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

  • PROCEEDINGS OF THE CONFERENCE “PHYSICAL CHEMISTRY IN RUSSIA AND BEYOND: FROM QUANTUM CHEMISTRY TO EXPERIMENT” (CHERNOGOLOVKA)
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Abstract

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.

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REFERENCES

  1. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976). https://doi.org/10.1016/0022-2836(76)90311-9

    Article  CAS  PubMed  Google Scholar 

  2. A. V. Nemukhin, B. L. Grigorenko, S. V. Lushchekina, et al., Russ. Chem. Rev. 81, 1011 (2012). https://doi.org/10.1070/RC2012v081n11ABEH004311

    Article  CAS  Google Scholar 

  3. E. D. Kots, M. G. Khrenova, A. V. Nemukhin, et al., Russ. Chem. Rev. 88, 1 (2019). https://doi.org/10.1070/RCR4842

    Article  CAS  Google Scholar 

  4. A. K. Mishra and D. G. Lambright, Biopolymers 105, 431 (2016). https://doi.org/10.1002/bip.22833

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  6. B. L. Grigorenko, E. D. Kots, and A. V. Nemukhin, Org. Biomol. Chem. 17, 4879 (2019). https://doi.org/10.1039/C9OB00463G

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  PubMed  Google Scholar 

  8. B. L. Grigorenko, M. G. Khrenova, and A. V. Nemukhin, Phys. Chem. Chem. Phys. 20, 23827 (2018). https://doi.org/10.1039/c8cp04817g

    Article  CAS  PubMed  Google Scholar 

  9. C. Kötting and K. Gerwert, Biol. Chem. 396, 131 (2015). https://doi.org/10.1515/hsz-2014-0219

    Article  CAS  PubMed  Google Scholar 

  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

    Article  CAS  Google Scholar 

  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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. T. Domratcheva, E. Hartmann, I. Schlichting, and T. Kottke, Sci. Rep. 6, 22669 (2016). https://doi.org/10.1038/srep22669

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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

    Article  CAS  Google Scholar 

  14. C. Adamo and V. Barone, J. Chem. Phys. 110, 6158 (1999). https://doi.org/10.1063/1.478522

    Article  CAS  Google Scholar 

  15. S. Grimme, J. Antony, S. Ehrlich, et al., J. Chem. Phys. 132, 154104 (2010). https://doi.org/10.1063/1.3382344

    Article  CAS  Google Scholar 

  16. W. D. Cornell, P. Cieplak, C. I. Bayly, et al., J. Am. Chem. Soc. 117, 5179 (1995). https://doi.org/10.1021/ja00124a002

    Article  CAS  Google Scholar 

  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

    Article  CAS  Google Scholar 

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ACKNOWLEDGMENTS

This work was supported by the Russian Scientific Foundation, project no. 19-73-20032. The calculations were performed on the equipment of the shared resource center of Moscow State University’s high-performance computing resources and the Russian Academy of Sciences’ Joint Supercomputer Center.

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Authors and Affiliations

  1. Department of Chemistry, Moscow State University, 119991, Moscow, Russia

    B. L. Grigorenko & A. V. Nemukhin

  2. Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia

    B. L. Grigorenko & A. V. Nemukhin

Authors
  1. B. L. Grigorenko
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  2. A. V. Nemukhin
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Correspondence to A. V. Nemukhin.

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Translated by K. Gumerov

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Grigorenko, B.L., Nemukhin, A.V. Theoretical Vibrational Spectra of Reaction Intermediates in the Active Site of Guanosine Triphosphate Binding Proteins. Russ. J. Phys. Chem. 94, 914–918 (2020). https://doi.org/10.1134/S0036024420050088

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  • DOI: https://doi.org/10.1134/S0036024420050088

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