Molecular dynamics simulations of glycosyltransferase LgtC

J 2004

Molecular dynamics simulations of glycosyltransferase LgtC

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA

Základní údaje

Originální název

Molecular dynamics simulations of glycosyltransferase LgtC

Název česky

MD simulace glycosyltransferasy LgtC

Autoři

ŠNAJDROVÁ, Lenka (203 Česká republika), Petr KULHÁNEK (203 Česká republika), Anne IMBERTY (250 Francie) a Jaroslav KOČA (203 Česká republika, garant)

Vydání

Carbohydrate Research, 2004, 0008-6215

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10401 Organic chemistry

Stát vydavatele

Nizozemské království

Utajení

není předmětem státního či obchodního tajemství

Odkazy

Science Direct - Carbohydrate Research: Molecular dynamics simulations of glycosyltransferase LgtC

Impakt faktor

Impact factor: 1.451

Kód RIV

RIV/00216224:14310/04:00009950

Organizační jednotka

Přírodovědecká fakulta

UT WoS

000220389100010

Klíčová slova anglicky

Galactosyltransferase; Molecular dynamics; Loops opening; Structural water molecules

Štítky

galactosyltransferase, Loops opening, molecular dynamics, structural water molecules

Změněno: 13. 2. 2005 16:31, prof. RNDr. Jaroslav Koča, DrSc.

Anotace

ORIG CZ

V originále

Molecular dynamics simulations have been performed on fully solvated alpha-(1->4)-galactosyltransferase LgtC from Neisseria meningitidis with and without the donor substrate UDP-Gal and in the presence of the manganese ion. The analysis of the trajectories revealed a limited movement in the loop X (residues 75-80) and a larger conformational change in the loop Y (residues 246-251) in the simulation, when UDP-Gal was not present. In this case, the loops X and Y open by almost 10 A, exposing the active site to the solvent. The 'hinge region' responsible for the opening is composed of residues 246-247. We have also analyzed the behavior of the manganese ion in the simulations. The coordination number is 6 when UDP-Gal is present and it increases to 7 when it is absent. In the latter case, three water molecules become coordinated to the ion. In both cases, the coordination is very stable implying that the manganese ion is tightly bound in the active site of the enzyme even if UDP-Gal is not present. Further analysis of the structural water molecules location confirmed that the mobility of water molecules in the active site and the accessibility of this site for solvent are higher in the absence of the substrate.

Česky

MD simulace glycosyltransferasy LgtC

Návaznosti

LN00A016, projekt VaV

Název: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Biomolekulární centrum

Citovat

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, roč. 339, č. 5, s. 995-1006. ISSN 0008-6215.

@article{549940,
   author = {Šnajdrová, Lenka and Kulhánek, Petr and Imberty, Anne and Koča, Jaroslav},
   article_number = {5},
   keywords = {Galactosyltransferase; Molecular dynamics; Loops opening; Structural water molecules},
   language = {eng},
   issn = {0008-6215},
   journal = {Carbohydrate Research},
   title = {Molecular dynamics simulations of glycosyltransferase LgtC},
   url = {http://www.sciencedirect.com/science/article/B6TFF-4BJX0MM-1/2/40cffae104186599da947477ce5752b7},
   volume = {339},
   year = {2004}
}

TY  - JOUR
ID  - 549940
AU  - Šnajdrová, Lenka - Kulhánek, Petr - Imberty, Anne - Koča, Jaroslav
PY  - 2004
TI  - Molecular dynamics simulations of glycosyltransferase LgtC
JF  - Carbohydrate Research
VL  - 339
IS  - 5
SP  - 995-1006
EP  - 995-1006
SN  - 00086215
KW  - Galactosyltransferase
KW  - Molecular dynamics
KW  - Loops opening
KW  - Structural water molecules
UR  - http://www.sciencedirect.com/science/article/B6TFF-4BJX0MM-1/2/40cffae104186599da947477ce5752b7
N2  - Molecular dynamics simulations have been performed on fully solvated alpha-(1->4)-galactosyltransferase LgtC from Neisseria meningitidis with and without the donor substrate UDP-Gal and in the presence of the manganese ion. The analysis of the trajectories revealed a limited movement in the loop X (residues 75-80) and a larger conformational change in the loop Y (residues 246-251) in the simulation, when UDP-Gal was not present. In this case, the loops X and Y open by almost 10 A, exposing the active site to the solvent. The 'hinge region' responsible for the opening is composed of residues 246-247. We have also analyzed the behavior of the manganese ion in the simulations. The coordination number is 6 when UDP-Gal is present and it increases to 7 when it is absent. In the latter case, three water molecules become coordinated to the ion. In both cases, the coordination is very stable implying that the manganese ion is tightly bound in the active site of the enzyme even if UDP-Gal is not present. Further analysis of the structural water molecules location confirmed that the mobility of water molecules in the active site and the accessibility of this site for solvent are higher in the absence of the substrate.
ER  -

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. \textit{Carbohydrate Research}. 2004, roč.~339, č.~5, s.~995-1006. ISSN~0008-6215.

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