Influence of protein environment on the electron paramagnetic resonance properties of flavoprotein radicals: A QM/MM study

Journal of Physical Chemistry B

Volumn 114, Issue 49, 2010, Pages 16655-16665

  Pauwels, Ewald ^a   Declerck, Reinout ^a,c   Verstraelen, Toon ^a   De Sterck, Bart ^a   Kay, Christopher W M ^b   Van Speybroeck, Veronique ^a   Waroquier, Michel ^a  

^a GHENT UNIVERSITY   (Belgium)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

^c BOSTON CONSULTING GROUP   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ELECTRON RESONANCE; ELECTRON SPIN RESONANCE SPECTROSCOPY; FUNCTIONAL GROUPS; GLUCOSE; GLUCOSE OXIDASE; GLUCOSE SENSORS; ISOMERS; MOLECULAR DYNAMICS; PARAMAGNETIC MATERIALS; PARAMAGNETISM; PROTEINS; TENSORS;

CATALYTIC SITES; COFACTORS; ELECTRON PARAMAGNETIC RESONANCE; EXPERIMENTAL CONDITIONS; FLAVIN ADENINE DINUCLEOTIDE; G TENSORS; GAUSSIANS; GEOMETRY OPTIMIZATION; GLOBAL FEATURE; HIGH RESOLUTION; HYPERFINE COUPLING; ISOTROPIC HYPERFINE COUPLINGS; MD SIMULATION; METHYL GROUP; MOLECULAR DYNAMICS SIMULATIONS; NIGER; ON THE FLIES; PRINCIPAL DIRECTIONS; PROTEIN STRUCTURES; PROTONATION STATE; SEMIQUINONE RADICALS; SPECTROSCOPIC CHARACTERISTICS;

PARAMAGNETIC RESONANCE;

EID: 78650167395     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp109763t     Document Type: Article

References (68)

1. Massey, V. Biochem. Soc. Trans. 2000, 28, 283-296
2. Fuchs, M. R.; Schleicher, E.; Schnegg, A.; Kay, C. W. M.; Torring, J. T.; Bittl, R.; Bacher, A.; Richter, G.; Mobius, K.; Weber, S. J. Phys. Chem. B 2002, 106, 8885-8890
3. Kay, C. W. M.; Bittl, R.; Bacher, A.; Richter, G.; Weber, S. J. Am. Chem. Soc. 2005, 127, 10780-10781
4. Kay, C. W. M.; Schleicher, E.; Hitomi, K.; Todo, T.; Bittl, R.; Weber, S. Magn. Reson. Chem. 2005, 43, S96-S102
5. Schnegg, A.; Kay, C. W. M.; Schleicher, E.; Hitomi, K.; Todo, T.; Mobius, K.; Weber, S. Mol. Phys. 2006, 104, 1627-1633
6. Kay, C. W. M.; Mkami, H. E.; Molla, G.; Pollegioni, L.; Ramsay, R. R. J. Am. Chem. Soc. 2007, 129, 16091-16097
7. Barquera, B.; Morgan, J. E.; Lukoyanov, D.; Scholes, C. P.; Gennis, R. B.; Nilges, M. J. J. Am. Chem. Soc. 2003, 125, 265-275
8. Okafuji, A.; Schnegg, A.; Schleicher, E.; Mobius, K.; Weber, S. J. Phys. Chem. B 2008, 112, 3568-3574
9. Schnegg, A.; Okafuji, A.; Bacher, A.; Bittl, R.; Fischer, M.; Fuchs, M. R.; Hegemann, P.; Joshi, M.; Kay, C. W. M.; Richter, G.; Schleicher, E.; Weber, S. Appl. Magn. Reson. 2006, 30, 345-358
10. For an example of a reference work, see
11. Parr, R. G.; Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: New York, 1989.
12. Kaupp, M.; Bühl, M.; Malkin, V. G. Calculation of NMR and EPR Parameters: Theory and Applications; Wiley-VCH: Weinheim, 2004.
13. Colombo, M. C.; VandeVondele, J.; Van Doorslaer, S.; Laio, A.; Guidoni, L.; Rothlisberger, U. Proteins 2008, 70, 1084-1098
14. Declerck, R.; Pauwels, E.; Van Speybroeck, V.; Waroquier, M. Phys. Rev. B 2006, 74, 245103
15. Weber, V.; Iannuzzi, M.; Giani, S.; Hutter, J.; Declerck, R.; Waroquier, M. J. Chem. Phys. 2009, 131 014106
16. http://cp2k.berlios.de.
17. Declerck, R.; Pauwels, E.; Van Speybroeck, V.; Waroquier, M. J. Phys. Chem. B 2008, 112, 1508-1514
18. Tarpan, M.; Sagstuen, E.; Pauwels, E.; Vrielinck, H.; Waroquier, M.; Callens, F. J. Phys. Chem. A 2008, 112, 3898-3905
19. Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249
20. Laino, T.; Mohamed, F.; Laio, A.; Parrinello, M. J. Chem. Theory Comput. 2005, 1, 1176-1184
21. Senn, H. M.; Thiel, W. Angew. Chem., Int. Ed. 2009, 48, 1198-1229
22. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Theory and Implementation. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John von Neumann-Institute for Computing: Jülich, 2000; p 301.
23. Salzmann, S.; Silva, M. R.; Thiel, W.; Marian, C. M. J. Phys. Chem. B 2009, 113, 15610-15618
24. Durbeej, B.; Eriksson, L. A. J. Am. Chem. Soc. 2000, 122, 10126-10132
25. Zheng, X. H.; Garcia, J.; Stuchebrukhov, A. A. J. Phys. Chem. B 2008, 112, 8724-8729
26. Eisenberg, A. S.; Schelvis, J. P. M. J. Phys. Chem. A 2008, 112, 6179-6189
27. Garcia, J. I.; Medina, M.; Sancho, J.; Alonso, P. J.; Gomez-Moreno, C.; Mayoral, J. A.; Martinez, J. I. J. Phys. Chem. A 2002, 106, 4729-4735
28. Weber, S.; Mobius, K.; Richter, G.; Kay, C. W. M. J. Am. Chem. Soc. 2001, 123, 3790-3798
29. http://www.rcsb.org.
30. Wohlfahrt, G.; Witt, S.; Hendle, J.; Schomburg, D.; Kalisz, H. M.; Hecht, H. Acta Crystallogr., Sect. D 1999, 55, 969-977
31. van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701-1718
32. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656-1676
33. van den Berg, P. A. W.; Feenstra, K. A.; Mark, A. E.; Berendsen, H. J. C.; Visser, A. J. W. G. J. Phys. Chem. B 2002, 106, 8858-8869
34. Perdew, J. P.; Burke, K.; Ernzerhof, M. Phys. Rev. Lett. 1996, 77, 3865-3868
35. Lippert, G.; Hutter, J.; Parrinello, M. Mol. Phys. 1997, 92, 477-487
36. Lippert, G.; Hutter, J.; Ballone, P.; Parrinello, M. J. Phys. Chem. 1996, 100, 6231-6235
37. Goedecker, S.; Teter, M.; Hutter, J. Phys. Rev. B 1996, 54, 1703-1710
38. Hartwigsen, C.; Goedecker, S.; Hutter, J. Phys. Rev. B 1998, 58, 3641-3662
39. Krack, M.; Parrinello, M. Phys. Chem. Chem. Phys. 2000, 2, 2105-2112
40. Godbout, N.; Salahub, D. R.; Andzelm, J.; Wimmer, E. Can. J. Chem. 1992, 70, 560-571
41. Nosé, S. J. Chem. Phys. 1984, 81, 511-519
42. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision D.01; Gaussian, Inc.: Wallingford, CT, 2004.
43. Neese, F. ORCA-an ab initio, Density Functional and Semiempirical program package, Version 2.7; University of Bonn: Germany, 2008.
44. Kaupp, M. Ab initio and Density Functional Calculations of Electronic g -Tensors for Organic Radicals. In EPR Spectroscopy of Free Radicals in Solids-Trends in Methods and Applications; Lund, A.; Shiotani, M., Eds.; Kluwer: Dordrecht, 2003; p 267.
45. Neese, F. J. Chem. Phys. 2001, 115, 11080-11096
46. Koseki, S.; Schmidt, M. W.; Gordon, M. S. J. Phys. Chem. 1992, 96, 10768-10772
47. Schreckenbach, G.; Ziegler, T. J. Phys. Chem. A 1997, 101, 3388-3399
48. Pickard, C. J.; Mauri, F. Phys. Rev. Lett. 2002, 88 08643
49. Neese, F. J. Chem. Phys. 2005, 122 034107
50. Keith, T. A.; Bader, R. F. W. Chem. Phys. Lett. 1993, 210, 223-231
51. Schleicher, E.; Wenzel, R.; Ahmad, M.; Batschauer, A.; Essen, L. O.; Hitomi, K.; Getzoff, E. D.; Bittl, R.; Weber, S.; Okafuji, A. Appl. Magn. Reson. 2010, 37, 339-352
52. Schleicher, E.; Hitomi, K.; Kay, C. W. M.; Getzoff, E. D.; Todo, T.; Weber, S. J. Biol. Chem. 2007, 282, 4738-4747
53. Su, Q.; Klinman, J. P. Biochemistry 1999, 38, 8572-8581
54. Roth, J. P.; Klinman, J. P. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 62-67
55. Wohlfahrt, G.; Trivic, S.; Zeremski, J.; Pericin, D.; Leskovac, V. Mol. Cell. Biochem. 2004, 260, 69-83
56. Leskovac, V.; Trivic, S.; Wohlfahrt, G.; Kandrac, J.; Pericin, D. Int. J. Biochem. Cell Biol. 2005, 37, 731-750
57. Zheng, Y. J.; Ornstein, R. L. J. Am. Chem. Soc. 1996, 118, 9402-9408
58. Kitzing, K.; Fitzpatrick, T. B.; Wilken, C.; Sawa, J.; Bourenkov, G. P.; Macheroux, P.; Clausen, T. J. Biol. Chem. 2005, 280, 27904-27913
59. Lyubimov, A. Y.; Heard, K.; Tang, H.; Sampson, N. S.; Vrielink, A. Protein Sci. 2007, 16, 2647-2656
60. van den Hemel, D.; Brigé, A.; Savvides, S. N.; Van Beeumen, J. J. Biol. Chem. 2006, 281, 28152-28161
61. Pauwels, E.; Van Speybroeck, V.; Waroquier, M. J. Phys. Chem. A 2004, 108, 11321-11332
62. Hermosilla, L.; Calle, P.; Garcia de la Vega, J. M.; Sieiro, C. J. Phys. Chem. A 2006, 110, 13600-13608
63. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2 nd ed.; Academic Press: New York, 2001.
64. De Cooman, H.; Vanhaelewyn, G.; Pauwels, E.; Sagstuen, E.; Waroquier, M.; Callens, F. J. Phys. Chem. B 2008, 112, 15045-15053
65. Pauwels, E.; De Cooman, H.; Vanhaelewyn, G.; Sagstuen, E.; Callens, F.; Waroquier, M. J. Phys. Chem. B 2008, 112, 15054-15063
66. Fittipaldi, M.; Steiner, R. A.; Matsushita, M.; Dijkstra, B. W.; Groenen, E. J. J.; Huber, M. Biophys. J. 2003, 85, 4047-4054
67. Sottini, S.; Gast, P.; Blok, A.; Canters, G. W.; Cavazzini, D.; Rossi, G. L.; Groenen, E. J. J. Appl. Magn. Reson. 2010, 37, 219-227
68. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38