Internal degrees of freedom, structural motifs, and conformational energetics of the 5′-deoxyadenosyl radical: Implications for function in adenosylcobalamin-dependent enzymes. A computational study

Journal of the American Chemical Society

Volumn 125, Issue 2, 2003, Pages 570-579

  Khoroshun, Dmitry V ^a,b   Warncke, Kurt ^a,b   Ke, Shyue Chu ^a,b   Musaev, Djamaladdin G ^a,b   Morokuma, Keiji ^a,b  

^a EMORY UNIVERSITY   (United States)

^b NATIONAL DONG HWA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

STRUCTURAL MOTIFS;

DEGREES OF FREEDOM (MECHANICS); FREE RADICALS; HYDROGEN BONDS; ISOMERS; PERTURBATION TECHNIQUES; POTENTIAL ENERGY; PROBABILITY DENSITY FUNCTION;

ENZYMES;

ADENINE; COBAMAMIDE; RIBOSE;

ARTICLE; CALCULATION; COENZYME; CONFORMATIONAL TRANSITION; CYCLIZATION; DENSITY FUNCTIONAL THEORY; ENERGY TRANSFER; ENZYME ACTIVITY; ENZYME KINETICS; HYDROGEN BOND; ISOMER; MATHEMATICAL ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN MOTIF; ROTATION; SECOND ORDER MOLLER PLESSET PERTURBATION THEORY; THEORETICAL MODEL; THEORY;

ADENINE; COBAMIDES; DEOXYADENINE NUCLEOTIDES; ENZYMES; FREE RADICALS; GASES; KINETICS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; RIBOSE; THERMODYNAMICS;

EID: 0037438391     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja028393k     Document Type: Article

References (98)

1. (a) Frey, P. A. Ann. Rev. Biochem. 2001, 70, 121.
2. 12; Banerjee, R., Ed.; Wiley: New York, 1999.
3. (c) Marsh, E. N. G.; Drennan, C. L. Curr. Opin. Chem. Biol. 2001, 5, 499.
4. Booker, S.; Licht, S.; Broderick, J.; Stubbe, J. Biochemistry 1994, 33, 12676.
5. Boas, J. F.; Hicks, P. R.; Pilbrow, J. R.; Smith, T. D. J. Chem. Soc., Faraday Trans. 2 1978, 74, 417.
6. Shibata, N.; Masuda, J.; Tobimatsu, T.; Toraya, T.; Suto, K.; Morimoto, Y.; Yasuoka, N. Structure 1999, 7, 997.
7. Canfield, J. M.; Warneke, K. J. Phys. Chem. B. 2002, 106, 8831.
8. (a) Buettner, G. R.; Coffman, R. E. Biochim. Biophys. Acta 1977, 480, 495.
9. (b) Gerfen, G. J.; Licht, S.; Willems, J.-P.; Hoffman, B. M.; Stubbe, J. J. Am. Chem. Soc. 1996, 118, 8192.
10. (c) Licht, S.; Gerfen, G. J.; Stubbe, J. Science 1996, 271, 477.
11. 12; Dolphin, D., Ed.; Wiley: New York. 1982; Vol. 2, pp 263-287.
12. 12; Banerjee, R., Ed.; Wiley: New York, 1999; pp 811-833.
13. Warncke, K.; Utada, A. S. J. Am. Chem. Soc. 2001, 123, 8564.
14. LoBrutto, R.; Bandarian, V.; Magnusson, O. T.; Chen, X.; Schramm, V. L.; Reed, G. H. Biochemistry 2001, 40, 9.
15. Structures FIZMUW in Cambridge Structural Database: (a) Savage, H. F. J.; Lindley, P. F.; Finney, J. L.; Timmins, P. A. Acta Crystallogr. 1987, B43, 280. (b) Allen, F. H.; Kennard, O. Chemical Design Automation News 1993, 8, 1.
16. Structures FIZMUW in Cambridge Structural Database: (a) Savage, H. F. J.; Lindley, P. F.; Finney, J. L.; Timmins, P. A. Acta Crystallogr. 1987, B43, 280. (b) Allen, F. H.; Kennard, O. Chemical Design Automation News 1993, 8, 1.
17. (a) Bothe, H.; Darley, D. J.; Albracht, S. P. J.; Gerfen, G. J.; Golding, B. T.; Buckel, W. Biochemistry 1998, 37, 4105.
18. (b) Mancia, F.; Smith, G. A.; Evans, P. R. Biochemistry 1999, 38, 7999.
19. (c) Mancia, F.; Keep, N. H.; Nakagawa, A.; Leadlay, P. F.; McSweeney, S.; Rasmussen, B.; Boesecke, P.; Diat, O.; Evans, P. R. Structure 1996, 4, 339.
20. (d) Mancia, F.; Evans, P. R. Structure 1998, 6, 711.
21. (e) Reitzer, R.; Grueber, K.; Jogl, G.; Wagner, U. G.; Bothe, H.; Buckel, W.; Kratky, C. Structure 1999, 7, 891.
22. 12: Banerjee, R., Ed.; Wiley: New York, 1999; pp 165-195.
23. Gruber, K.; Reitzer, R.; Kratky, C. Angew. Chem., Int, Ed. 2001, 40, 3377.
24. (a) Finke. R. G.; Hay, B. P. Inorg. Chem. 1984, 23, 3041.
25. (b) Hay, B. P.; Finke, R. G. J. Am. Chem. Soc. 1987, 109, 8012.
26. (c) Garr, C. D.; Sirovatka, J. M.; Finke. R. G. J. Am. Chem. Soc. 1996, 118, 11142.
27. (a) Pett, V. B.; Liebman, M. N.; Murray-Rust, P.; Prasad, K.; Glusker, J. P. J. Am. Chem. Soc. 1987, 109, 3207.
28. (b) Masuda, J.; Shibata, N.; Morimoto, Y.; Toraya, T.; Yasuoka, N. Structure 2000. 8, 775.
29. (a) Toraya, T.; Matsumoto, T.; Ichikawa, M.; Itoh, T.; Sugawara, T.; Mizuno, Y. J. Biol. Chem. 1986, 261, 9289.
30. (b) Toraya, T.; Watanabe, N.; Ichikawa, M.; Matsumoto, T.; Ushio, K.; Fukui, S. J. Biol. Chem. 1987, 262, 8544.
31. 12; Dolphin, D., Ed.; Wiley: New York, 1982; Vol. 1, pp 325-392.
32. (b) Pratt, J. M. J. Mol. Catal. 1984, 23, 187.
33. (c) Pratt, J. M. Chem. Soc. Rev. 1985, 14, 161.
34. Sando, G. N.; Blakley, R. L.; Hogenkamp, H. P. C.; Hoffmann, P. J. J. Biol. Chem. 1975, 250, 8774.
35. (a) Christianson, D. W.; Lipscomb, W. N. J. Am. Chem. Soc. 1985, 107, 2682.
36. (b) Mealli, C.; Sabat, M.; Marzilli, L. G. J. Am. Chem. Soc. 1987, 109, 1593.
37. (c) Zhu, L.; Kostic, N. M. Inorg. Chem. 1987, 26, 4194.
38. (d) Hansen, L. M.; Kumar, P. N. V. P.; Marynick, D. S. Inorg. Chem. 1994, 33, 728.
39. (e) Hansen, L. M.; Derecskei-Kovacs, A.; Marynick, D. S. J. Mol. Struct. 1998, 431, 53.
40. (f) Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. Chem. Phys. Lett. 2000, 331, 509.
41. (g) Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. J. Phys. Chem. B 2000, 104, 10921.
42. (h) Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. J. Am. Chem. Soc. 2001, 123, 2679.
43. (i) Kozlowski, P. M. Curr. Opin. Chem. Biol. 2001, 5, 736.
44. (j) Andruniow, T.; Zgierski, M. Z.; Kozlowski, P. M. J. Phys. Chem. A 2002, 106, 1365.
45. (k) Doelker, N.; Maseras, F.; Lledos, A. J. Phys. Chem. B 2001, 105, 7564.
46. (a) Torrent, M.; Musaev, D. G.; Morokuma, K.; Ke, S.-C.; Wamcke, K. J. Phys. Chem. B 1999, 103, 8618.
47. (b) Ke, S.-C.; Torrent, M.; Musaev, D. G.; Morokuma, K.; Warncke, K. Biochemistry 1999, 38, 12681.
48. (a) Golding, B. T.; Radom, L. J. Chem, Soc., Chem. Commun. 1973, 939.
49. (b) Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1976, 98, 6331.
50. 12; Dolphin, D., Ed.; Wiley: New York, 1982; Vol. 1, pp 543-582.
51. (d) Smith, D. M.; Nicolaides, A.; Golding, B. T.; Radom.; L. J. Am. Chem. Soc. 1998, 120, 10223.
52. (e) Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1999, 121, 1037.
53. (f) Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem, Soc. 1999, 121, 1383.
54. (g) Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1999, 121, 5700.
55. (h) Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 1999, 121, 9388.
56. (i) Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 2001, 123, 1664.
57. (j) Wetmore, S. D.; Smith, D. M.; Golding, B. T.; Radom, L. J. Am. Chem. Soc. 2001, 123, 7963.
58. (k) Wetmore, S. D.; Smith, D. M.; Radom, L. J. Am. Chem. Soc. 2001, 123, 8678.
59. (l) Semialjac, M.; Schwarz, H. J. Am. Chem. Soc. 2002, 124, 8974.
60. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain. M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian98, revision A.7; Gaussian, Inc.: Pittsburgh, PA, 1998.
61. (a) Becke, A. D. Phys. Rev. A 1988, 38, 3098.
62. (b) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
63. (c) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
64. (d) Hertwig, R. H.; Koch, W. Chem. Phys. Lett. 1997, 268, 345.
65. (a) Hehre, W. J.; Ditchfield, R.; Pople, J. A. J. Chem. Phys. 1972, 56, 2257.
66. (b) Hariharan, P. C.; Pople, J. A. Theor. Chim. Acta. 1973, 28, 213.
67. Clark, T.; Chandrasekhar, J.; Spitznagel, G. W.; Schleyer, P. v. R. J. Comput. Chem. 1983, 4, 294.
68. Head-Gordon, M.; Pople, J. A.; Frisch, M. J. Chem. Phys. Lett. 1988, 153, 503.
69. (a) Schlegel, H. B. J. Phys. Chem. 1988, 92, 3075.
70. (b) Schlegel, H. B. J. Chem. Phys. 1986, 84, 4530.
71. (a) Csonka, G. I.; Anh, N.; Angyan, J.; Csizmadia, I. G. Chem. Phys. Lett. 1995, 245, 129.
72. (b) Csonka, G. I.; Csizmadia, I. G. Chem. Phys. Lett. 1995, 243, 419.
73. (c) Topol, I. A.; Burt, S. K.; Rashin, A. A. Chem. Phys. Lett. 1995, 247, 112.
74. (d) Jeanvoine, Y.; Bohr, F.; Ruiz-Lopez, M. F. Can. J. Chem. 1995, 73, 710.
75. (e) Florian, J.; Johnson, B. G. J. Phys. Chem. 1995, 99, 5899.
76. (f) Novoa, J. J.; Sosa, C. J. Phys. Chem. 1995, 99, 15837.
77. (g) Han, W.-G.; Suhai, S. J. Phys. Chem. 1996, 100, 3942.
78. (h) Kang, H. C. Chem. Phys. Lett. 1996, 254, 135.
79. (i) Jeong, H. Y.; Han, Y.-K. Chem. Phys. Lett. 1996, 263, 345.
80. (j) Kang, H. C. Chem. Phys. Lett. 1996, 263, 348.
81. (k) Zhang, Q.; Bell, R.; Truong, T. N. J. Phys. Chem. 1995, 99, 592.
82. Callam, C. S.; Singer, S. J.; Lowary, T. L.; Hadad, C. M. J. Am. Chem. Soc. 2001, 123, 11743.
83. Pullman. B.: Saran, A. Prog.Nucleic Acid Res. Mol. Biol.1976, 18, 215.
84. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94, 8205.
85. Brameld, K. A.; Goddard, W. A., III. J. Am. Chem. Soc. 1999, 121, 985.
86. (a) Morokuma, K.; Umeyama, H. Chem. Phys. Lett. 1977, 49, 333.
87. (b) Pophristic, V.; Goodman, L. J. Phys. Chem. A 2002, 106, 1642.
88. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235.
89. Pullman, B.; Berthod, H. Jerusalem Symp. Quantum Chem. Biochem. 1973, 5, 209.
90. (a) Witzel, H. Prog. Nucleic Acid Res. 1963, 2, 221.
91. (b) Ts'o, P. O. P.; Rapaport, S. A.; Bollum, F. J. Biochemistry 1966, 5, 4153.
92. (c) Broom, A. D.; Schweizer, M. P.; Ts'o, P. O. P. J. Am. Chem. Soc. 1967, 89, 3612.
93. (d) Pitha, J. Biochemistry 1970, 9, 3678.
94. (e) Ts'o, P. O. P. Monomeric Units of Nucleic Acids - Bases, Nucleosides, and Nucleotides. In Fine Structure of Proteins and Nucleic Acids; Fasman, G. D.; Timasheff, S. N. Eds.; Marcel Dekker: New York, 1970; p 49.
95. (a) Zagalak, B.; Pawelkiewicz, J. Acta Biochim. Pol. 1965, 12, 219.
96. (b) Toraya, T.; Ushio, K.; Fukui, S.; Hogenkamp, H. P. C. J. Biol. Chem. 1977, 252, 963.
97. (c) Ichikawa, M.; Toraya, T. Biochim. Biophys. Acta 1988, 952, 191.
98. (d) Calafat, A. M.; Taoka, S.; Puckett, J. M., Jr., Semerad, C.; Yan, H.; Luo, L.; Chen, H.; Banerjee, R.; Marzilli, L. G. Biochemistry 1995, 34, 14125.