gelasco, P. J.; Shu, L.; Chen, S.; Burdi, D.; Huynh, B. H.; Que, L., Jr.; Stubbe, J. J. Am. Chem. Soc. 1998, 120, 849-860.
30. Burdi, D.; Willems, J. P.; Riggs-Gelasco, P. J.; Antholine, W. E.; Stubbe, J.; Hoffman, B. M. J. Am. Chem. Soc. 1998, 120, 12910-12919.
31. Hsu, H. F.; Dong, Y.; Shu, L.; Young, V. G., Jr.; Que, L., Jr. J. Am. Chem. Soc. 1999, 121, 5230-5237.
32. (a) Siegbahn, P. E. M. Inorg. Chem. 1999, 38, 2880-2889.
33. (b) Siegbahn, P. E. M. Chem. Phys. Lett. 2002, 351, 311-318.
34. (c) Siegbahn, P. E. M. Q. Rev. Biophys. 2003, 36, 91-145.
35. Han, W.-G.; Lovell T.; Liu, T.; Noodleman, L. Inorg. Chem. 2003, 42, 2751-2758.
36. Noodleman, L.; Lovell T.; Han, W.-G.; Li, J.; Himo, F. Chem. Rev. 2004, 104, 459-508.
37. Han, W.-G.; Lovell T.; Liu, T.; Noodleman, L. Inorg. Chem. 2004, 43, 613-621.
38. Han, W.-G.; Tajkhorshid, E.; Suhai, S. J. Biol. Struct. Dyn. 1999, 16, 1019-1032.
39. ADF2003.01 and ADF2004.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands (http://www.scm.com).
40. (a) Fonseca Guerra, C.; Snijders, J. G.; te Velde, G.; Baerends, E. J. Theor. Chem. Acc. 1998, 99, 391-403.
41. (b) te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Guerra, C. F.; van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. J. Comput. Chem. 2001, 22, 931-967.
42. (c) van Lenthe, E.; van der Avoird, A.; Wormer, P. E. S. J. Chem. Phys. 1998, 108, 4783-4796.
43. (a) Klamt, A.; Schrüümann, G. J. Chem. Soc., Perkin Trans. 1993, 2, 799-805.
44. (b) Klamt, A. J. Phys. Chem. 1995, 99, 2224-2235.
45. (c) Klamt, A.; Jones, V. J. Chem. Phys. 1996, 105, 9972-9981.
46. (d) Pye, C. C.; Ziegler, T. Theor. Chem. Acc. 1999, 101, 396-408.
47. (a) Liu, T.; Han, W.-G.; Himo, F.; Ullmann, G. M.; Bashford, D.; Toutchkine, A.; Hahn, K. M.; Noodleman, L. J. Phys. Chem. A 2004, 108, 3545-3555.
48. (b) Han, W.-G.; Liu, T.; Himo, F.; Toutchkine, A.; Bashford, D.; Hahn, K. M.; Noodleman, L. ChemPhysChem 2003, 4, 1084-1094.
49. Vosko, S. H.; Wilk, L.; Nusair, M. Can. J. Phys. 1980, 58, 1200-1211.
50. Perdew, J. P.; Chekavry, J. A.; Vosko, S. H.; Jackson, K. A.; Perderson, M. R.; Singh, D. J.; Fioihais, C. Phys. Rev. B 1992, 46, 6671-6687.
51. (a) Noodleman, L.; Case, D. A. Adv. Inorg. Chem. 1992, 38, 423-470.
52. (b) Noodleman, L.; Chen, J.-L.; Case, D. A.; Giori, C.; Rius, G.; Mouesca, J.-M.; Lamotte, B. In Nuclear Magnetic Resonance of Paramagnetic Macromolecules; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1995; pp 339-367.
53. (c) Kuramochi, H.; Noodleman, L.; Case, D. A. J. Am. Chem. Soc. 1997, 119, 11442-11451.
54. (d) Adams, D. A.; Noodleman, L.; Hendrickson, D. N. Inorg. Chem. 1997, 36, 3966-3984.
55. (e) Case, D. A.; Noodleman, L.; Li, J. In Metal-Ligand Interactions in Chemistry, Physics and Biology; Russo, N., Salahub, D. R., Eds.: Kluwer Academic Publishers: Dordrecht, The Netherlands. 2000; pp 19-47.
56. (f) Cheng, R.-J.; Chen, P.-Y.; Lovell, T.; Liu, T.; Noodleman, L.; Case, D. A. J. Am. Chem. Soc. 2003, 125, 6774-6783.
57. Mouesca, J.-M.; Chen, J. L.; Noodleman, L.; Bashford, D.; Case, D. A. J. Am. Chem. Soc. 1994, 116, 11898-11914.
58. Zhao, X. G.; Richardson, W. H.; Chen, J.-L.; Li, J.; Noodleman, L.; Tsai, H.-L.; Hendrickson, D. N. Inorg. Chem. 1997, 36, 1198-1217.
59. Li, J.; Noodleman, L. In Spectroscopic Methods in Bioinorganic Chemistry; Solomon, E. I., Hodgson, K. O., Eds.; ACS Symposium Series 692; American Chemical Society: Washington. DC, 1998; Chapter 9, pp 179-195.
60. (a) Lovell, T.; Li, J.; Noodleman, L. Inorg. Chem. 2001, 40, 5267-5278.
61. (b) Lovell, T.; Torres, R. A.; Han, W.-G.; Liu, T.; Case, D. A.; Noodleman, L. Inorg. Chem. 2002, 41, 5744-5753.
62. (c) Lovell, T.; Li, J.; Case, D. A.; Noodleman, L. J. Biol. Inorg. Chem. 2002, 7, 735-749.
63. (a) Lovell, T.; Han, W.-G.; Liu, T.; Noodleman, L. J. Am. Chem. Soc. 2002, 124, 5890-5894.
64. (b) Liu, T.; Lovell, T.; Han, W.-G.; Noodleman, L. Inorg. Chem. 2003, 42, 5244-5251:
65. Inorg. Chem. 2004, 43, 6858.
66. (a) Sinnecker, S.; Neese, F.; Noodleman, L.; Lubitz, W. J. Am. Chem. Soc. 2004, 126, 2613-2622.
67. (b) Noodleman, L.; Baerends, E. J. J. Am. Chem. Soc. 1984, 106, 2316-2327.
68. (a) Vogel, E.; Will, S.; Tilling, A. S.; Neumann, L.; Lex, J.; Bill, E.; Trautwein, A. X.; Wieghardt, K. Angew. Chem., Int. Ed. Engl. 1994, 33, 731-735.
69. (b) Kostka, K. L.; Fox, B. G.; Hendrich, M. P.; Collins, T. J.; Rickard, C. E. F.; Wright, L. J.; Münck, E. J. Am. Chem. Soc. 1993, 115, 6746-6757.
70. (a) Fox, B. G.; Hendrich, M. P.; Surerus, K. K.; Andersson, K. K.; Froland, W. A.; Lipscomb, J. D.; Münck, E. J. Am. Chem. Soc. 1993, 115, 3688-3701.
71. (b) Lynch, J. B.; Juarez-Garcia, C.; Münck, E.; Que, L. J., Jr. Biol. Chem. 1989, 264, 8091-8096.
72. (c) Martínez-Pinedo, G.; Schwerdtfeger, P.; Caurier, E.; Langanke, K.; Nazarewicz, W.; Söhnel, T. Phys. Rev. Lett. 2001, 87, 062701(1-4).
73. (a) Neese, F. Inorg. Chim. Acta 2002, 337, 181-192.
74. (b) Neese, F. Curr. Opin. Chem. Biol. 2003, 7, 125-135.
75. (c) Godbout, N.; Havlin, R.; Salzmann, R.; Debrunner, P. G.; Oldfield, E. J. Am. Chem. Soc. 1998, 102, 2342-2350.
76. (d) Havlin, R.; Godbout, N.; Salzmann, R.; Wojdelski, M.; Arnold, W.; Schulz, C. E.; Oldfield, E. J. Am. Chem. Soc. 1998, 120, 3144-3151.
77. (e) Zhang, Y.; Mao, J.; Oldfield, E. J. Am. Chem. Soc. 2002, 124, 7829-7839.
78. (a) Richardson, W. H.; Peng, C.; Bashford, D.; Noodleman, L.; Case, D. A. Int. J. Quantum Chem. 1997, 61, 207-217.
79. (b) Li, J.; Fisher, C. L.; Konecny, R.; Bashford, D.; Noodleman, L. Inorg. Chem. 1999, 38, 929-939.
80. (c) Huang, H.; Han, W.-G.; Noodleman, L.; Grynszpan, F. Bioorg. Med. Chem. 2001, 9, 3185-3195.
81. (d) Han, W.-G.; Lovell, T.; Noodleman, L. Inorg. Chem. 2002, 41, 205-218.
82. Noyes, R. M. J. Am. Chem. Soc. 1962, 84, 512-522.
83. Reiss, H.; Heller, A. J. Phys. Chem. 1985, 89, 4207-4213.
84. Tawa, G. J.; Topol, I. A.; Burt, S. K.; Caldwell, R. A.; Rashin, A. A. J. Chem. Phys. 1998, 109, 4852-4863.
85. (a) Liptak, M. D.; Shields, G. C. J. Am. Chem. Soc. 2001, 123, 7314-7319.
86. (b) Palascak, M. W.; Shields, G. C. J. Phys. Chem. A 2004, 108, 3692-3694.
87. (a) Wilk, L.; Vosko, S. H. Phys. Rev. A 1977, 15, 1839-1846.
88. (b) Neese, F. J. Chem. Phys. 2003, 118, 3939-3948.
89. Valentine, A. M.; Tavares, P.; Pereira, A. S.; Davydov, R.; Krebs, C.; Hoffman, B. M.; Edmondson, D. E.; Huynh, B. H.; Lippard, S. J. J. Am. Chem. Soc. 1998, 120, 2190-2191.
90. Baik, M.-H.; Newcomb, M.; Friesner, R. A.; Lippard, S. J. Chem. Rev. 2003, 103, 2385-2419.