About: Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation.

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About: Conformational free energy surface of a-N-acetylneuraminic acid: An interplay between hydrogen bonding and solvation. Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
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 (en)
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. (en)
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. (en)
skos:notation	RIV/60461373:22330/09:00022337!RIV10-MSM-22330___
http://linked.open...avai/riv/aktivita	Z
http://linked.open...avai/riv/aktivity	Z(MSM6046137305)
http://linked.open...iv/cisloPeriodika	113
http://linked.open...vai/riv/dodaniDat	2010
http://linked.open...aciTvurceVysledku	Spiwok, Vojtěch
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Vysoká škola chemicko-technologická v Praze / Fakulta potravinářské a biochemické technologie
http://linked.open...dnocenehoVysledku	308070
http://linked.open...ai/riv/idVysledku	RIV/60461373:22330/09:00022337
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	Free energy; metadynamics; sialic acid (en)
http://linked.open.../riv/klicoveSlovo	metadynamics Free energy sialic acid
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[C0CBA35500A2]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF PHYSICAL CHEMISTRY B
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...UplatneniVysledku	2009
http://linked.open...iv/tvurceVysledku	Spiwok, Vojtěch Tvaroška, Igor
http://linked.open...ain/vavai/riv/wos	000268139000033
http://linked.open...n/vavai/riv/zamer	Teoretické základy potravinářských a biochemických technologií
issn	1520-6106
number of pages	6 (xsd:int)
http://localhost/t...ganizacniJednotka	22330

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