Journal of Molecular Modeling

, Volume 19, Issue 11, pp 4701–4711 | Cite as

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

  • Morteza Khabiri
  • Babak Minofar
  • Jan Brezovský
  • Jiří Damborský
  • Rudiger Ettrich
Original Paper


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.


Molecular dynamics Non-aqueous media Organic solvents Solvent orientation 



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


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Morteza Khabiri
    • 1
    • 2
  • Babak Minofar
    • 1
  • Jan Brezovský
    • 3
    • 4
  • Jiří Damborský
    • 3
    • 4
  • Rudiger Ettrich
    • 1
    • 2
  1. 1.Institute of Nanobiology and Structural Biology of GCRCAcademy of Sciences of the Czech RepublicNove HradyCzech Republic
  2. 2.Faculty of SciencesUniversity of South Bohemia in Ceske BudejoviceNove HradyCzech Republic
  3. 3.Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of ScienceMasaryk UniversityBrnoCzech Republic
  4. 4.International Clinical Research CenterSt. Anne’s University Hospital BrnoBrnoCzech Republic

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