J 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.

Abstract

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

.......................................................................................................................................................................................

Links

GA201/07/0927, research and development project
Name: Vizualizace proteinových struktur
Investor: Czech Science Foundation, Visualization of protein structures
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
LC06010, research and development project
Name: Centrum biokatalýzy a biotransformací
Investor: Ministry of Education, Youth and Sports of the CR, Center of Biocatalysis and Biotransformation
MSM0021622412, plan (intention)
Name: Interakce mezi chemickými látkami, prostředím a biologickými systémy a jejich důsledky na globální, regionální a lokální úrovni (INCHEMBIOL) (Acronym: INCHEMBIOL)
Investor: Ministry of Education, Youth and Sports of the CR, Interactions among the chemicals, environment and biological systems and their consequences on the global, regional and local scales (INCHEMBIOL)
MSM0021622413, plan (intention)
Name: Proteiny v metabolismu a při interakci organismů s prostředím
Investor: Ministry of Education, Youth and Sports of the CR, Proteins in metabolism and interaction of organisms with the environment