2014
Catalytic Mechanism of the ppGalNAcT2 Retaining Glycosyltransferase Inferred From QM/MM Calculations
TRNKA, Tomáš, Stanislav KOZMON, Igor TVAROŠKA a Jaroslav KOČAZákladní údaje
Originální název
Catalytic Mechanism of the ppGalNAcT2 Retaining Glycosyltransferase Inferred From QM/MM Calculations
Autoři
TRNKA, Tomáš (203 Česká republika, domácí), Stanislav KOZMON (703 Slovensko, domácí), Igor TVAROŠKA (703 Slovensko, domácí) a Jaroslav KOČA (203 Česká republika, garant, domácí)
Vydání
GLYCO-T 2014: 9th International Symposium on Glycosyltransferases, 2014
Další údaje
Jazyk
angličtina
Typ výsledku
Prezentace na konferencích
Obor
10403 Physical chemistry
Stát vydavatele
Portugalsko
Utajení
není předmětem státního či obchodního tajemství
Kód RIV
RIV/00216224:14740/14:00079625
Organizační jednotka
Středoevropský technologický institut
Klíčová slova anglicky
glycosyltransferases;reaction mechanism;quantum chemistry
Příznaky
Mezinárodní význam
Změněno: 19. 3. 2015 17:32, Ing. Tomáš Trnka, Ph.D.
Anotace
V originále
To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals.
Návaznosti
ED1.1.00/02.0068, projekt VaV |
| ||
LH13055, projekt VaV |
| ||
286154, interní kód MU |
|