Interaction of Organic Solvents with Protein Structures at
Protein-Solvent Interface

J 2013

Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface

KHABIRI, M.; B. MINOFAR; Jan BREZOVSKÝ; Jiří DAMBORSKÝ; R. ETTRICH et. al.

Basic information

Original name

Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface

Authors

KHABIRI, M.; B. MINOFAR; Jan BREZOVSKÝ; Jiří DAMBORSKÝ and R. ETTRICH

Edition

Journal of Molecular Modeling, du bureau d'adresse, 2013, 1610-2940

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

is not subject to a state or trade secret

Impact factor

Impact factor: 1.867

RIV identification code

RIV/00216224:14310/13:00065827

Organization unit

Faculty of Science

DOI

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

UT WoS

000326193200010

Keywords in English

haloalkane dehalogenases

Abstract

In the original language

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.

Links

ED0001/01/01, research and development project

Name: CETOCOEN

GA203/08/0114, research and development project

Name: Specifické iontové efekty pro proteiny v roztocích a podobné biologicky relevantní systémy.

Investor: Czech Science Foundation, Specific ion effects for proteins in solutions and related biologically relevant systems

IAA401630901, research and development project

Name: Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami

Investor: Academy of Sciences of the Czech Republic, Evolution of substrate specificity in enzymes acting on xenobiotic compounds

Cite

KHABIRI, M.; B. MINOFAR; Jan BREZOVSKÝ; Jiří DAMBORSKÝ and R. ETTRICH. Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. Journal of Molecular Modeling. du bureau d'adresse, 2013, vol. 19, No 11, p. 4701-4711. ISSN 1610-2940. Available from: https://doi.org/10.1007/s00894-012-1507-z.

@article{1138894,
   author = {Khabiri, M. and Minofar, B. and Brezovský, Jan and Damborský, Jiří and Ettrich, R.},
   article_number = {11},
   doi = {https://doi.org/10.1007/s00894-012-1507-z},
   keywords = {haloalkane dehalogenases},
   language = {eng},
   issn = {1610-2940},
   journal = {Journal of Molecular Modeling},
   title = {Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface},
   volume = {19},
   year = {2013}
}

TY  - JOUR
ID  - 1138894
AU  - Khabiri, M. - Minofar, B. - Brezovský, Jan - Damborský, Jiří - Ettrich, R.
PY  - 2013
TI  - Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface
JF  - Journal of Molecular Modeling
VL  - 19
IS  - 11
SP  - 4701-4711
EP  - 4701-4711
PB  - du bureau d'adresse
SN  - 16102940
KW  - haloalkane dehalogenases
N2  - 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.
ER  -

KHABIRI, M.; B. MINOFAR; Jan BREZOVSKÝ; Jiří DAMBORSKÝ and R. ETTRICH. Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. \textit{Journal of Molecular Modeling}. du bureau d'adresse, 2013, vol.~19, No~11, p.~4701-4711. ISSN~1610-2940. Available from: https://doi.org/10.1007/s00894-012-1507-z.

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