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Russian Journal of Physical Chemistry A

, Volume 88, Issue 7, pp 1248–1254 | Cite as

The effect of glutamic acid side chain on acidity constant of lysine in beta-sheet: A density functional theory study

  • M. SargolzaeiEmail author
  • M. Afshar
  • M. S. Sadeghi
  • M. Kavee
Biophysical Chemistry

Abstract

In this work, the possibility of proton transfer between side chain of lysine and glutamic acid in peptide of Glu-Ala-Lys+ was demonstrated using density functional theory (DFT). We have shown that the proton transfer takes place between side chain of glutamic and lysine residues through the hydrogen bond formation. The structures of transition state for proton transfer reaction were detected in gas and solution phases. Our kinetic studies show that the proton transfer reaction rate in gas phase is higher than solution phase. The ionization constant (pK a) value of lysine residue in peptide was estimated 1.039 which is lower than intrinsic pK a of lysine amino acid.

Keywords

ionization constants ab initio Gibbs free energy density functional calculations 

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References

  1. 1.
    M. Namazian and H. Heidary, J. Mol. Struct. (Theochem) 620, 257 (2003).CrossRefGoogle Scholar
  2. 2.
    K. B. Schowen, H. H. Limbach, G. S. Denisov, and R. L. Schowen, Biochim. Biophys. Acta 1458, 43 (2000).CrossRefGoogle Scholar
  3. 3.
    L. Sirovich and J. D. Rodriguez, Phys. Lett. A 120, 211 (1987).CrossRefGoogle Scholar
  4. 4.
    G. Schüürmann, M. Cossi, V. Barone, and J. Tomasi, J. Phys. Chem. A 102, 6706 (1998).CrossRefGoogle Scholar
  5. 5.
    R. E. Georgescu, E. G. Alexov, and M. R. Gunner, Biophys. J. 83, 1731 (2002).CrossRefGoogle Scholar
  6. 6.
    A. Warshel, Biochem. J. 20, 3167 (1981).CrossRefGoogle Scholar
  7. 7.
    C. Lim, D. Bashford, and M. Karplus, J. Phys. Chem. 95, 5610 (1991).CrossRefGoogle Scholar
  8. 8.
    P.-T. Chen, C.-C. Wang, J.-C. Jiang, H.-K. Wang, and M. Hayashi, J. Phys. Chem. B 115, 1485 (2011).CrossRefGoogle Scholar
  9. 9.
    P. Kulhánek, E. W. Schlag, and J. Koca, J. Am. Chem. Soc. 125, 13678 (2003).CrossRefGoogle Scholar
  10. 10.
    P. Hudáky and A. Perczel, J. Phys. Chem. A 108, 6195 (2004).CrossRefGoogle Scholar
  11. 11.
    R. I. Najafabadi, M. R. Housaindokht, M. S. Sadeghi Googheri, M. Sargolzaei, and M. Izadyar, Int. J. Quantum Chem. 112, 2675 (2012).CrossRefGoogle Scholar
  12. 12.
    M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian 03, Revision B.03 (Gaussian Inc., Wallingford, CT, 2004).Google Scholar
  13. 13.
    A. D. Becke, J. Chem. Phys. 98, 5648 (1993).CrossRefGoogle Scholar
  14. 14.
    R. G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford Univ. Press, New York, 1989).Google Scholar
  15. 15.
    S. Miertuš, E. Scrocco, and J. Tomasi, Chem. Phys. 55, 117 (1981).CrossRefGoogle Scholar
  16. 16.
    A. E. Reed, L. A. Curtiss, and F. Weinhold, Chem. Rev. 88, 899 (1988).CrossRefGoogle Scholar
  17. 17.
    R. F. W. Bader, Atoms in Molecules: A Quantum Theory (Oxford Univ. Press, UK (1990)).Google Scholar
  18. 18.
    R. Bader, Atoms in Molecules: A Quantum Theory (Oxford Univ. Press, USA, 1994).Google Scholar
  19. 19.
    R. F. W. Bader, Chem. Rev. 91, 893 (1991).CrossRefGoogle Scholar
  20. 20.
    R. F. W. Bader, Acc. Chem. Res. 18, 9 (1985).CrossRefGoogle Scholar
  21. 21.
    H. Eyring, J. Chem. Phys. 3, 107 (1935).CrossRefGoogle Scholar
  22. 22.
    E. Espinosa, E. Molins, and C. Lecomte, Chem. Phys. Lett. 285, 170 (1998).CrossRefGoogle Scholar
  23. 23.
    Y. Nozaki and C. Tanford, Meth. Enz. 11, 715734 (1967).Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2014

Authors and Affiliations

  • M. Sargolzaei
    • 1
    Email author
  • M. Afshar
    • 2
  • M. S. Sadeghi
    • 3
  • M. Kavee
    • 4
  1. 1.Department of ChemistryShahrood University of TechnologyShahroodIran
  2. 2.Department of PhysicsIran University of Science and TechnologyNarmak TehranIran
  3. 3.Department of ChemistryIslamic Azad University, Science and Research, Sirjan BranchArakIran
  4. 4.Department of ChemistryIslamic Azad University, Marvdasht BranchArakIran

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