About: Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.

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About: Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. Goto Sponge NotDistinct Permalink

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Description	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. 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. (en)
Title	Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. (en)
skos:prefLabel	Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. (en)
skos:notation	RIV/00216224:14310/09:00028564!RIV13-AV0-14310___
http://linked.open...avai/riv/aktivita	P S Z
http://linked.open...avai/riv/aktivity	P(GA201/07/0927), P(GA203/08/0114), P(IAA401630901), P(LC06010), S, Z(AV0Z40500505), Z(AV0Z60870520), Z(MSM0021622412), Z(MSM0021622413)
http://linked.open...iv/cisloPeriodika	00
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Koudeláková, Táňa Prokop, Zbyněk Klvaňa, Martin Pavlová, Martina Kutá-Smatanová, Ivana Kutý, Michal Damborský, Jiří Dvořák, Pavel Kulhánek, Petr Chaloupková, Radka
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykova univerzita / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	332836
http://linked.open...ai/riv/idVysledku	RIV/00216224:14310/09:00028564
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	DhaA haloalkane dehalogenase; mutations; ubstrate 1.2.3-trichloropropane (en)
http://linked.open.../riv/klicoveSlovo	DhaA haloalkane dehalogenase ubstrate 1.2.3-trichloropropane mutations
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[7115D77228FD]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF MOLECULAR BIOLOGY
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	10 (xsd:int)
http://linked.open...cetTvurcuVysledku	13 (xsd:int)
http://linked.open...vavai/riv/projekt	Specific ion effects for proteins in solutions and related biologically relevant systems. Evolution of substrate specificity in enzymes acting on xenobiotic compounds Center of Biocatalysis and Biotransformation Visualization of protein structures
http://linked.open...UplatneniVysledku	2009
http://linked.open...v/svazekPeriodika	2009
http://linked.open...iv/tvurceVysledku	Chaloupková, Radka Damborský, Jiří Dvořák, Pavel Kulhánek, Petr Kutá-Smatanová, Ivana Klvaňa, Martin Koudeláková, Táňa Pavlová, Martina Prokop, Zbyněk Stsiapanava, A. Kutý, Michal Dohnálek, J. Wade, R.
http://linked.open...ain/vavai/riv/wos	000270624100020
http://linked.open...n/vavai/riv/zamer	Progresivní makromolekulární materiály a supramolekulární systémy: syntéza a studium vlastností, jevů a možností využití pro speciální aplikace a moderní technologie Spatial and functional dynamics of biological, ecological and socio-economic systems interacting with global climatic change Interactions among the chemicals, environment and biological systems and their consequences on the global, regional and local scales (INCHEMBIOL) Proteiny v metabolismu a při interakci organismů s prostředím
issn	0022-2836
number of pages	10 (xsd:int)
http://localhost/t...ganizacniJednotka	14310
is http://linked.open...avai/riv/vysledek of	Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations.

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