title: 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.
authors: Institute of Nanobiology and Structural Biology of GCRC, Academy of Sciences of the Czech Republic, Zamek 136, 373 33, Nove Hrady, Czech Republic.
authors: Morteza
authors: M
authors: Khabiri
authors: Babak
authors: B
authors: Minofar
authors: Jan
authors: J
authors: Brezovský
authors: Jiří
authors: J
authors: Damborský
authors: Rudiger
authors: R
authors: Ettrich
mesh_terms: D019840:2-Propanol / Q000737:chemistry* / Q000494:pharmacology; D000096:Acetone / Q000737:chemistry* / Q000494:pharmacology; D018360:Crystallography, X-Ray; D005559:Formamides / Q000737:chemistry* / Q000494:pharmacology; D006867:Hydrolases / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D020836:Protein Structure, Quaternary / Q000187:drug effects; D017434:Protein Structure, Tertiary / Q000187:drug effects; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
chemical_list: D005559:Formamides; D012997:Solvents; D014867:Water; D000096:Acetone; C031066:formamide; D006867:Hydrolases; C046137:haloalkane dehalogenase; D019840:2-Propanol