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

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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.

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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

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Authors and Affiliations

  1. Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 373 33, Nove Hrady, Czech Republic

    Morteza Khabiri, Babak Minofar & Rudiger Ettrich

  2. Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, 373 33, Nove Hrady, Czech Republic

    Morteza Khabiri & Rudiger Ettrich

  3. Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic

    Jan Brezovský & Jiří Damborský

  4. International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic

    Jan Brezovský & Jiří Damborský

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  1. Morteza Khabiri
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  2. Babak Minofar
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Correspondence to Rudiger Ettrich.

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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

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

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