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The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal H-NMR coupling constants.
Carbohydr Res
October 2020
Aspen Oss B.V, Kloosterstraat 6, 5349 AB, Oss, the Netherlands. Electronic address:
The idopyranose ring plays a pivotal role in the conformational, dynamical, and intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate and it was early on assigned a role in the Sugar Code governing biological recognition processes. There is consensus that next to the two canonical C and C chair conformations, the conformational space accessible to the idopyranose ring entails a S skew-boat conformation, but the equilibrium between these three ring puckers has evaded satisfactory quantification. In this study a meta-analysis of X-ray solid-state data and vicinal NMR coupling constants is presented, based on the Truncated Fourier Puckering (TFP) formalism and the generalized Karplus (CAGPLUS) equation.
View Article and Find Full Text PDFMolecular modeling and MM-PBSA free energy analysis of endo-1,4-β-xylanase from Ruminococcus albus 8.
Int J Mol Sci
September 2014
Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China.
Endo-1,4-β-xylanase (EC 3.2.1.
View Article and Find Full Text PDFNMR characterization of the binding properties and conformation of glycosaminoglycans interacting with interleukin-10.
Glycobiology
November 2014
Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstraße 16/18, D-04107 Leipzig, Germany Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India.
The cytokine interleukin-10 (IL-10) is an important regulator of the host immune system with both pro- and anti-inflammatory functions. Glycosaminoglycans (GAGs) play a decisive role in the biology of many growth factors, e.g.
View Article and Find Full Text PDFStructural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 β-D-mannosidase.
Acta Crystallogr D Biol Crystallogr
October 2013
School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
Article Synopsis
- Rice Os7BGlu26 is a glycoside hydrolase enzyme with a much higher efficiency for breaking down β-D-mannoside compared to β-D-glucoside, demonstrated by its kcat/Km values.
- Structural analyses, including crystal structures, show that Os7BGlu26 has a unique (β/α)8-barrel configuration and a narrower active-site cleft, which influences its substrate selectivity.
- Mutations in specific residues (like Tyr134 and Cys182) significantly affect the enzyme's activity and selectivity, indicating that interactions with the catalytic acid/base are crucial for substrate recognition.
Conformations of the iduronate ring in short heparin fragments described by time-averaged distance restrained molecular dynamics.
Glycobiology
November 2013
Glycosystems Laboratory, Instituto de Investigaciones Quimicas, CSIC - US, Americo Vespucio, 49, E-41092 Sevilla, Spain.
The polyconformational behavior of L-iduronic acid (L-IdoA2S) in heparin derivatives has been previously analyzed in terms of intra-ring proton-proton vicinal coupling constants ((3)JHH) through mathematical fit of experimental and theoretical values (Ferro DR, Provasoli A, Ragazzi M, Casu B, Torri G, Bossennec V, Perly B, Sinay P, Petitou M, Choay J. 1990. Conformer Populations of L-Iduronic Acid Residues in Glycosaminoglycan Sequences.
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