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Статья
2020

Theoretical Vibrational Spectra of Reaction Intermediates in the Active Site of Guanosine Triphosphate Binding Proteins


B. L. GrigorenkoB. L. Grigorenko, A. V. NemukhinA. V. Nemukhin
Российский журнал физической химии А
https://doi.org/10.1134/S0036024420050088
Abstract / Full Text

Calculations of the structures and energies of intermediates of the enzymatic hydrolysis of guanosine triphosphate, performed by means of quantum mechanics and molecular mechanics (QM/MM), suggest a mechanism for chemical transformations of reaction particles in an active site that assumes an amide-imide tautomerism of the side chain of glutamine residue. Positions of vibrational bands and a corresponding band shift upon isotopic substitution 14N → 15N in the side chain of glutamine residue in the active site are predicted for experimental verification of the given mechanism via IR spectroscopy.

Author information
  • Department of Chemistry, Moscow State University, 119991, Moscow, RussiaB. L. Grigorenko & A. V. Nemukhin
  • Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119334, Moscow, RussiaB. L. Grigorenko & A. V. Nemukhin
References
  1. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976). https://doi.org/10.1016/0022-2836(76)90311-9
  2. A. V. Nemukhin, B. L. Grigorenko, S. V. Lushchekina, et al., Russ. Chem. Rev. 81, 1011 (2012). https://doi.org/10.1070/RC2012v081n11ABEH004311
  3. E. D. Kots, M. G. Khrenova, A. V. Nemukhin, et al., Russ. Chem. Rev. 88, 1 (2019). https://doi.org/10.1070/RCR4842
  4. A. K. Mishra and D. G. Lambright, Biopolymers 105, 431 (2016). https://doi.org/10.1002/bip.22833
  5. A. T. P. Carvalho, K. Szeler, K. Vavitsas, et al., Arch. Biochem. Biophys. 582, 80 (2015). https://doi.org/10.1016/j.abb.2015.02.027
  6. B. L. Grigorenko, E. D. Kots, and A. V. Nemukhin, Org. Biomol. Chem. 17, 4879 (2019). https://doi.org/10.1039/C9OB00463G
  7. M. G. Khrenova, B. L. Grigorenko, A. B. Kolomeisky, and A. V. Nemukhin, J. Phys. Chem. B 119, 12838 (2015). https://doi.org/10.1021/acs/jpcb.5b07238
  8. B. L. Grigorenko, M. G. Khrenova, and A. V. Nemukhin, Phys. Chem. Chem. Phys. 20, 23827 (2018). https://doi.org/10.1039/c8cp04817g
  9. C. Kötting and K. Gerwert, Biol. Chem. 396, 131 (2015). https://doi.org/10.1515/hsz-2014-0219
  10. M. G. Khrenova, B. L. Grigorenko, and A. V. Nemukhin, Spectrochim. Acta, Part A 166, 68 (2016). https://doi.org/10.1016/j.saa.2016.04.056
  11. T. Domratcheva, B. L. Grigorenko, I. Schlichting, and A. V. Nemukhin, Biophys. J. 94, 3872 (2008). https://doi.org/10.1529/biophysj.107.124172
  12. T. Domratcheva, E. Hartmann, I. Schlichting, and T. Kottke, Sci. Rep. 6, 22669 (2016). https://doi.org/10.1038/srep22669
  13. A. K. Scheffzek, M. R. Ahmadian, W. Kabsch, et al., Science (Washington, D.C., U. S.) 277, 333 (1997). https://doi.org/10.1126/science.277.5324.333
  14. C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999). https://doi.org/10.1063/1.478522
  15. S. Grimme, J. Antony, S. Ehrlich, et al., J. Chem. Phys. 132, 154104 (2010). https://doi.org/10.1063/1.3382344
  16. W. D. Cornell, P. Cieplak, C. I. Bayly, et al., J. Am. Chem. Soc. 117, 5179 (1995). https://doi.org/10.1021/ja00124a002
  17. M. Valiev, E. J. Bylaska, N. Govind, et al., Comput. Phys. Commun. 181, 1477 (2010). https://doi.org/10.1016/j.cpc.2010.04.018