Iranian Journal of Chemistry

Iranian Journal of Chemistry

Theoretical Study of the kinetic-isotope effect on the catalytic reaction of the Escherichia coli Glyoxalase I

Document Type : Original Article

Authors
Khaled Hoseyni 1
Behnaz Farshidfar 1
Mehdi Irani 2
1 Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran
2 Department of Chemistry, Faculty of Science, University of Kurdistan ,Sanandaj , Iran
10.22036/cr.2021.284416.1142
Abstract
In this work, the density functional theory is used to study the kinetic-isotope effect on the catalytic reaction on the S-substrate of Escherichia coli Glyoxalase I. The quantum mechanical cluster approach was used to model the enzyme’s active site based on its crystal structure. Energies of the stationary structure along the reaction path were optimized, and their energies were calculated. The effect of the solvent on the energy profiles was calculated by the CPCM model. Results show that replacing H1 (hydrogen atom attached to the chiral carbon of substrate) with deuterium increases the activation energy of the reaction and gives a value greater than 2 for kH/kD. This result confirms that breaking the H1-C1 happens in the rate-determining step of the reaction. Also, results showed that replacing the H2 atom (hydrogen atom of the alcohol group of the substrate) gives a kH/kD less than 1.0 and introduces a reverse isotopic effect to the reaction.

Graphical Abstract

Theoretical Study of the kinetic-isotope effect on the catalytic reaction of the Escherichia coli Glyoxalase I
Keywords
DFT
Glyoxalase I
Kinetic-Isotope
Mechanism
  1. D. Roston, Z. Islam, A. Kohen, Mol. 18, (2013).
  2. P. Georgieva, F. Himo, J. Comput. Chem. 31, 1707, (2010).
  3. P.E.M. Siegbahn, F. Himo, Wiley Interdiscip. Rev. Comput. Mol. Sci. 1, 323, (2011).
  4. A.T. Lee, A. Plump, C. DeSimone, A. Cerami, R. Bucala, Diabetes. 44, 20, (1995).
  5. N. Murata-Kamiya, H. Kamiya, H. Kaji, H. Kasai, Mutat. Res. Genet. Toxicol. Environ. Mutagen. 468, 173, (2000).
  6. C. Sibbersen, J. Palmfeldt, J. Hansen, N. Gregersen, K.A. Jørgensen, M. Johannsen, Chem. Commun. 49, 4012, (2013).
  7. S. Yamazoye, J. Biochem. 23, 319, (1936).
  8. M.M. He, S.L. Clugston, J.F. Honek, B.W. Matthews, Biochemistry. 39, 8719, (2000).
  9. A.D. Cameron, M. Ridderström, B. Olin, M.J. Kavarana, D.J. Creighton, B. Mannervik, Biochemistry. 38, 13480, (1999).
  10. S. Jafari, U. Ryde, A.E.A. Fouda, F.S. Alavi, G. Dong, M. Irani, Inorg. Chem. 59, 2594, (2020).
  11. U. Richter, M. Krauss, J. Am. Chem. Soc. 123, 6973, (2001).
  12. D.J. Creighton, D.S. Hamilton, Arch. Biochem. Biophys. 387, 1, (2001).
  13. A.D. Becke, Phys. Rev. A. 38, 3098, (1988).
  14. C. Lee, W. Yang, R.G. Parr, Phys. Rev. B. 37, 785, (1988).
  15. D.J. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenb, Gaussian, Inc. Wallingford CT. (2009).
  16. G.A. Petersson, M.A. Al‐Laham, J. Chem. Phys. 94, 6081, (1991).
  17. P.J. Hay, W.R. Wadt, J. Chem. Phys. 82, 270, (1985).
  18. V.B. and M. Cossi, V. Barone, M. Cossi, J. Phys. Chem. A. 102, 1995, (1998).
  19. S. Parvaneh, H. Parsa, M. Irani, Comput. Theor. Chem. 1188, 112944, (2020).
  20. P.E.M. Siegbahn, ChemPhysChem. 12, 3274, (2011).
  21. F. Himo, P.E.M. Siegbahn, J. Am. Chem. Soc. 123, 10280, (2001).
  22. I. Feierberg, A.D. Cameron, J. Åqvist, FEBS Lett. 453, 90, (1999).
  23. K.Y. Mullings, N. Sukdeo, U. Suttisansanee, Y. Ran, J.F. Honek, J. Inorg. Biochem. 108, 133, (2012).
  24. M.J. Maroney, S. Ciurli, Chem. Rev. 114, 4206, (2014).
Iranian Journal of Chemistry
Volume 4, Issue 2 - Serial Number 7
February 2022
Pages 103-107

  • Receive Date 03 May 2021
  • Revise Date 09 October 2021
  • Accept Date 23 October 2021