Second Step of Hydrolytic Dehalogenation in Haloalkane
Dehalogenase Investigated by QM/MM Methods

J 2008

Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods

OTYEPKA, Michal; Pavel BANÁŠ; A. MAGISTRATO; P. CARLONI; Jiří DAMBORSKÝ et. al.

Základní údaje

Originální název

Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods

Název česky

Druhý krok hydrolytické dehalogenace v haloalkan dehalogenáze prováděný metodou QM/MM

Autoři

OTYEPKA, Michal; Pavel BANÁŠ; A. MAGISTRATO; P. CARLONI a Jiří DAMBORSKÝ

Vydání

Proteins: Structure, Function, and Bioinformatics, 2008, 0887-3585

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

Odkazy

URL

Impakt faktor

Impact factor: 3.419

Kód RIV

RIV/00216224:14310/08:00025615

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000252836300009

Klíčová slova anglicky

dehalogenase; LinB; Sphingomonas paucimobilis UT26; quantum-mechanical/molecular mechanics (QM/MM) simulations

Štítky

dehalogenase, LINB, Sphingomonas paucimobilis UT26

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 7. 2009 10:42, prof. Mgr. Jiří Damborský, Dr.

Anotace

ORIG CZ

V originále

We investigate mechanism and energetics of the hydrolytic dehalogenation catalyzed by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 by Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) simulations, QM calculations and classical molecular dynamics. We focus on the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate to alcohol and free enzyme. In this step, a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the ester intermediate. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5_2 kcal.mol-1. The lowering of the energy barrier of catalyzed reaction is caused by strong stabilization of the reaction intermediate and transition state by local electrostatic field of the enzyme, while its intrinsic dynamics plays a minor role. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme.

Česky

V článku jsou popisovány výpočty mechanismů a energii při hydrolytické dehalogenaci katalyyované pomocí haloalkan dehalogenázou LinB z bakterie Sphingomonas paucimobilis UT26

Návaznosti

LC06010, projekt VaV

Název: Centrum biokatalýzy a biotransformací

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Centrum biokatalýzy a biotransformací

MSM0021622413, záměr

Název: Proteiny v metabolismu a při interakci organismů s prostředím

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Proteiny v metabolismu a při interakci organismů s prostředím

Citovat

OTYEPKA, Michal; Pavel BANÁŠ; A. MAGISTRATO; P. CARLONI a Jiří DAMBORSKÝ. Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. Proteins: Structure, Function, and Bioinformatics. 2008, roč. 70, č. 000, s. 707-717. ISSN 0887-3585.

@article{721204,
   author = {Otyepka, Michal and Banáš, Pavel and Magistrato, A. and Carloni, P. and Damborský, Jiří},
   article_number = {000},
   keywords = {dehalogenase; LinB; Sphingomonas paucimobilis UT26; quantum-mechanical/molecular mechanics (QM/MM) simulations},
   language = {eng},
   issn = {0887-3585},
   journal = {Proteins: Structure, Function, and Bioinformatics},
   title = {Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods},
   url = {http://loschmidt.chemi.muni.cz/peg/abstracts/prot07b.html},
   volume = {70},
   year = {2008}
}

TY  - JOUR
ID  - 721204
AU  - Otyepka, Michal - Banáš, Pavel - Magistrato, A. - Carloni, P. - Damborský, Jiří
PY  - 2008
TI  - Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods
JF  - Proteins: Structure, Function, and Bioinformatics
VL  - 70
IS  - 000
SP  - 707-717
EP  - 707-717
SN  - 08873585
KW  - dehalogenase
KW  - LinB
KW  - Sphingomonas paucimobilis UT26
KW  - quantum-mechanical/molecular mechanics (QM/MM) simulations
UR  - http://loschmidt.chemi.muni.cz/peg/abstracts/prot07b.html
N2  - We investigate mechanism and energetics of the hydrolytic dehalogenation catalyzed by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 by Car-Parrinello (CP) and ONIOM hybrid quantum-mechanical/molecular mechanics (QM/MM) simulations, QM calculations and classical molecular dynamics. We focus on the second reaction step of the catalytic cycle, which comprises a general base-catalyzed hydrolysis of an ester intermediate to alcohol and free enzyme. In this step, a histidine residue (His272), polarized by glutamate (Glu132), acts as a base, accepting a proton from the catalytic water molecule and transferring it to an alcoholate ion. The reaction proceeds through a metastable tetrahedral intermediate, which shows an easily reversed reaction to the ester intermediate. The overall free energy barrier of the reaction calculated by potential of the mean force integration using CP-QM/MM calculations is equal to 19.5_2 kcal.mol-1. The lowering of the energy barrier of catalyzed reaction is caused by strong stabilization of the reaction intermediate and transition state by local electrostatic field of the enzyme, while its intrinsic dynamics plays a minor role. In the formation of the products, the protonated aspartic acid (Asp108) can easily adopt conformation of the relaxed state found in the free enzyme.
ER  -

OTYEPKA, Michal; Pavel BANÁŠ; A. MAGISTRATO; P. CARLONI a Jiří DAMBORSKÝ. Second Step of Hydrolytic Dehalogenation in Haloalkane Dehalogenase Investigated by QM/MM Methods. \textit{Proteins: Structure, Function, and Bioinformatics}. 2008, roč.~70, č.~000, s.~707-717. ISSN~0887-3585.

Přehled o publikaci