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.

Základní údaje

Originální název

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

Autoři

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

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 1.867

Kód RIV

RIV/00216224:14310/13:00065827

Organizační jednotka

Přírodovědecká fakulta

DOI

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

UT WoS

000326193200010

Klíčová slova anglicky

haloalkane dehalogenases

Štítky

AKR, rivok

Změněno: 29. 4. 2014 14:33, Ing. Zdeňka Rašková

Anotace

V originále

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.

Návaznosti

ED0001/01/01, projekt VaV

Název: CETOCOEN

GA203/08/0114, projekt VaV

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

Investor: Grantová agentura ČR, Specifické iontové efekty pro proteiny v roztocích a podobné biologicky relevantní systémy

IAA401630901, projekt VaV

Název: Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami

Investor: Akademie věd ČR, Evoluce substrátové specifity u enzymů aktivních s xenobiotickými látkami

Citovat

KHABIRI, M.; B. MINOFAR; Jan BREZOVSKÝ; Jiří DAMBORSKÝ a R. ETTRICH. Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. Journal of Molecular Modeling. du bureau d'adresse, 2013, roč. 19, č. 11, s. 4701-4711. ISSN 1610-2940. Dostupné z: 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 a R. ETTRICH. Interaction of Organic Solvents with Protein Structures at Protein-Solvent Interface. \textit{Journal of Molecular Modeling}. du bureau d'adresse, 2013, roč.~19, č.~11, s.~4701-4711. ISSN~1610-2940. Dostupné z: https://doi.org/10.1007/s00894-012-1507-z.

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