Team:NRP-UEA-Norwich/Modeling/Simulation
Acylation simulation
Bacterial glycogen and plant starch consist of chains of glucose residues connected by alpha-1,4-glycosidic linkages with alpha-1,6-glycosidic linkages forming branch points. Our main aim was to produce acylated or butrylated starch. As plants are more difficult to work with, we initially expressed four putative acyltransferases in E. coli to see if we could modify bacterial glycogen. However, the activity on these enzymes is still unknown. We don't know at which position in the glucose molecule that the enzyme might add the acyl group. If the group is added to the free end available at a growing branch, it will compete with the glycogen synthase and disrupt the growth of the molecule.
Even though glycogen acylation has not yet been described, phosphorylation of glycogen has been studied previously in both muscle and bacterial glycogen. Tagliabracci V. S. et al showed that the phosphate in glycogen is present as C2 and C3 phosphomonoesters 1 . Phosphorylation of starch has been also characterized2. According to Blennow A. et al, the phosphate groups bind at the free C6 and C3 hydroxyl groups of the glucose units. Both groups are located at the hydrophilic surface of the double helix, which might affect the stability of the molecule 2.
We therefore needed to model the putative changes in glycogen structure depending on the location of the modification. Our aim was to produce carbohydrate molecules with 5-10% of the residues modified since this level of butrylation (achieved by chemical modification) has positive benefits to the colon of rats 3 Our model indicates that this level of modification is only viable if the enzyme can modify any base - If it can only use the carbon-4 position it would impact on the growth of the molecule.
To create the glycogen structures we made the following assumptions:
•C1 doesn't get modified as it's forming a bond in all the residues expect the 1st one. C2, C3, C4 and C6 might get modified.
• The branching occurs in a one-by-one glucose addition, even though the branching enzyme (GlgB) would cut an oligosaccharide from the linear molecule and add it at a branching point 4
Results from the simulation
Glyco2D does work!
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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam.
You can learn more by clicking on the image on the right.
Acylation on carbon 4
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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam.
You can learn more by clicking on the image on the right.
Acylation in any available position
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Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam.
You can learn more by clicking on the image on the right.
References
1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, Optimization of molecular design in the evolution of metabolism: The glycogen molecule , Biochem Journal, 295, p. 477–83
2. Meléndez R, Meléndez-Hevia E, Mas F, Mach J, Cascante M: Physical constraints in the synthesis of glycogen that influence its structural homogeneity: A two-dimensional approach. Biophys J 1998, 75:106–14.
