J 2015

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

TRNKA, Tomáš; Stanislav KOZMON; Igor TVAROŠKA a Jaroslav KOČA

Základní údaje

Originální název

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

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

PLoS Computational Biology, SAN FRANCISCO, PUBLIC LIBRARY SCIENCE, 2015, 1553-734X

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

Impakt faktor

Impact factor: 4.587

Kód RIV

RIV/00216224:14310/15:00083119

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000354517600002

EID Scopus

2-s2.0-84929493591

Klíčová slova anglicky

POLYPEPTIDE N-ACETYLGALACTOSAMINYLTRANSFERASE; ENZYMATIC GLYCOSYL TRANSFER; ACETYL-D-GALACTOSAMINE; UDP-GALNAC; GALACTOSYLTRANSFERASE LGTC; DENSITY FUNCTIONALS; INTEGRATION SCHEME; CORRELATION-ENERGY; TRANSITION-STATE; LECTIN DOMAIN

Štítky

Příznaky

Mezinárodní význam, Recenzováno
Změněno: 12. 4. 2016 13:04, Ing. Andrea Mikešková

Anotace

V originále

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. 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
Název: CEITEC - central european institute of technology
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

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