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Oligosaccharide Assembly01:24

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Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
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Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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Polysaccharides such as glycogen and starch are synthesized from nucleoside diphosphate sugars, primarily uridine diphosphate glucose (UDPG) and adenosine diphosphate glucose (ADPG). These activated glucose donors act as key intermediates in carbohydrate metabolism and biosynthesis. UDPG primarily involves glycogen synthesis in animals and many bacteria, while ADPG plays a fundamental role in starch synthesis in plants and certain bacteria.UDPG is formed when glucose-1-phosphate reacts with...
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Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
Chemistry of Carbohydrates03:25

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Carbohydrates are an essential part of the diet in humans and animals. Grains, fruits, and vegetables are natural sources of carbohydrates that provide energy to the body, particularly through glucose, a simple sugar that is a component of starch and an ingredient in many staple foods. The stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule represents carbohydrates. In other words, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This...
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Biochemical and Structural Characterization of the Carbohydrate Transport Substrate-binding-protein SP0092
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Searching and optimizing structure ensembles for complex flexible sugars.

Junchao Xia1, Claudio J Margulis, David A Case

  • 1BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States. junchao-xia@biomaps.rutgers.edu

Journal of the American Chemical Society
|August 26, 2011
PubMed
Summary
This summary is machine-generated.

Nuclear Magnetic Resonance (NMR) methods can now determine molecular geometry by analyzing ensembles of flexible carbohydrate conformers. This study introduces a novel computational approach to accurately weight these conformers for human milk sugars.

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Area of Science:

  • Carbohydrate chemistry
  • Structural biology
  • Computational chemistry

Background:

  • Nuclear Magnetic Resonance (NMR) restrictions are typically used for molecular geometry determination when a single, low-energy conformation dominates.
  • Flexible molecules like carbohydrates often exist as an ensemble of low-energy conformers, complicating direct structural analysis using NMR.
  • Residual dipolar couplings (RDCs) and scalar couplings are NMR observables sensitive to molecular conformation.

Purpose of the Study:

  • To develop and validate a novel computational procedure for identifying and weighting conformer contributions within an ensemble.
  • To apply this method to human milk oligosaccharides to determine their conformational populations.
  • To assess the rigidity of glycosidic linkages in histo-blood group epitopes.

Main Methods:

  • Utilized a genetic algorithm to globally minimize the R factor between calculated and experimental RDCs.
  • Employed the Fast Sugar Structure Prediction Software (FSPS) for exhaustive local minima conformational searches.
  • Optimized conformer weights based on comparisons with NMR observables like RDCs and scalar couplings.

Main Results:

  • Successfully applied the framework to six human milk sugars (LND-1, LNF-1, LNF-2, LNF-3, LNnT, LNT).
  • Determined population weights for the ensemble of conformers for each sugar.
  • Demonstrated that RDCs can be accurately represented by a small subset of dominant conformers.

Conclusions:

  • The developed procedure effectively models conformational ensembles of flexible carbohydrates using NMR data.
  • A few key conformers are sufficient to represent the RDCs of the studied human milk sugars.
  • The results suggest significant rigidity in several, but not all, glycosidic linkages within histo-blood group epitopes.