Dynamic investigation of protein metal active sites: Interplay of XANES and molecular dynamics simulations

Journal of the American Chemical Society

Volumn 132, Issue 42, 2010, Pages 14901-14909

  D'Angelo, Paola ^a   Della Longa, Stefano ^b   Arcovito, Alessandro ^c   Anselmi, Massimiliano ^a   Di Nola, Alfredo ^a   Chillemi, Giovanni ^d  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF L'AQUILA   (Italy)

^c CATHOLIC UNIVERSITY   (Italy)

^d CASPUR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; AXIAL LIGAND; BIOLOGICAL FUNCTIONS; COORDINATION GEOMETRY; DYNAMIC INFORMATION; EXPERIMENTAL VALIDATIONS; GEOMETRICAL CONFIGURATIONS; HEME PROTEINS; LOW ENERGIES; MD SIMULATION; METAL CENTERS; METALLO-PROTEINS; METALLOPROTEIN; MOLECULAR DYNAMICS SIMULATIONS; NEUROGLOBIN; NOVEL STRATEGIES; QUANTITATIVE ANALYSIS; STRUCTURAL DISORDERS; STRUCTURAL INFORMATION; STRUCTURAL PARAMETER; X-RAY ABSORPTION NEAR-EDGE STRUCTURE; XANES; XANES SPECTRA;

ABSORPTION SPECTROSCOPY; MOLECULAR DYNAMICS; PORPHYRINS; STRUCTURAL DYNAMICS; STRUCTURAL OPTIMIZATION; SYSTEMATIC ERRORS;

PROTEINS;

CARBON MONOXYNEUROGLOBIN; HEMOPROTEIN; IRON; METALLOPROTEIN; NEUROGLOBIN; UNCLASSIFIED DRUG;

ARTICLE; MOLECULAR DYNAMICS; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; RELIABILITY; ROENTGEN SPECTROSCOPY; STRUCTURE ANALYSIS; SYSTEMATIC ERROR; XANES SPECTROSCOPY;

CATALYTIC DOMAIN; METALS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEINS; SPECTRUM ANALYSIS; X-RAYS;

EID: 77958481880     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja1056533     Document Type: Article

References (53)

1. Cook, J. D., Penner-Hahn, J. E., and Stemmler, T. L. Methods Cell. Biol. 2008, 90, 199-216
2. Strange, R. W. and Feiters, M. C. Curr. Opin. Struct. Biol. 2008, 18, 609-616
3. Lee, P. A. and Pendry, J. B. Phys. Rev. B 1975, 11, 2795-2811
4. Rehr, J. J. and Albers, R. C. Rev. Mod. Phys. 2000, 72, 621-654
5. Natoli, C. R., Benfatto, M., Della Longa, S., and Hatada, K. J. Synchrotron Radiat. 2003, 10, 26-42
6. Rehr, J. J. and Ankudinov, A. L. Coord. Chem. 2005, 249, 131-140
7. D'Angelo, P., Roscioni, O. M., Chillemi, G., Della Longa, S., and Benfatto, M. J. Am. Chem. Soc. 2006, 128, 1853-1858
8. D'Angelo, P., Zitolo, A., Migliorati, V., Mancini, G., Persson, I., and Chillemi, G. Inorg. Chem. 2009, 48, 10239-10248
9. D'Angelo, P., Migliorati, V., Mancini, G., Barone, V., and Chillemi, G. J. Chem. Phys. 2008, 128 084502-6
10. D'Angelo, P., Migliorati, V., Mancini, G., and Chillemi, G. J. Phys. Chem. A 2008, 112, 11833-11841
11. van Gunsteren, W. F., Dolenc, J., and Mark, A. E. Curr. Opin. Struct. Biol. 2008, 18, 149-153
12. Burmester, T., Weich, B., Reinhardt, S., and Hankeln, T. Nature 2000, 407, 520-523
13. Vallone, B., Nienhaus, K., Brunori, M., and Nienhaus, G. U. Proteins 2004, 56, 85-92
14. Pesce, A., Dewilde, S., Nardini, M., Moens, L., Ascenzi, P., Hankeln, T., Burmester, T., and Bolognesi, M. Structure 2003, 11, 1087-1095
15. Dewilde, S., Kiger, L., Burmester, T., Hankeln, T., Baudin-Creuza, V., Aerts, T., Marden, M. C., Caubergs, R., and Moens, L. J. Biol. Chem. 2001, 276, 38949-38955
16. Nienhaus, K., Kriegl, J. M., and Nienhaus, G. U. J. Biol. Chem. 2004, 279, 22944-22952
17. Sun, Y., Jin, K., Mao, X., Zhu, Y., and Greenberg, D. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 15306-15311
18. Sun, Y., Jin, K., Peel, A., Mao, X. O., Xie, L., and Greenberg, D. A. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3497-3500
19. Vallone, B., Nienhaus, K., Matthes, A., Brunori, M., and Nienhaus, G. U. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 17351-17356
20. Anselmi, M., Brunori, M., Vallone, B., and Di Nola, A. Biophys. J. 2007, 93, 434-441
21. Anselmi, M., Brunori, M., Vallone, B., and Di Nola, A. Biophys. J. 2008, 95, 4157-4162
22. Arcovito, A., Moschetti, T., D'Angelo, P., Mancini, G., Vallone, B., Brunori, M., and Della Longa, S. Arch. Biochem. Biophys. 2008, 475, 7-13
23. Benfatto, M. and Della Longa, S. J. Synchrotron Radiat. 2001, 8, 1087-1094
24. Della Longa, S., Arcovito, A., Girasole, M., Hazemann, J. L., and Benfatto, M. Phys. Rev. Lett. 2001, 87, 155501-04
25. D'Angelo, P., Lapi, A., Migliorati, V., Arcovito, A., Benfatto, M., Roscioni, O. M., Meyer-Klaucke, W., and Della Longa, S. Inorg. Chem. 2008, 47, 9905-9918
26. Scherk, C. G., Ostermann, A., Achterhold, K., Iakovleva, O., Nazikkol, C., Krebs, B., Knapp, E. W., Meyer-Klaucke, W., and Parak, F. G. Eur. Biophys. J. 2001, 30, 393-403
27. Green, M. T., Dawson, J. H., and Gray, H. B. Science 2004, 304, 1653-1656
28. Proux, O. Phys. Scr. 2005, T115, 970-973
29. Muller, J. B., Jepsen, O., and Wilkins, J. W. Solid State Commun. 1982, 42, 365-368
30. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
31. Lee, C., Yang, W., and Parr, R. G. Phys. Rev. B 1988, 37, 785-789
32. Schaefer, A., Horn, H., and Ahlrichs, R. J. Chem. Phys. 1992, 97, 2571-2577
33. Loew, G. H. and Harris, D. L. Chem. Rev. 2000, 100, 407-420
34. Smith, D. M. A., Dupuis, M., and Straatsma, T. P. Mol. Phys. 2005, 103, 273-278
35. Harvey, J. N. J. Am. Chem. Soc. 2000, 122, 12401-12402
36. McMahon, B. H., Stojkovic, B. P., Hay, P. J., Martin, R. L., and Garcia, A. E. J. Chem. Phys. 2000, 113, 6831-6850
37. Li, J., Ai, Y. J., Xie, Z. Z., and Fang, W. H. J. Phys. Chem. B 2008, 112, 8715-8723
38. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., and Su, S. J. Comput. Chem. 1993, 14, 1347-1363
39. Breneman, C. M. and Wiberg, K. B. J. Comput. Chem. 1990, 11, 361-373
40. Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., and Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel Publishing Co.: Dordrecht, The Netherlands, 1981; pp 331 - 342.
41. Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. Comput. Phys. Commun. 1995, 91, 43-56
42. van Gunsteren, W. F., Billeter, S., Eising, A., Hunenberger, P., Kruger, P., Mark, A. E., Scott, W., and Tironi, I. Biomolecular Simulations: The GROMOS96 Manual and User Guide; BIOMOS BV: Zurich/Groningen, 1996.
43. Oostenbrink, C., Villa, A., Mark, A. E., and van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656-1676
44. Brown, D. and Clarke, J. H. R. Mol. Phys. 1984, 51, 1243-1252
45. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
46. Amadei, A., Linssen, A. B., and Berendsen, H. J. Proteins 1993, 17, 412-425
47. D'Angelo, P., Zitolo, A., Migliorati, V., and Persson, I. Chem.-Eur. J. 2010, 16, 684-692
48. Chillemi, G., Mancini, G., Sanna, N., Barone, V., Della Longa, S., Benfatto, M., Pavel, N. V., and D'Angelo, P. J. Am. Chem. Soc. 2007, 129, 5430-5436
49. Hayakawa, K., Hatada, K., D'Angelo, P., Della Longa, S., Natoli, C. R., and Benfatto, M. J. Am. Chem. Soc. 2004, 126, 15618-15623
50. D'Angelo, P., Benfatto, M., Della Longa, S., and Pavel, N. V. Phys. Rev. B 2002, 66 064209
51. Arcovito, A., Ardiccioni, C., Cianci, M., D'Angelo, P., Vallone, B., and Della Longa, S. J. Phys. Chem. B [Online early access]. DOI: 10.1021/jp104395g. Published Online: Sept 29, 2010.
52. Banci, L. Curr. Opin. Chem. Biol. 2003, 7, 143-149
53. Shi, W. and Chance, M. R. Cell. Mol. Life Sci. 2008, 65, 3040-3048