A strenuous experimental journey searching for spectroscopic evidence of a bridging nickel-iron-hydride in [NiFe] hydrogenase

Journal of Synchrotron Radiation

Volumn 22, Issue , 2015, Pages 1334-1344

  Wang, Hongxin ^a,b   Yoda, Yoshitaka ^c   Ogata, Hideaki ^d   Tanaka, Yoshihito ^c,e   Lubitz, Wolfgang ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c Institute of Physical and Chemical Research   (Japan)

^d MAX PLANCK INSTITUTE FOR CHEMICAL ENERGY CONVERSION   (Germany)

^e UNIVERSITY OF HYOGO   (Japan)

Author keywords

iron hydride; Ni H Fe wag mode; Ni R; NRVS; nuclear resonance vibrational spectroscopy; ultra weak signal; NiFe hydrogenase

Indexed keywords

DENSITY FUNCTIONAL THEORY; HYDRIDES; IRON; PROBABILITY DENSITY FUNCTION; SPECTROSCOPY; SYNCHROTRON RADIATION; VIBRATIONAL SPECTROSCOPY;

IRON HYDRIDE; NRVS; NUCLEAR RESONANCE VIBRATIONAL SPECTROSCOPY; ULTRA-WEAK; [NIFE]-HYDROGENASE;

NICKEL;

HYDROGEN; HYDROGENASE; NICKEL-IRON HYDROGENASE; PROTEIN BINDING;

BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ENZYME ACTIVATION; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROCEDURES;

BINDING SITES; COMPUTER SIMULATION; ENZYME ACTIVATION; HYDROGEN; HYDROGEN BONDING; HYDROGENASE; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; PROTEIN BINDING;

EID: 84946716106     PISSN: 09090495     EISSN: 16005775     Source Type: Journal    
DOI: 10.1107/S1600577515017816     Document Type: Article

References (61)

1. Amara, P., Volbeda, A., Fontecilla-Camps, J. C. & Field, M. J. (1999). J. Am. Chem. Soc. 121, 4468-4477.
2. Armstrong, F. A. (2009). Photosynth. Res. 102, 541-550.
3. Armstrong, F. A., Belsey, N. A., Cracknell, J. A., Goldet, G., Parkin, A., Reisner, E., Vincent, K. A. & Wait, A. F. (2009). Chem. Soc. Rev. 38, 36-51.
4. Barilone, J. L., Ogata, H., Lubitz, W. & van Gastel, M. (2015). Phys. Chem. Chem. Phys. 17, 16204-16212.
5. Barton, B. E., Whaley, C. M., Rauchfuss, T. B. & Gray, D. L. (2009). J. Am. Chem. Soc. 131, 6942-6943.
6. Bergmann, U., Sturhahn, W., Linn, D. E., Jenney, F. E., Adams, M. W. W., Rupnik, K., Hales, B. J., Alp, E. E., Mayse, A. & Cramer, S. P. (2003). J. Am. Chem. Soc. 125, 4016-4017.
7. Brecht, M., van Gastel, M., Buhrke, T., Friedrich, B. & Lubitz, W. (2003). J. Am. Chem. Soc. 125, 13075-13083.
8. Cammack, R., Frey, M. & Robson, R. (2001). Editors. Hydrogen as a Fuel: Learning from Nature. New York: Taylor & Francis.
9. Cramer, S. P., Xiao, Y., Wang, H., Guo, Y. & Smith, M. C. (2007). Hyperfine Interact. 170, 47-54.
10. Crossland, J. L., Young, D. M., Zakharov, L. N. & Tyler, D. R. (2009). Dalton Trans. 2009, 9253-9259.
11. De Lacey, A. L., Fernández, V. M., Rousset, M. & Cammack, R. (2007). Chem. Rev. 107, 4304-4330.
12. Do, L. H.,Wang, H., Tinberg, C. E., Dowty, E., Yoda, Y., Cramer, S. P. & Lippard, S. J. (2011). Chem. Commun. 47, 10945-10947.
13. Dole, F., Fournel, A., Magro, V., Hatchikian, E. C., Bertrand, P. & Guigliarelli, B. (1997). Biochemistry, 36, 7847-7854.
14. Dong, W., He, P., Wang, J., Zhou, Z. & Wang, H. (2013). Infrared Phys. Technol. 56, 51-56.
15. Evans, R. M., Parkin, A., Roessler, M. M., Murphy, B. J., Adamson, H., Lukey, M. J., Sargent, F., Volbeda, A., Fontecilla-Camps, J. C. & Armstrong, F. A. (2013). J. Am. Chem. Soc. 135, 2694-2707.
16. Foerster, S., Stein, M., Brecht, M., Ogata, H., Higuchi, Y. & Lubitz, W. (2003). J. Am. Chem. Soc. 125, 83-93.
17. Fontecilla-Camps, J. C., Volbeda, A., Cavazza, C. & Nicolet, Y. (2007). Chem. Rev. 107, 4273-4303.
18. Fritsch, J., Lenz, O. & Friedrich, B. (2013). Nat. Rev. Microbiol. 11, 106-114.
19. Gastel,M. van, Stein, M., Brecht, M., Schröder, O., Lendzian, F., Bittl, R., Ogata, H., Higuchi, Y. & Lubitz, W. (2005). J. Biol. Inorg. Chem., 11, 41-51.
20. Goto, S., Ishikawa, T., Kitamura, H. & Takahashi, S. (2000). SPring-8 Annual Report pp. 30-35. SPring-8, Hyogo, Japan.
21. Gu, W., Jacquamet, L., Patil, D. S., Wang, H. -X., Evans, D. J., Smith, M. C.,Millar, M., Koch, S., Eichhorn, D. M., Latimer, M. & Cramer, S. P. (2003). J. Inorg. Biochem. 93, 41-51.
22. Guiral, M., Tron, P., Belle, V., Aubert, C., Leger, C., Guigliarelli, B. & Giudici-Orticoni, M. (2006). Int. J. Hydrogen Energy, 31, 1424-1431.
23. Hara, T., Yabashi,M., Tanaka, T., Bizen, T., Goto, S., Marechal, X. M., Seike, T., Tamasaku, K., Ishikawa, T. & Kitamura, H. (2002). Rev. Sci. Instrum. 73, 1125-1128.
24. Heinekey, D. M. (2009). J. Organomet. Chem. 694, 2671-2680.
25. Inada, T., Namba, T., Asai, S., Kobayashi, T., Tanaka, Y., Tamasaku, K., Sawada, K. & Ishikawa, T. (2013). Phys. Lett. B, 722, 301-304.
26. Jayapal, P., Robinson, D., Sundararajan, M., Hillier, I. H. & McDouall, J. J. W. (2008). Phys. Chem. Chem. Phys. 10, 1734-1738.
27. Jugder, B. E., Welch, J., Aguey-Zinsou, K. F. & Marquis, C. P. (2013). RSC Adv. 3, 8142-8159.
28. Kamali, S., Wang, H., Mitra, D., Ogata, H., Lubitz, W., Manor, B. C., Rauchfuss, T. B., Byrne, D., Bonnefoy, V., Jenney, F. E. Jr, Adams, M. W. W., Yoda, Y., Alp, E., Zhao, J. & Cramer, S. P. (2013). Angew. Chem. Int. Ed. 52, 724-728.
29. Kim, J. Y. H. & Cha, H. J. (2013). Korean J. Chem. Eng. 30, 1-10.
30. Lauterbach, L.,Wang, H., Horch, M., Gee, L. B., Yoda, Y., Tanaka, Y., Zebger, I., Lenz, O. & Cramer, S. P. (2015). Chem. Sci. 6, 1055-1060.
31. Lubitz,W. & Ogata, H. (2013). Encyclopedia of Biological Chemistry, edited by W. J. Lennarz and M. D. Lane, pp. 562-567. London: Academic Press.
32. Lubitz, W., Ogata, H., Rüdiger, O. & Reijerse, E. (2014). Chem. Rev. 114, 4081-4148.
33. Matsumoto, T., Kim, K., Nakai, H., Hibino, T. & Ogo, S. (2013). Chem. Cat. Chem. 5, 1368-1373.
34. Mertens, R. & Liese, A. (2004). Curr. Opin. Biotechnol. 15, 343-348.
35. Ogata, H., Hirota, S., Nakahara, A., Komori, H., Shibata, N., Kato, T., Kano, K. & Higuchi, Y. (2005). Structure, 13, 1635-1642.
36. Ogata, H., Kramer, T., Wang, H., Schilter, D., Pelmenschikov, V., van Gastel, M., Neese, F., Rauchfuss, T. B., Gee, L. B., Scott, A. D., Yoda, Y., Tanaka, Y., Lubitz, W. & Cramer, S. P. (2015). Nat. Commun. 6, 7890.
37. Ogata, H., Nishikawa, K. & Lubitz, W. (2015). Nature, 520, 571-574.
38. Pelmenschikov, V., Guo, Y., Wang, H., Cramer, S. P. & Case, D. A. (2011). Faraday Discuss. 148, 409-420.
39. Schilter, D., Nilges, M. J., Chakrabarti, M., Lindahl, P. A., Rauchfuss, T. B. & Stein, M. (2012). Inorg. Chem. 51, 2338-2348.
40. Seto, M., Yoda, Y., Kikuta, S., Zhang, X. W. & Ando, M. (1995). Phys. Rev. Lett. 74, 3828-3831.
41. Shafaat, H. S., Rüdiger, O., Ogata, H. & Lubitz, W. (2013). Biochim. Biophys. Acta, 1827, 986-1002.
42. Shafaat, H. S., Weber, K., Petrenko, T., Neese, F. & Lubitz, W. (2012). Inorg. Chem. 51, 11787-11797.
43. Simmons, T. R. & Artero, V. (2013). Angew. Chem. Int. Ed. 52, 6143-6145.
44. Smith, M. C., Xiao, Y. M.,Wang, H. X., George, S. J., Coucouvanis, D., Koutmos, M., Sturhahn, W., Alp, E. E., Zhao, J. Y. & Cramer, S. P. (2005). Inorg. Chem. 44, 5562-5570.
45. Sturhahn, W., Toellner, T. S., Alp, E. E., Zhang, X., Ando, M., Yoda, Y., Kikuta, S., Seto, M., Kimball, C. W. & Dabrowski, B. (1995). Phys. Rev. Lett. 74, 3832-3835.
46. Takahashi, S., Aoyagi, H., Mochizuki, T., Oura, M., Sakurai, Y., Watanabe, A. & Kitamura, H. (2001). Nucl. Instrum. Methods Phys. Res. A, 467-468, 758-761.
47. Tanaka, Y., Uozaki, Y., Nozaki, K., Ito, K., Yamasaki, K., Terauchi, H., Takahashi, I. & Ishikawa, T. (2011). J. Phys. Conf. Ser. 278, 012018.
48. Tard, C. & Pickett, C. J. (2009). Chem. Rev. 109, 2245-2274.
49. Tinberg, C. E., Tonzetich, Z. J., Wang, H., Do, L. H., Yoda, Y., Cramer, S. P. & Lippard, S. J. (2010). J. Am. Chem. Soc. 132, 18168-18176.
50. Volbeda, A., Martin, L., Barbier, E., Gutiérrez-Sanz, O., De Lacey, A., Liebgott, P., Dementin, S., Rousset, M. & Fontecilla-Camps, J. (2015). J. Biol. Inorg. Chem. 20, 11-22.
51. Wang, H., Alp, E., Yoda, Y. & Cramer, S. (2014). Methods in Molcular Cell Biology, Vol. 1122, Metalloproteins, edited by J. C. Fontecilla-Camps and Y. Nicolet, pp. 125-137. New Jersey: Humana Press.
52. Wang, H., Patil, D. S., Gu, W., Jacquamet, L., Friedrich, S., Funk, T. & Cramer, S. P. (2001). J. Electron Spectrosc. Relat. Phenom. 114-116, 855-863.
53. Wang, H., Patil, D. S., Ralston, C. Y., Bryant, C. & Cramer, S. P. (2001). J. Electron Spectrosc. Relat. Phenom. 114-116, 865-871.
54. Wang, H. X., Ralston, C. Y., Patil, D. S., Jones, R. M., Gu, W., Verhagen, M., Adams, M., Ge, P., Riordan, C., Marganian, C. A., Mascharak, P., Kovacs, J., Miller, C. G., Collins, T. J., Brooker, S., Croucher, P. D., Wang, K., Stiefel, E. I. & Cramer, S. P. (2000). J. Am. Chem. Soc. 122, 10544-10552.
55. Wang, H., Yoda, Y., Dong, W. & Huang, S. D. (2013). J. Synchrotron Rad. 20, 683-690.
56. Wang, H., Yoda, Y., Kamali, S., Zhou, Z. -H. & Cramer, S. P. (2012). J. Synchrotron Rad. 19, 257-263.
57. Xiao, Y. M., Wang, H. X., George, S. J., Smith, M. C., Adams, M. W. W., Jenney, F. E., Sturhahn, W., Alp, E. E., Zhao, J. O., Yoda, Y., Dey, A., Solomon, E. I. & Cramer, S. P. (2005). J. Am. Chem. Soc. 127, 14596-14606.
58. Yabashi, M., Mochizuki, T., Yamazaki, H., Goto, S., Ohashi, H., Takeshita, K., Ohata, T., Matsushita, T., Tamasaku, K., Tanaka, Y. & Ishikawa, T. (2001). Nucl. Instrum. Methods Phys. Res. A, 467-468, 678-681.
59. Yang, J. Y., Bullock, M., DuBois, M. R. & DuBois, D. L. (2011). MRS Bull. 36, 39-47.
60. Yoda, Y., Imai, Y., Kobayashi, H., Goto, S., Takeshita, K. & Seto, M. (2012). Nucl. Instrum. Methods Phys. Res. A, 206, 83.
61. Yoda, Y., Yabashi, M., Izumi, K., Zhang, X. W., Kishimoto, S., Kitao, S., Seto, M., Mitsui, T., Harami, T., Imai, Y. & Kikuta, S. (2001). Nucl. Instrum. Methods Phys. Res. A, 467-468, 715-718.