The 2SO Skew‐Boat Conformation in <scp>L</scp>‐Iduronic Acid

Ochsenbein, Philippe; Bonin, Michel; Schenk‐Joß, Kurt; El-Hajji, Mohamed

doi:10.1002/ange.201105172

Cited by 4 publications

(2 citation statements)

References 28 publications

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“…5 B ). This trajectory, which is plausible as it contains only conformations accessible to the d -glucuronyl ring in solution (44, 45), appears to be highly conducive to UXS catalysis in each step. The 4 C 1 → B O,3 transition serves to align the catalytic groups for NAD + -dependent oxidation at C 4 , however, already in expectation of the subsequent decarboxylation because the carboxylate group at C 5 is brought into an axial position that makes it an excellent leaving group.…”

Section: Resultsmentioning

confidence: 91%

Structure and Mechanism of Human UDP-xylose Synthase

Eixelsberger

Sykora

Egger

et al. 2012

Journal of Biological Chemistry

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Background: Human UDP-xylose synthase (hUXS1) is responsible for conversion of UDP-glucuronic acid to UDP-xylose.Results: Crystal structure, molecular dynamics simulations, and reaction course analysis give conclusive insight into the enzymatic mechanism in three catalytic steps.Conclusion: Distortion of sugar pyranose ring in bound substrate facilitates enzymatic reaction.Significance: A detailed mechanism for catalysis by hUXS1 is proposed.

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Section: Resultsmentioning

confidence: 91%

Structure and Mechanism of Human UDP-xylose Synthase

Eixelsberger

Sykora

Egger

et al. 2012

Journal of Biological Chemistry

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“…We believe that the enhanced conformational flexibility is captured by the accurate description of the interactions between the hydroxyl groups of the carbohydrates and the surrounding solvent in the Drude simulations, which in turn influences the conformational behavior of polysaccharides. The inherent flexibility and ring puckering of the carbohydrate ring is also found to be important in xylose or heparin and their derivatives. , In Figure S5 of the Supporting Information file, we plot the Mercator plots obtained from the additive and Drude simulations. The distribution of the Cremer–Pople puckering parameters highlights the higher ring flexibility in the Drude simulations.…”

Section: Resultsmentioning

confidence: 99%

Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives

Pandey

Aytenfisu

MacKerell

et al. 2019

J. Chem. Theory Comput.

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In this work, we report the development of Drude polarizable force field parameters for the carboxylate and N-acetyl amine derivatives, extending the functionality of the existing Drude polarizable carbohydrate force field. The force field parameters have been developed in a hierarchical manner, reproducing the quantum mechanical gas-phase properties of small model compounds representing the key functional group in the carbohydrate derivatives, including optimization of the electrostatic and bonded parameters. The optimized parameters were then used to generate the models for carboxylate and Nacetyl amine carbohydrate derivatives. The transferred parameters were further tested and optimized to reproduce crystal geometries and J-coupling data from nuclear magnetic resonance experiments. The parameter development resulted in the incorporation of D-glucuronate, L-iduronate, N-acetyl-D-glucosamine (GlcNAc), and N-acetyl-D-galactosamine (GalNAc) sugars into the Drude polarizable force field. The parameters developed in this study were then applied to study the conformational properties of glycosaminoglycan polymer hyaluronan, composed of D-glucuronate and N-acetyl-D-glucosamine, in aqueous solution. Upon comparing the results from the additive and polarizable simulations, it was found that the inclusion of polarization improved the description of the electrostatic interactions observed in hyaluronan, resulting in enhanced conformational flexibility. The developed Drude polarizable force field parameters in conjunction with the remainder of the Drude polarizable force field parameters can be used for future studies involving carbohydrates and their conjugates in complex, heterogeneous systems.

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Conformational Studies of Oligosaccharides

Yang

Delbianco

2020

Chemistry A European J

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The conformation of am olecule strongly affects its function, as demonstrated for peptides and nucleic acids. This correlation is much less establishedf or carbohydrates, the most abundant organic materials in nature. Recent advances in synthetic and analytical techniques have enabled the study of carbohydrates at the molecular level. Recurrent structural features were identified as responsible for particular biological activities or materialp roperties. In this Minireview,r ecent achievements in the structuralc haracterization of carbohydrates, enabled by systematic studies of chemically defined oligosaccharides, are discussed. These findings can guide the development of more potent glycomimetics. Synthetic carbohydrate materials by design can be envisioned.

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The ²S_O Skew‐Boat Conformation in L‐Iduronic Acid

Cited by 4 publications

References 28 publications

Structure and Mechanism of Human UDP-xylose Synthase

Structure and Mechanism of Human UDP-xylose Synthase

Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives

Conformational Studies of Oligosaccharides

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The 2SO Skew‐Boat Conformation in L‐Iduronic Acid

Cited by 4 publications

References 28 publications

Structure and Mechanism of Human UDP-xylose Synthase

Structure and Mechanism of Human UDP-xylose Synthase

Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives

Conformational Studies of Oligosaccharides

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The ²S_O Skew‐Boat Conformation in L‐Iduronic Acid