Skip to main content

Interaction of organic solvents with protein structures at protein-solvent interface

Abstract

The effect of non-denaturing concentrations of three different organic solvents, formamide, acetone and isopropanol, on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA at the protein-solvent interface was studied using molecular dynamics simulations. Analysis of B-factors revealed that the presence of a given organic solvent mainly affects the dynamical behavior of the specificity-determining cap domain, with the exception of DbjA in acetone. Orientation of organic solvent molecules on the protein surface during the simulations was clearly dependent on their interaction with hydrophobic or hydrophilic surface patches, and the simulations suggest that the behavior of studied organic solvents in the vicinity of hyrophobic patches on the surface is similar to the air/water interface. DbjA was the only dimeric enzyme among studied haloalkane dehalogenases and provided an opportunity to explore effects of organic solvents on the quaternary structure. Penetration and trapping of organic solvents in the network of interactions between both monomers depends on the physico-chemical properties of the organic solvents. Consequently, both monomers of this enzyme oscillate differently in different organic solvents. With the exception of LinB in acetone, the structures of studied enzymes were stabilized in water-miscible organic solvents.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

References

  1. Fetzner S, Lingens F (1994) Bacterial dehalogenases: biochemistry, genetics, and biotechnological applications. Microbiol Mol Biol Rev 58:641–685

    CAS  Google Scholar 

  2. Damborský J, Rorije E, Jesenská A, Nagata Y, Klopman G, Peijnenburg WJ (2001) Structure-specificity relationships for haloalkane dehalogenases. Environ Toxicol Chem 20:2681–2689

    Google Scholar 

  3. Stucki G, Thueer M (1995) Experiences of a large-scale application of 1,2-dichloroethane degradation microorganisms for groundwater treatment. Environ Sci Technol 29:2339–2345

    Article  CAS  Google Scholar 

  4. Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, Harel M, Remington SJ, Silman I, Schrag J (1992) The alpha/beta hydrolase fold. Protein Eng 5:197–211

    Article  CAS  Google Scholar 

  5. Janssen DB (2004) Evolving haloalkane dehalogenases. Curr Opin Chem Biol 8:150–159

    Article  CAS  Google Scholar 

  6. Chovancova E, Kosinski J, Bujnicki JM, Damborsky J (2007) Phylogenetic analysis of haloalkane dehalogenases. Proteins 67:305–316

    Article  CAS  Google Scholar 

  7. Kaur J, Sharma R (2006) Directed evolution: an approach to engineer enzymes. Crit Rev Biotechnol 26:165–199

    Article  CAS  Google Scholar 

  8. Prokop Z, Sato Y, Brezovsky J, Mozga T, Chaloupkova R, Koudelakova T, Jerabek P, Stepankova V, Natsume R, van Leeuwen JG, Janssen DB, Florian J, Nagata Y, Senda T, Damborsky J (2010) Enantioselectivity of haloalkane dehalogenases and its modulation by surface loop engineering. Angew Chem Int Ed Engl 49:6111–6115

    Google Scholar 

  9. Newman J, Peat TS, Richard R, Kan L, Swanson PE, Affholter JA, Holmes IH, Schindler JF, Unkefer CJ, Terwilliger TC (1999) Haloalkane dehalogenases: structure of a Rhodococcus enzyme. Biochemistry 38:16105–16114

    Article  CAS  Google Scholar 

  10. Marek J, Vévodová J, Smatanová IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborský J (2000) Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39:14082–14086

    Article  CAS  Google Scholar 

  11. Chaloupkova R, Sykorova J, Prokop Z, Jesenska A, Monincova M, Pavlova M, Tsuda M, Nagata Y, Damborsky J (2003) Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. J Biol Chem 278:52622–52628

    Google Scholar 

  12. Štěpánková V, Khabiri M, Brezovský J, Pavelka A, Sýkora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Damborský J, Chaloupková R (2012) Expansion of tunnels and active-site cavities influence catalytic activity of haloalkane dehalogenases in organic co-solvents. submitted

  13. Halling PJ (2004) What can we learn by studying enzymes in non-aqueous media? Philos Trans R Soc Lond B Biol Sci 359:1287–1296

    Article  CAS  Google Scholar 

  14. Charles T (1973) The hydrophobic effect: formation of micelles and biological membranes. John Wiley & Sons, New York, p 220

    Google Scholar 

  15. Klibanov AM (2001) Improving enzymes by using them in organic solvents. Nature 409:241–246

    Article  CAS  Google Scholar 

  16. Torres S, Castro G (2004) Non-aqueous biocatalysis in homogeneous solvent systems. Food Technol Biotechnol 42:271–277

    CAS  Google Scholar 

  17. Maurel P, Douzou P, Waldmann J, Yonetani T (1978) Enzyme behaviour and molecular environment. The effects of ionic strength, detergents, linear polyanions and phospholipids on the pH profile of soluble cytochrome oxidase. Biochim Biophys Acta 525:314–324

    Article  CAS  Google Scholar 

  18. Yang L, Dordick JS, Garde S (2004) Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity. Biophys J 87:812–821

    Article  CAS  Google Scholar 

  19. Soares CM, Teixeira VH, Baptista AM (2003) Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys J 84:1628–1641

    Article  CAS  Google Scholar 

  20. Hudson EP, Eppler RK, Clark DS (2005) Biocatalysis in semi-aqueous and nearly anhydrous conditions. Curr Opin Biotechnol 16:637–643

    Article  CAS  Google Scholar 

  21. Micaêlo NM, Soares CM (2007) Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS J 274:2424–2436

    Article  Google Scholar 

  22. Serdakowski AL, Dordick JS (2008) Enzyme activation for organic solvents made easy. Trends Biotechnol 26:48–54

    Article  CAS  Google Scholar 

  23. Boas FE, Harbury PB (2007) Potential energy functions for protein design. Curr Opin Struct Biol 17:199–204

    Article  CAS  Google Scholar 

  24. Patargias GN, Harris SA, Harding JH (2010) A demonstration of the inhomogeneity of the local dielectric response of proteins by molecular dynamics simulations. J Chem Phys 132:235103–235111

    Article  Google Scholar 

  25. Frisch MJ et al. (2004) Gaussian 03. Gaussian Inc, Wallingford

    Google Scholar 

  26. Horta BAC, Alencastro RBD, Ribeiro AAST (2008) MKTOP: a program for automatic construction of molecular topologies. J Braz Chem Soc 19:1433–1435

    Article  Google Scholar 

  27. Bruice TC, Kahn K (2002) Parameterization of OPLS-AA force field for the conformational analysis of macrocyclic polyketides. J Comput Chem 23:977–996

    Article  Google Scholar 

  28. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225–11236

    Article  CAS  Google Scholar 

  29. Puhovski YP, Rode BM (1995) Structure and dynamics of liquid formamide. Chem Phys 190:61–82

    Article  CAS  Google Scholar 

  30. Kulakova AN, Larkin MJ, Kulakov LA (1997) The plasmid-located haloalkane dehalogenase gene from Rhodococcus rhodochrous NCIMB 13064. Microbiology 143:109–115

  31. Krieger E, Koraimann G, Vriend G (2002) Increasing the precision of comparative models with YASARA NOVA–a self-parameterizing force field. Proteins 47:393–402

    Article  CAS  Google Scholar 

  32. Berendsen HJC, Grigera JR, Straatsma TP (1987) The missing term in effective pair potential. J Phys Chem 91:6269–6271

    Article  CAS  Google Scholar 

  33. Berendsen HJC, van der Spoel D, van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:43–56

    Article  CAS  Google Scholar 

  34. Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317

    CAS  Google Scholar 

  35. Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690

    Article  CAS  Google Scholar 

  36. Essmann U, Perera L, Berkowitz M (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8592

    Article  CAS  Google Scholar 

  37. Hess B, Bekker H, Berendsen HJC, Fraaije JG (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1742

    Article  CAS  Google Scholar 

  38. Humphrey W, Dalke A, Schulten K (1996) VMD-visual molecular dynamics. J Mol Graph 14:33–38

    Article  CAS  Google Scholar 

  39. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos

    Google Scholar 

  40. Kovacs H, Mark AE, van Gunsteren WF (1997) Solvent structure at a hydrophobic protein surface. Proteins 27:395–404

    Article  CAS  Google Scholar 

  41. Oberbrodhage J, Morgner H, Tapia O, Siegbahn HOG (1997) Molecular dynamics simulation of the free surface of liquid formamide. Int J Quantum Chem 63:1123–1131

    Article  CAS  Google Scholar 

  42. Andersson G (2007) Angle resolved ion scattering spectroscopy at surfaces of pure liquids: topography and orientation of molecules. Phys Chem Chem Phys 7:2942–2947

    Article  Google Scholar 

  43. Chen H, Gan W, Wu BH, Wu D, Guo Y, Wang HF (2005) Determination of structure and energetics for Gibbs surface adsorption layers of binary liquid mixture 1. Acetone + water. J Phys Chem B 109:8053–8063

    Article  CAS  Google Scholar 

  44. Simonson T, Brooks LC (1996) Charge screening and the dielectric constant of proteins: Insights from molecular dynamics. J Am Chem Soc 118:8452–8458

    Article  CAS  Google Scholar 

  45. Kataoka S (2006) Cremer PS Probing molecular structure at interfaces for comparison with bulk solution behavior: water/2-propanol mixtures monitored by vibrational sum frequency spectroscopy. J Am Chem Soc 128:5516–5522

    Article  CAS  Google Scholar 

  46. Chovancová E, Pavelka A, Beneš P, Strnad O, Brezovský J, Kozlíková B, Gora A, Šustr V, Klvaňa M, Medek P, Biedermannová L, Sochor J, Damborský J (2012) CAVER 3.0: a tool for analysis of transport pathways in dynamic protein structures. PLOS Computational Biology, under review

Download references

Acknowledgments

M.K. and R.E. acknowledge support from the Czech Science Foundation, Grants 203/08/0114 and P207/10/1934, the Academy of Sciences of the Czech Republic, Grants AV0Z60870520 and IAA401630901, and the Ministry of Education, Youth and Sports of the Czech Republic, (projects No. ME09062 and MSM6007665808), and the European Regional Development Fund, Grants CZ.1.05/2.1.00/01.0001 and CZ.1.05/1.1.00/02.0123. Additionally, M.K. was supported by the University of South Bohemia, Grant GAJU 170/2010/P. Access to the National Grid Infrastructure -MetaCentrum- is highly appreciated

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Rudiger Ettrich.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Khabiri, M., Minofar, B., Brezovský, J. et al. Interaction of organic solvents with protein structures at protein-solvent interface. J Mol Model 19, 4701–4711 (2013). https://doi.org/10.1007/s00894-012-1507-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-012-1507-z

Keywords

  • Molecular dynamics
  • Non-aqueous media
  • Organic solvents
  • Solvent orientation