Journal of Structural Chemistry

, Volume 60, Issue 6, pp 942–951 | Cite as

Mobility of Water, Urea and Trimethylamine-N-Oxide Molecules in the Vicinity of Globular Protein

  • V. P. Voloshin
  • N. N. MedvedevEmail author


Molecular mobility in the hydration shell of the SNase globular protein in an aqueous solution with cosolvents (urea and trimethylamine oxide) is studied using all-atom molecular dynamic simulations. Average displacements of the molecules initially located in the successive layers around the protein are calculated over the same short period of time to characterize the diffusion mobility of the molecules depending on the distance to the protein. It is shown that solvent molecules have lower mobility near the protein, and the mobility of more distant molecules increases irregularly and correlates with the positions of the distribution function maxima of these molecules around the protein. After the second maximum of these functions, the mobility reaches its bulky values both for water and the cosolvent.


molecular dynamic modeling aqueous solutions trimethylamine-N-oxide urea hydration shell cosolvents 


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  1. 1.
    P. H. Yancey, M. E. Clark, S. C. Hand, R. D. Bowlus, and G. N. Somero. Science, 1982, 217, 1214.CrossRefGoogle Scholar
  2. 2.
    D. W. Bolen and G. Rose. Annu. Rev. Biochem., 2008, 77, 339.CrossRefGoogle Scholar
  3. 3.
    P. H. Schummel, A. Haag, W. Kremer, H. R. Kalbitzer, and R. Winter. J. Phys. Chem. B, 2016, 120, 6575.CrossRefGoogle Scholar
  4. 4.
    D. R. Canchi, P. Jayasimha, D. C. Rau, G. I. Makhatadze, and F. E. Garcia. J. Phys. Chem. B, 2012, 116, 12095.CrossRefGoogle Scholar
  5. 5.
    E. Schneck, D. Horinek, and R. R. Netz. J. Phys. Chem. B, 2013, 117, 8310.CrossRefGoogle Scholar
  6. 6.
    P. Ganguly, N. F. A. van der Vegt, and J.-E. Shea. J. Phys. Chem. Lett., 2016, 7, 3052.CrossRefGoogle Scholar
  7. 7.
    B. Moeser and D. Horinek. J. Phys. Chem. B, 2014, 118, 107.CrossRefGoogle Scholar
  8. 8.
    D. R. Canchi and A. E. Garcia. Annu. Rev. Phys. Chem., 2013, 64, 273.CrossRefGoogle Scholar
  9. 9.
    L. Larini and J.-E. Shea. J. Phys. Chem. B, 2013, 117, 13268.CrossRefGoogle Scholar
  10. 10.
    M. V. Fedotova, S. E. Kruchinin, and G. N. Chuev. New J. Chem., 2017, 41, 1219.CrossRefGoogle Scholar
  11. 11.
    D. W. Bolen and I. V. Baskakov. J. Mol. Biol, 2001, 310, 955.CrossRefGoogle Scholar
  12. 12.
    S. Paul and G. N. Patey. J. Phys. Chem. B, 2007, 111, 7932.CrossRefGoogle Scholar
  13. 13.
    P. Ganguly, T. Hajari, J.-E. Shea, and N. F. A. van der Vegt. J. Phys. Chem. Lett., 2015, 6, 581.CrossRefGoogle Scholar
  14. 14.
    N. Smolin, V. P. Voloshin, A. V. Anikeenko, A. Geiger, R. Winter, and N. N. Medvedev. Phys. Chem. Chem. Phys., 2017, 19(9), 6345.CrossRefGoogle Scholar
  15. 15.
    E. D. Kadtsyn, A. V. Anikeenko, and N. N. Medvedev. J. Strust. Chem., 2018, 59(2), 347.CrossRefGoogle Scholar
  16. 16.
    B. Bagchi. Chem. Rev., 2005, 105, 3197.CrossRefGoogle Scholar
  17. 17.
    M.-C. Bellissent-Funel, A. Hassanali, M. Havenith, R. Henchman, P. Pohl, F. Sterpone, D. van der Spoel, Y. Xu, and A. E. Garcia. Chem. Rev., 2016, 116, 7611.CrossRefGoogle Scholar
  18. 18.
    D. Laage, T. Elsaesser, and J. T. Hynes. Chem. Rev., 2017, 117, 10694.CrossRefGoogle Scholar
  19. 19.
    A. R. Bizzarri and S. Cannistraro. Phys. Rev. E, 1996, 53(4), R3040.CrossRefGoogle Scholar
  20. 20.
    S. G. Dastidar and C. Mukhopadhyay. Phys. Rev. E, 2003, 68, 021921.CrossRefGoogle Scholar
  21. 21.
    P. Rani and P. Biswas. J. Phys. Chem. B, 2015, 119, 13262.CrossRefGoogle Scholar
  22. 22.
    R. Chitra and S. Yashonath. J. Phys. Chem. B, 1997, 101, 5437.CrossRefGoogle Scholar
  23. 23.
    L. van Hove. Phys. Rev., 1954, 95, 249.CrossRefGoogle Scholar
  24. 24.
    P. Hopkins, A. Fortini, A. J. Archer, and M. Schmidt. J. Chem. Phys., 2010, 133, 224505.CrossRefGoogle Scholar
  25. 25.
    W. Kob and H. C. Andersen. Phys. Rev. E, 1995, 51, 4626.CrossRefGoogle Scholar
  26. 26.
    P. Gallo, R. Pellarin, and M. Rovere. Phys. Rev. E, 2003, 7, 041202.CrossRefGoogle Scholar
  27. 27.
    B. P. Bhowmik, I. Tah, and S Karmakar. Phys. Rev. E, 2018, 98, 022122.CrossRefGoogle Scholar
  28. 28.
    F. Sciortino, P. Gallo, P. Tartaglia, and S.-H. Chen. Phys. Rev., 1996, 54(6), 6331.Google Scholar
  29. 29.
    M. De Marzio, G. Camisasca, M. Rovere, and P. Gallo. J. Chem. Phys., 2017, 146, 084502.CrossRefGoogle Scholar
  30. 30.
    B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. J. Chem. Theory Comput., 2008, 4, 435.CrossRefGoogle Scholar
  31. 31.
    S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl. Bioinformatics, 2013, 29, 845.CrossRefGoogle Scholar
  32. 32.
    W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives. J. Am. Chem. Soc, 1996, 118, 11225.CrossRefGoogle Scholar
  33. 33.
    H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma. J. Phys. Chem., 1987, 91, 6269.CrossRefGoogle Scholar
  34. 34.
    S. Weerasinghe and P. E. Smith. J. Phys. Chem. B, 2003, 107, 3891.CrossRefGoogle Scholar
  35. 35.
    L. Larini and J.-E. Shea. J. Phys. Chem. B, 2013, 117, 13268.CrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Inc. 2019

Authors and Affiliations

  1. 1.Voevodsky Institute of Chemical Kinetics and Combustion, Siberian BranchRussian Academy of SciencesNovosibirskRussia
  2. 2.Novosibirsk State UniversityNovosibirskRussia

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