Difference between revisions of "Team:NRP-UEA-Norwich/Modeling/Simulation"
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<p class="space10">To create the glycogen structures we made the following assumptions: </p> | <p class="space10">To create the glycogen structures we made the following assumptions: </p> | ||
| − | <p class="space10">•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.<br/>• 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 <sub><a data-id="ref" class="scroll-link">4</a></sub></p> | + | <p class="space10">• 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.<br/>• 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 <sub><a data-id="ref" class="scroll-link">4</a></sub></p> |
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<h4 class="title2">Glyco2D does work!</h4> | <h4 class="title2">Glyco2D does work!</h4> | ||
| − | <p class="space20"> | + | <p class="space20">When we increase the initial percentage of random acylation, the total number of modified glucoses increased. We showed a great linear correlation between both (see figure 1) </p> |
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<h4 class="title2">Acylation on carbon 4</h4> | <h4 class="title2">Acylation on carbon 4</h4> | ||
| − | <p class="space20"> | + | <p class="space20">As we're using putative acyltransferases, we don't know the carbon in the glucose molecule that gets acylated. If it binds to C4, the acylation will restrict further growth of the glycogen molecule. </p> |
| − | <p class="space20"> | + | <p class="space20">As we can see, by having a chance of acylation of 1% at C4, the glucose lost is around 50%. By 'glucose lost' we mean all the glucose molecules that could haven been added to the unmodified molecule (see figure 2). </p> |
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| + | <p class="space20">Therefore, if the acyl group always binds to C4, we won't have a viable glycogen molecule. </p> | ||
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<div class="col-md-6 left"> | <div class="col-md-6 left"> | ||
| − | <h4 class="title2">Acylation in any available position</h4> | + | <h4 class="title2">Acylation can happen in any available position</h4> |
| − | <p class="space20"> | + | <p class="space20">Another hypothesis is that the acyltransferase can add the group to any carbon on the glucose molecule. We assume a random chance of a group being added on the 4 carbons available in the molecule. If it is added to C4, it will restrict growth. If it is added to C6, it might restrict branching if it binds to the glucose molecule in the 5th or 10th position in the chain (branching points). The normal growth will not be altered if it binds C2 or C3.</p> |
| − | + | ||
| − | + | ||
| − | <p class="space20"> | + | <p class="space20">We ran the simulation 300 times for each % of acylation and calculated the average for all the possible randomly generated molecules. We observed a good correlation between the final % of acylated glucose residues and the % of glucose molecules that are lost in comparison to the unmodified molecule (see figure 3). |
| + | </p> | ||
| + | <p class="space20">As we can see, when a 5% of final acylation is achieved, only a 22 % of the glucose in the molecule is lost, and this give rise to a valid glycogen molecule. This model allowed us to define the optimal value so that the minimum amount of glucose units are lost from the glycogen molecule but we achieve the desired level of acylation. </p> | ||
Revision as of 11:36, 15 September 2015
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!
When we increase the initial percentage of random acylation, the total number of modified glucoses increased. We showed a great linear correlation between both (see figure 1)
Acylation on carbon 4
As we're using putative acyltransferases, we don't know the carbon in the glucose molecule that gets acylated. If it binds to C4, the acylation will restrict further growth of the glycogen molecule.
As we can see, by having a chance of acylation of 1% at C4, the glucose lost is around 50%. By 'glucose lost' we mean all the glucose molecules that could haven been added to the unmodified molecule (see figure 2).
Therefore, if the acyl group always binds to C4, we won't have a viable glycogen molecule.
Acylation can happen in any available position
Another hypothesis is that the acyltransferase can add the group to any carbon on the glucose molecule. We assume a random chance of a group being added on the 4 carbons available in the molecule. If it is added to C4, it will restrict growth. If it is added to C6, it might restrict branching if it binds to the glucose molecule in the 5th or 10th position in the chain (branching points). The normal growth will not be altered if it binds C2 or C3.
We ran the simulation 300 times for each % of acylation and calculated the average for all the possible randomly generated molecules. We observed a good correlation between the final % of acylated glucose residues and the % of glucose molecules that are lost in comparison to the unmodified molecule (see figure 3).
As we can see, when a 5% of final acylation is achieved, only a 22 % of the glucose in the molecule is lost, and this give rise to a valid glycogen molecule. This model allowed us to define the optimal value so that the minimum amount of glucose units are lost from the glycogen molecule but we achieve the desired level of acylation.
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.
