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Statements

Subject Item
n2:RIV%2F60461373%3A22330%2F09%3A00022337%21RIV10-MSM-22330___
rdf:type
skos:Concept n15:Vysledek
dcterms:description
The conformational free energy surface of alpha-N-acetylneuraminic acid (Neu5Ac, sialic acid) in the space of ring-puckering coordinates was calculated using the metadynamics method. Free energy surfaces in vacuum and with an explicit solvent were calculated in GLYCAM 06 force field. In vacuum three structures are almost equivalently populated, namely, the 2C5 chair and the B3,6/2S6 and OS3 boat/skew-boat conformations. The B3,6/2S6 structure is stabilized by an ionic hydrogen bond between the amide N-H bond and the carboxylic group. However, this structure is unfavorable in a water environment in which the experimentally observed 2C5 chair conformation is predicted to be more stable than the other structures. These results indicate that environment significantly influences conformation of Neu5Ac and that Neu5Ac-processing enzymes might modify a conformation of their substrates solely by a changing polarity of the environment. The structure of Neu5Ac bound in influenza neuraminidase (4S2/B2,5) belongs The conformational free energy surface of alpha-N-acetylneuraminic acid (Neu5Ac, sialic acid) in the space of ring-puckering coordinates was calculated using the metadynamics method. Free energy surfaces in vacuum and with an explicit solvent were calculated in GLYCAM 06 force field. In vacuum three structures are almost equivalently populated, namely, the 2C5 chair and the B3,6/2S6 and OS3 boat/skew-boat conformations. The B3,6/2S6 structure is stabilized by an ionic hydrogen bond between the amide N-H bond and the carboxylic group. However, this structure is unfavorable in a water environment in which the experimentally observed 2C5 chair conformation is predicted to be more stable than the other structures. These results indicate that environment significantly influences conformation of Neu5Ac and that Neu5Ac-processing enzymes might modify a conformation of their substrates solely by a changing polarity of the environment. The structure of Neu5Ac bound in influenza neuraminidase (4S2/B2,5) belongs
dcterms:title
Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation. Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation.
skos:prefLabel
Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation. Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation.
skos:notation
RIV/60461373:22330/09:00022337!RIV10-MSM-22330___
n3:aktivita
n4:Z
n3:aktivity
Z(MSM6046137305)
n3:cisloPeriodika
113
n3:dodaniDat
n6:2010
n3:domaciTvurceVysledku
n10:9836861
n3:druhVysledku
n17:J
n3:duvernostUdaju
n13:S
n3:entitaPredkladatele
n12:predkladatel
n3:idSjednocenehoVysledku
308070
n3:idVysledku
RIV/60461373:22330/09:00022337
n3:jazykVysledku
n8:eng
n3:klicovaSlova
Free energy; metadynamics; sialic acid
n3:klicoveSlovo
n14:Free%20energy n14:metadynamics n14:sialic%20acid
n3:kodStatuVydavatele
US - Spojené státy americké
n3:kontrolniKodProRIV
[C0CBA35500A2]
n3:nazevZdroje
JOURNAL OF PHYSICAL CHEMISTRY B
n3:obor
n7:CE
n3:pocetDomacichTvurcuVysledku
1
n3:pocetTvurcuVysledku
2
n3:rokUplatneniVysledku
n6:2009
n3:tvurceVysledku
Spiwok, Vojtěch Tvaroška, Igor
n3:wos
000268139000033
n3:zamer
n11:MSM6046137305
s:issn
1520-6106
s:numberOfPages
6
n16:organizacniJednotka
22330