Molecular dynamics simulations of glycosyltransferase LgtC

J 2004

Molecular dynamics simulations of glycosyltransferase LgtC

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

Basic information

Original name

Molecular dynamics simulations of glycosyltransferase LgtC

Name in Czech

MD simulace glycosyltransferasy LgtC

Authors

ŠNAJDROVÁ, Lenka (203 Czech Republic), Petr KULHÁNEK (203 Czech Republic), Anne IMBERTY (250 France) and Jaroslav KOČA (203 Czech Republic, guarantor)

Edition

Carbohydrate Research, 2004, 0008-6215

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10401 Organic chemistry

Country of publisher

Netherlands

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

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

Impact factor

Impact factor: 1.451

RIV identification code

RIV/00216224:14310/04:00009950

Organization unit

Faculty of Science

UT WoS

000220389100010

Keywords in English

Galactosyltransferase; Molecular dynamics; Loops opening; Structural water molecules

Abstract

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.

In Czech

MD simulace glycosyltransferasy LgtC

Links

LN00A016, research and development project

Name: BIOMOLEKULÁRNÍ CENTRUM

Investor: Ministry of Education, Youth and Sports of the CR, Biomolecular Center

Citovat

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, vol. 339, No 5, p. 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 and Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. \textit{Carbohydrate Research}. 2004, vol.~339, No~5, p.~995-1006. ISSN~0008-6215.

Detailed Information on Publication Record