About: Toward an Accurate Conformational Modeling of Iduronic Acid

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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	Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of C-1(4), C-4(1) and S-2(O) conformations of alpha-L-IdoA-OMe and alpha-L-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1-4 interaction) were tested. It was found that scaling (reduction) of 1-4 electrostatic interactions significantly changes conformational preferences toward the C-4(1) conformation. More interestingly, scaling of 1-4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1-4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments. Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of C-1(4), C-4(1) and S-2(O) conformations of alpha-L-IdoA-OMe and alpha-L-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1-4 interaction) were tested. It was found that scaling (reduction) of 1-4 electrostatic interactions significantly changes conformational preferences toward the C-4(1) conformation. More interestingly, scaling of 1-4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1-4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments. (en)
Title	Toward an Accurate Conformational Modeling of Iduronic Acid Toward an Accurate Conformational Modeling of Iduronic Acid (en)
skos:prefLabel	Toward an Accurate Conformational Modeling of Iduronic Acid Toward an Accurate Conformational Modeling of Iduronic Acid (en)
skos:notation	RIV/60461373:22330/13:43896536!RIV14-MSM-22330___
http://linked.open...avai/predkladatel	Fakulta potravinářské a biochemické technologie
http://linked.open...avai/riv/aktivita	Z
http://linked.open...avai/riv/aktivity	Z(MSM6046137305)
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Oborský, Pavel Spiwok, Vojtěch Králová, Blanka
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	111327
http://linked.open...ai/riv/idVysledku	RIV/60461373:22330/13:43896536
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	SIMULATION; FLEXIBILITY; GLYCOSAMINOGLYCANS; RING; GAS-PHASE; HEPARIN DISACCHARIDE; METHYL 2-O-SULFO-ALPHA-L-IDURONATE; MOLECULAR-DYNAMICS; FREE-ENERGY; SPIN COUPLING-CONSTANT (en)
http://linked.open.../riv/klicoveSlovo	SIMULATION GAS-PHASE FLEXIBILITY FREE-ENERGY GLYCOSAMINOGLYCANS HEPARIN DISACCHARIDE METHYL 2-O-SULFO-ALPHA-L-IDURONATE RING SPIN COUPLING-CONSTANT MOLECULAR-DYNAMICS
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[40AEEE49FD42]
http://linked.open...i/riv/nazevZdroje	JOURNAL OF PHYSICAL CHEMISTRY B
http://linked.open...in/vavai/riv/obor	CE
http://linked.open...ichTvurcuVysledku	3 (xsd:int)
http://linked.open...cetTvurcuVysledku	4 (xsd:int)
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	117
http://linked.open...iv/tvurceVysledku	Spiwok, Vojtěch Králová, Blanka Tvaroška, Igor Oborský, Pavel
http://linked.open...ain/vavai/riv/wos	000314492300005
http://linked.open...n/vavai/riv/zamer	Teoretické základy potravinářských a biochemických technologií
issn	1520-6106
number of pages	7 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp3100552
http://localhost/t...ganizacniJednotka	22330

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