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.Základní údaje
Originální název
Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.
Název česky
Cesta a mechanismus vzniku produktu v inženýrství haloalkán dehalogenáz použitím klasické a zrychlené molekulárně-dynamické simulace.
Autoři
KLVAŇA, Martin (203 Česká republika), Martina PAVLOVÁ (203 Česká republika), Táňa KOUDELÁKOVÁ (203 Česká republika), Radka CHALOUPKOVÁ (203 Česká republika), Pavel DVOŘÁK (203 Česká republika), Zbyněk PROKOP (203 Česká republika), A. STSIAPANAVA (804 Ukrajina), Michal KUTÝ (203 Česká republika), Ivana KUTÁ-SMATANOVÁ (203 Česká republika), J. DOHNÁLEK (203 Česká republika), Petr KULHÁNEK (203 Česká republika), R. WADE (276 Německo) a Jiří DAMBORSKÝ (203 Česká republika, garant)
Vydání
JOURNAL OF MOLECULAR BIOLOGY, 2009, 0022-2836
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: 3.871
Kód RIV
RIV/00216224:14310/09:00028564
Organizační jednotka
Přírodovědecká fakulta
UT WoS
000270624100020
Klíčová slova anglicky
DhaA haloalkane dehalogenase; mutations; ubstrate 1.2.3-trichloropropane
Příznaky
Mezinárodní význam, Recenzováno
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.
Česky
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Návaznosti
| GA201/07/0927, projekt VaV |
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| GA203/08/0114, projekt VaV |
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| IAA401630901, projekt VaV |
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| LC06010, projekt VaV |
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| MSM0021622412, záměr |
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| MSM0021622413, záměr |
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