Conformational behavior of nucleotide-sugar in solution:
Molecular dynamics and NMR study of solvated
uridinediphosphate-glucose in the presence of monovalent
cations

J 2001

Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations

PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA, Anne IMBERTY et. al.

Základní údaje

Originální název

Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations

Autoři

PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA a Anne IMBERTY

Vydání

Biopolymers, John Wiley & Sons, Inc, 2001, 0006-3525

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

Impakt faktor

Impact factor: 1.845

Kód RIV

RIV/00216224:14310/01:00004134

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

cations; molecular dynamics; NMR spectroscopy; nucleotide-sugars; UDP-glucose

Štítky

Cations, molecular dynamics, NMR Spectroscopy, nucleotide-sugars, UDP-glucose

Změněno: 5. 4. 2001 10:26, prof. RNDr. Jaroslav Koča, DrSc.

Anotace

V originále

The nucleotide-sugars are metabolites of primary importance in the biosynthesis of polysaccharides and glycoconjugates since they serve as sugar donors in the reactions of glycosyltransferases, enzymes that displays a high specificity for both donors and acceptors. In order to determine the conformational behavior of uridinediphosphoglucose in dilute aqueous solution that includes a physiologically relevant concentration of salt, parallel NMR and molecular modeling investigations have been conducted. Nine molecular dynamics trajectories of 3 ns each were calculated in presence of explicit water and monovalent cations with the use of the AMBER force field with recently developed energy parameters for nucleotide-sugars (P. Petrova, J. Koca, and A. Imberty, Journal of American Chemical Society, 1999, vol. 121, pp. 5535-5547). Theoretical nuclear Overhauser effect data were calculated from these simulations using a model-free approach that takes into account internal motions. Comparison of theoretical and experimental data gives excellent agreement for the region surrounding the glucose-phosphate linkage including the pyrophosphate linkage itself. Less satisfactory agreement is obtained for the ribose ring and the base orientations. On the whole, both NMR and molecular dynamics simulations predict the molecule to be flexible, and to visit a large number of conformations while maintaining an extended overall shape

Návaznosti

MSM 143100005, záměr

Název: Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Strukturně-funkční vztahy biomolekul a jejich role v metabolismu

Citovat

PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA a Anne IMBERTY. Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations. Biopolymers. John Wiley & Sons, Inc, 2001, roč. 58, č. 7, s. 617-635. ISSN 0006-3525.

@article{360014,
   author = {Petrová, Pavla and Monteiro, Celine and Herve du Penhoat, Catherine and Koča, Jaroslav and Imberty, Anne},
   article_number = {7},
   keywords = {cations; molecular dynamics; NMR spectroscopy; nucleotide-sugars; UDP-glucose},
   language = {eng},
   issn = {0006-3525},
   journal = {Biopolymers},
   title = {Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations},
   volume = {58},
   year = {2001}
}

TY  - JOUR
ID  - 360014
AU  - Petrová, Pavla - Monteiro, Celine - Herve du Penhoat, Catherine - Koča, Jaroslav - Imberty, Anne
PY  - 2001
TI  - Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations
JF  - Biopolymers
VL  - 58
IS  - 7
SP  - 617
EP  - 617
PB  - John Wiley & Sons, Inc
SN  - 00063525
KW  - cations
KW  - molecular dynamics
KW  - NMR spectroscopy
KW  - nucleotide-sugars
KW  - UDP-glucose
N2  - The nucleotide-sugars are metabolites of primary importance in the biosynthesis of polysaccharides and glycoconjugates since they serve as sugar donors in the reactions of glycosyltransferases, enzymes that displays a high specificity for both donors and acceptors. In order to determine the conformational behavior of uridinediphosphoglucose in dilute aqueous solution that includes a physiologically relevant concentration of salt, parallel NMR and molecular modeling investigations have been conducted. Nine molecular dynamics trajectories of 3 ns each were calculated in presence of explicit water and monovalent cations with the use of the AMBER force field with recently developed energy parameters for nucleotide-sugars (P. Petrova, J. Koca, and A. Imberty, Journal of American Chemical Society, 1999, vol. 121, pp. 5535-5547). Theoretical nuclear Overhauser effect data were calculated from these simulations using a model-free approach that takes into account internal motions. Comparison of theoretical and experimental data gives excellent agreement for the region surrounding the glucose-phosphate linkage including the pyrophosphate linkage itself. Less satisfactory agreement is obtained for the ribose ring and the base orientations. On the whole, both NMR and molecular dynamics simulations predict the molecule to be flexible, and to visit a large number of conformations while maintaining an extended overall shape
ER  -

PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA a Anne IMBERTY. Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations. \textit{Biopolymers}. John Wiley \&{} Sons, Inc, 2001, roč.~58, č.~7, s.~617-635. ISSN~0006-3525.

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