Skip to main content
SpringerLink
Log in

Calculation of mobility and entropy of the binding of molecules by crystals

  • Structural and Functional Analysis of Biopolymers and Their Complexes
  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

A simple method for evaluating a range of molecular movements in crystals has been developed. This estimate is needed to calculate the entropy of binding, in particular in protein–ligand complexes. The estimate is based on experimental data concerning the enthalpy of sublimation and saturated vapor pressure obtained for 15 organic crystals with melting temperatures of 25–80°С. For this set, we calculated the values of the average range and the corresponding average amplitude of molecular movements in crystals that constituted 0.75 ± 0.14 Å and 0.18 ± 0.03 Å, respectively. The entropy of sublimation calculated based on the average range of molecular movements in crystals was well consistent with the experimental data.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Shaw D.E., Maragakis P., Lindorff-Larsen K., Piana S., Dror R.O., Eastwood M.P., Bank J.A., Jumper J.M., Salmon J.K., Shah Y., Wriggers W. 2010. Atom-level characterization of structural dynamics of proteins. Science. 330, 341–346.

    Article  CAS  PubMed  Google Scholar 

  2. Abagyan R. 2012. Computational chemistry in 25 years. J. Comput. Aided Mol. Des. 26, 9–10.

    Article  CAS  PubMed  Google Scholar 

  3. Bajorath J. 2012. Computational chemistry in pharmaceutical research: At the crossroads. J. Comput. Aided Mol. Des. 26, 11–12.

    Article  CAS  PubMed  Google Scholar 

  4. Huang N., Jacobson M.P. 2007. Physics-based methods for studying protein–ligand interactions. Curr. Opin. Drug Discov. Dev. 10, 325–331.

    CAS  Google Scholar 

  5. Borhani D.W., Shaw D.E. 2012. The future of molecular dynamics simulations in drug discovery. J. Comput. Aided Mol. Des. 26, 15–26.

    Article  CAS  PubMed  Google Scholar 

  6. Steinbrecher T., Labahn A. 2010. Towards accurate free energy calculations in ligand–protein binding studies. Curr. Med. Chem. 17, 767–785.

    Article  CAS  PubMed  Google Scholar 

  7. Muzzioli E., Del Rio A., Rastelli G. 2011. Assessing protein kinase selectivity with molecular dynamics and mm-pbsa binding free energy calculations. Chem. Biol. Drug Des. 78, 252–259.

    Article  CAS  PubMed  Google Scholar 

  8. Jain A.N. 2006. Scoring functions for protein-ligand docking. Curr. Protein Pept. Sci. 7, 407–420.

    Article  CAS  PubMed  Google Scholar 

  9. Joseph-McCarthy D., Baber J.C., Feyfant E., Thompson D.C., Humblet C. 2007. Lead optimization via high-throughput molecular docking. Curr. Opin. Drug Discov. Devel. 10, 264–274.

    CAS  PubMed  Google Scholar 

  10. Clark R.D., Waldman M. 2012. Lions and tigers and bears, oh my! Three barriers to progress in computeraided molecular design. J. Comput. Aided Mol. Des. 26, 29–34.

    Article  CAS  PubMed  Google Scholar 

  11. Gao C., Park M.-S., Stern H.A. 2010. Accounting for ligand conformational restriction in calculations of protein–ligand binding affinities. Biophys. J. 98, 901–910.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Pickett, S. D., and M. J. Sternberg. 1993. Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 231, 825–839.

    Article  CAS  PubMed  Google Scholar 

  13. Finkelstein A.V., Janin J. 1989. The price of lost freedom. Protein Eng. 3, 1–3.

    Article  CAS  PubMed  Google Scholar 

  14. Kortemme T, Baker D. 2002. A simple physical model for binding energy hot spots in protein-protein complexes. Proc. Natl. Acad. Sci. U. S. A. 99, 14116–14121.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Lee J., Seok C. 2008. A statistical rescoring scheme for protein–ligand docking: Consideration of entropic effect. Proteins. 15, 1074–1083.

    Google Scholar 

  16. Wang J., Hou T. 2012. Develop and test a solvent accessible surface area-based model in conformational entropy calculations. J. Chem. Inf. Model. 25, 1199–1212.

    Article  Google Scholar 

  17. Chiba S., Harano Y., Roth R., Kinoshita M., Sakurai M. 2012. Evaluation of protein–ligand binding free energy focused on its entropic components. J. Comput. Chem. 15, 550–560.

    Article  Google Scholar 

  18. Kamisetty H., Ramanathan A., Bailey-Kellogg C., Langmead C.J. 2011. Accounting for conformational entropy in predicting binding free energies of protein–protein interactions. Proteins. 79, 444–462.

    Article  CAS  PubMed  Google Scholar 

  19. Perola, E., Charifson P. S. 2004. Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding. J. Med. Chem. 47, 2499–2510.

    Article  CAS  PubMed  Google Scholar 

  20. Marshall G.R. 2012. Limiting assumptions in structure- based design: binding entropy. J. Comput. Aided. Mol. Des. 26, 3–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Zidek L., Novotny M.V., Stone M.J. 1999. Increased protein backbone conformational entropy upon hydrophobic ligand binding. Nat. Struct. Biol. 6, 1118–1121.

    Article  CAS  PubMed  Google Scholar 

  22. Tang Y.T., Marshall G.R. 2010. PHOENIX: A scoring function derived using high-resolution crystal structures and calorimetric measurements. J. Chem. Inf. Model. 51, 214–228.

    Article  Google Scholar 

  23. Balog E., Perahia D., Smith J.C., Merzel F. 2011. Vibrational softening of a protein on ligand binding. J. Phys. Chem. B. 115, 6811–6817.

    Article  CAS  PubMed  Google Scholar 

  24. Long D., Yang D. 2010. Millisecond timescale dynamics of human liver fatty acid binding protein: Testing of its relevance to the ligand entry process. Biophys. J. 16, 3054–3061.

    Article  Google Scholar 

  25. Piana S., Klepeis J.L., Shaw D.E. 2014. Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations. Curr. Opin. Struct. Biol. 24, 98–105.

    Article  CAS  PubMed  Google Scholar 

  26. Landau L.D., Lifshitz E.M. 1969). Statistical Physics, vol. 5 of A Course of Theoretical Physics. New York: Pergamon.

    Google Scholar 

  27. Pereyaslavets L.B., Finkelstein A.V. 2010. Atomic force field FFsol for calculating molecular interactions in water environment. Mol. Biol. (Moscow). 44, 303–316.

    Article  CAS  Google Scholar 

  28. Pereyaslavets L.B., Finkelstein A.V. 2012. Development and testing of PFFsol1.1, a new polarizable atomic force field for calculation of molecular interactions in implicit water environment. J. Phys. Chem. B. 116, 4646–4654.

    Article  CAS  PubMed  Google Scholar 

  29. Pereyaslavets L.B., Finkelstein A.V. 2011. Database A2 on thermodynamic characteristics of molecular, crystals. Annex to the paper by the same authors in Mol. Biol. (Moscow). 44, 303–316 (2010. http://physprotresru/resources/FFS/A2pdf

    Article  Google Scholar 

  30. Finkelstein A.V. 2014. Appended database A2 on characteristics of molecular crystals. http://physprotres. ru/resources/FFS/Addition%20to%20A2pdf

  31. Allen F.H. 2002). The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Cryst. B58, 380–388.

    Article  CAS  Google Scholar 

  32. Levitt M., Hirshberg M., Sharon R., Daggett V. 1995. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comput. Physics Commun. 91, 215–231.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow oblast, 142290, Russia

    S. O. Garbuzynskiy & A. V. Finkelstein

Authors
  1. S. O. Garbuzynskiy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. V. Finkelstein
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S. O. Garbuzynskiy.

Additional information

Original Russian Text © S.O. Garbuzynskiy, A.V. Finkelstein, 2016, published in Molekulyarnaya Biologiya, 2016, Vol. 50, No. 3, pp. 520–529.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Garbuzynskiy, S.O., Finkelstein, A.V. Calculation of mobility and entropy of the binding of molecules by crystals. Mol Biol 50, 452–461 (2016). https://doi.org/10.1134/S0026893316020060

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026893316020060

Keywords

Search

Navigation