A QM/MM Investigation of the Catalytic Mechanism of
Metal-Ion-Independent Core 2
beta1,6-N-Acetylglucosaminyltransferase

J 2013

A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ a Jaroslav KOČA

Základní údaje

Originální název

A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase

Autoři

TVAROŠKA, Igor (703 Slovensko, domácí), Stanislav KOZMON (703 Slovensko, domácí), Michaela WIMMEROVÁ (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, garant, domácí)

Vydání

Chemistry - A European Journal, Weinheim, WILEY-VCH Verlag, 2013, 0947-6539

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10600 1.6 Biological sciences

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.696

Kód RIV

RIV/00216224:14740/13:00068539

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1002/chem.201300383

UT WoS

000320134200020

Klíčová slova anglicky

computer chemistry; density functional calculations; molecular modeling; reaction mechanisms; transferases; transition state

Štítky

ok, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 11. 4. 2014 01:04, Olga Křížová

Anotace

V originále

Beta 1,6-GlcNAc-transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O-glycans. The catalytic mechanism of this metal-ion-independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme-substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted SN2-like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously.

Návaznosti

ED1.1.00/02.0068, projekt VaV

Název: CEITEC - central european institute of technology

2SGA2747, interní kód MU

Název: Saccharide - protein dispersion interactions involved in the bacterial recognition processes (Akronym: SaProDI)

Investor: Jihomoravský kraj, Saccharide - protein dispersion interactions involved in the bacterial recognition processes, Granty pro zahraniční vědce

286154, interní kód MU

Název: SYLICA - Synergies of Life and Material Sciences to Create a New Future (Akronym: SYLICA)

Investor: Evropská unie, SYLICA - Synergies of Life and Material Sciences to Create a New Future, Kapacity

Citovat

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ a Jaroslav KOČA. A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase. Chemistry - A European Journal. Weinheim: WILEY-VCH Verlag, 2013, roč. 19, č. 25, s. 8153-8162. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201300383.

@article{1111000,
   author = {Tvaroška, Igor and Kozmon, Stanislav and Wimmerová, Michaela and Koča, Jaroslav},
   article_location = {Weinheim},
   article_number = {25},
   doi = {http://dx.doi.org/10.1002/chem.201300383},
   keywords = {computer chemistry; density functional calculations; molecular modeling; reaction mechanisms; transferases; transition state},
   language = {eng},
   issn = {0947-6539},
   journal = {Chemistry - A European Journal},
   title = {A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase},
   url = {http://onlinelibrary.wiley.com/doi/10.1002/chem.201300383/abstract},
   volume = {19},
   year = {2013}
}

TY  - JOUR
ID  - 1111000
AU  - Tvaroška, Igor - Kozmon, Stanislav - Wimmerová, Michaela - Koča, Jaroslav
PY  - 2013
TI  - A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase
JF  - Chemistry - A European Journal
VL  - 19
IS  - 25
SP  - 8153-8162
EP  - 8153-8162
PB  - WILEY-VCH Verlag
SN  - 09476539
KW  - computer chemistry
KW  - density functional calculations
KW  - molecular modeling
KW  - reaction mechanisms
KW  - transferases
KW  - transition state
UR  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201300383/abstract
L2  - http://onlinelibrary.wiley.com/doi/10.1002/chem.201300383/abstract
N2  - Beta 1,6-GlcNAc-transferase (C2GnT) is an important controlling factor of biological functions for many glycoproteins and its activity has been found to be altered in breast, colon, and lung cancer cells, in leukemia cells, in the lymhomonocytes of multiple sclerosis patients, leukocytes from diabetes patients, and in conditions causing an immune deficiency. The result of the action of C2GnT is the core 2 structure that is essential for the further elongation of the carbohydrate chains of O-glycans. The catalytic mechanism of this metal-ion-independent glycosyltransferase is of paramount importance and is investigated here by using quantum mechanical (QM) (density functional theory (DFT))/molecular modeling (MM) methods with different levels of theory. The structural model of the reaction site used in this report is based on the crystal structures of C2GnT. The entire enzyme-substrate system was subdivided into two different subsystems: the QM subsystem containing 206 atoms and the MM region containing 5914 atoms. Three predefined reaction coordinates were employed to investigate the catalytic mechanism. The calculated potential energy surfaces discovered the existence of a concerted SN2-like mechanism. In this mechanism, a nucleophilic attack by O6 facilitated by proton transfer to the catalytic base and the separation of the leaving group all occur almost simultaneously.
ER  -

TVAROŠKA, Igor, Stanislav KOZMON, Michaela WIMMEROVÁ a Jaroslav KOČA. A QM/MM Investigation of the Catalytic Mechanism of Metal-Ion-Independent Core 2 beta1,6-N-Acetylglucosaminyltransferase. \textit{Chemistry - A European Journal}. Weinheim: WILEY-VCH Verlag, 2013, roč.~19, č.~25, s.~8153-8162. ISSN~0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201300383.

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