Detailed Information on Publication Record
2009
Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.
KLVAŇA, Martin, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Pavel DVOŘÁK et. al.Basic information
Original name
Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.
Name in Czech
Cesta a mechanismus vzniku produktu v inženýrství haloalkán dehalogenáz použitím klasické a zrychlené molekulárně-dynamické simulace.
Authors
KLVAŇA, Martin (203 Czech Republic), Martina PAVLOVÁ (203 Czech Republic), Táňa KOUDELÁKOVÁ (203 Czech Republic), Radka CHALOUPKOVÁ (203 Czech Republic), Pavel DVOŘÁK (203 Czech Republic), Zbyněk PROKOP (203 Czech Republic), A. STSIAPANAVA (804 Ukraine), Michal KUTÝ (203 Czech Republic), Ivana KUTÁ-SMATANOVÁ (203 Czech Republic), J. DOHNÁLEK (203 Czech Republic), Petr KULHÁNEK (203 Czech Republic), R. WADE (276 Germany) and Jiří DAMBORSKÝ (203 Czech Republic, guarantor)
Edition
JOURNAL OF MOLECULAR BIOLOGY, 2009, 0022-2836
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10600 1.6 Biological sciences
Country of publisher
United States of America
Confidentiality degree
není předmětem státního či obchodního tajemství
Impact factor
Impact factor: 3.871
RIV identification code
RIV/00216224:14310/09:00028564
Organization unit
Faculty of Science
UT WoS
000270624100020
Keywords in English
DhaA haloalkane dehalogenase; mutations; ubstrate 1.2.3-trichloropropane
Tags
International impact, Reviewed
Změněno: 11/8/2009 13:26, prof. Mgr. Jiří Damborský, Dr.
V originále
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein crystallography, were constructed and biochemically characterized. The mutants showed distinct catalytic efficiencies with the halogenated substrate 1,2,3-trichloropropane. Release pathways for the two dehalogenation products, 2,3-dichloropropane-1-ol and the chloride ion, as well as water molecules, were studied using classical and random acceleration molecular dynamics simulations. Five different pathways, denoted p1, p2a, p2b, p2c and p3, were identified. The individual pathways showed differing selectivity for the products: the chloride ion releases solely through p1 whereas the alcohol releases through all five pathways. Water molecules play a crucial role for release of both products by breakage of their hydrogen bonding interactions with the active site residues and shielding the charged chloride ion during its passage through a hydrophobic tunnel. Exchange of the chloride ions, the alcohol product and the waters between the buried active site and the bulk solvent can be realized by three different mechanisms: (i) passage through a permanent tunnel, (ii) passage through a transient tunnel and (iii) migration through a protein matrix. We demonstrate that the accessibility of the pathways and the mechanisms of ligand exchange were modified by mutations. Insertion of bulky aromatic residues in the tunnel corresponding to pathway p1 leads to reduced accessibility to the ligands and a change in mechanism of opening from permanent to transient. We propose that engineering the accessibility of tunnels and the mechanisms of ligand exchange is a powerful strategy for modification of the functional properties of enzymes with buried active sites.
In Czech
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Links
| GA201/07/0927, research and development project |
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| GA203/08/0114, research and development project |
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| IAA401630901, research and development project |
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| LC06010, research and development project |
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| MSM0021622412, plan (intention) |
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| MSM0021622413, plan (intention) |
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