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Related Concept Videos

Chemistry of Carbohydrates03:25

Chemistry of Carbohydrates

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

Chemistry of Carbohydrates

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

Chemistry of Carbohydrates

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...
Biosynthesis of Polysaccharides01:26

Biosynthesis of Polysaccharides

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...
Oligosaccharide Assembly01:24

Oligosaccharide Assembly

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.
Multiple sugar molecules that may or may...
What are Carbohydrates?01:44

What are Carbohydrates?

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Hierarchical and Programmable One-Pot Oligosaccharide Synthesis
09:56

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Published on: September 6, 2019

Multiscale coarse-graining of monosaccharides.

Pu Liu1, Sergei Izvekov, Gregory A Voth

  • 1Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.

The Journal of Physical Chemistry. B
|September 14, 2007
PubMed
Summary

A new multiscale coarse-graining (MS-CG) algorithm efficiently models monosaccharides in water. This method significantly speeds up simulations for carbohydrate systems, enabling large-scale studies.

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Area of Science:

  • Computational Chemistry
  • Biomolecular Modeling
  • Carbohydrate Chemistry

Background:

  • Accurate simulation of carbohydrate systems is crucial for understanding biological processes.
  • Atomistic simulations are computationally expensive, limiting their application to large-scale systems.
  • Coarse-graining methods offer a way to reduce computational cost by representing groups of atoms as single beads.

Purpose of the Study:

  • To develop and validate a systematic multiscale coarse-graining (MS-CG) algorithm for monosaccharides in aqueous solution.
  • To demonstrate the transferability and efficiency of the MS-CG model for simulating carbohydrate systems.
  • To apply the MS-CG algorithm to a larger saccharide system, alpha-(1-->4)-d-glucan.

Main Methods:

  • Developed a systematic multiscale coarse-graining (MS-CG) algorithm.
  • Derived nonbonded interactions using the force-matching approach.
  • Obtained bonded interactions via Boltzmann statistical analyses of atomistic trajectories.
  • Validated the model using alpha-D-glucopyranose in aqueous solution under NPT ensemble.

Main Results:

  • The MS-CG model accurately reproduces structural and thermodynamic properties of alpha-D-glucopyranose.
  • The model shows reasonable transferability to different thermodynamic states.
  • Simulations using the MS-CG model are approximately 3 orders of magnitude more efficient than atomistic simulations.
  • The MS-CG algorithm was successfully applied to an alpha-(1-->4)-d-glucan system.

Conclusions:

  • The developed MS-CG algorithm is effective for coarse-graining monosaccharides and related saccharide systems.
  • The MS-CG model significantly enhances computational efficiency, making it suitable for large-scale and long-time simulations of carbohydrates.
  • This approach facilitates the study of complex carbohydrate behavior in biological and chemical contexts.