Difference between revisions of "Team:NRP-UEA-Norwich/Modeling/Glyco2D"
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| − | We built Glyco2D based on the mathematical model described by Meléndez-Hevia <i> et al. </i> <sub><a | + | We built Glyco2D based on the mathematical model described by Meléndez-Hevia <i> et al. </i> <sub><a data-id="team">1</a></sub>. This model described the structural properties of glycogen based on different parameters such as chain length, branching degree and the number of tiers. The model was able to demonstrate the optimal values of these parameters for maximizing the glucose stored in the smallest volume and the number of non-reducing ends. These optimal values were branching degree of 2, chain length of 13 glucose units and approximately 12 tiers <sub><a href="#1">1</a></sub>. |
The software we developed uses these properties to predict the structure of the molecule<sub><a href="#2">2</a></sub>. | The software we developed uses these properties to predict the structure of the molecule<sub><a href="#2">2</a></sub>. | ||
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<h2 class="title1"><a name="1"></a>References</h2> | <h2 class="title1"><a name="1"></a>References</h2> | ||
| − | <p>1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, <i> Optimization of molecular design in the evolution of metabolism: The glycogen molecule </i>, Biochem Journal, 295, p. 477–83</p> | + | <p id="1">1. Meléndez-Hevia E., Waddell T.G., and Shelton E.D., 1993, <i> Optimization of molecular design in the evolution of metabolism: The glycogen molecule </i>, Biochem Journal, 295, p. 477–83</p> |
<p><a name="2"></a>2. Meléndez R, Meléndez-Hevia E, Mas F, Mach J, Cascante M: <i>Physical constraints in the synthesis of glycogen that influence its structural homogeneity: A two-dimensional approach</i>. Biophys J 1998, 75:106–14.</p> | <p><a name="2"></a>2. Meléndez R, Meléndez-Hevia E, Mas F, Mach J, Cascante M: <i>Physical constraints in the synthesis of glycogen that influence its structural homogeneity: A two-dimensional approach</i>. Biophys J 1998, 75:106–14.</p> | ||
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Revision as of 10:20, 15 September 2015
Glyco2D
We built Glyco2D based on the mathematical model described by Meléndez-Hevia et al. 1. This model described the structural properties of glycogen based on different parameters such as chain length, branching degree and the number of tiers. The model was able to demonstrate the optimal values of these parameters for maximizing the glucose stored in the smallest volume and the number of non-reducing ends. These optimal values were branching degree of 2, chain length of 13 glucose units and approximately 12 tiers 1. The software we developed uses these properties to predict the structure of the molecule2.
The software was created in C++ using openGL. The individual glucose molecules are represented by black squares and they are used as building blocks for the chains and branches.
To create the glycogen structures we made the following assumptions:
•The branching points on the chain are always the 5th and 9th glucose molecule on the chain.
• All chains are equal in length.
• The branching degree is 2 on each chain, except on the final tier.
The software creates a pool of glucose units which are used to build the structure one tier at a time. Each time a new chain is about to be built, the software checks from a total of 24 possible directions and eliminates those that would grow toward the inner parts of the structure as it is not physically possible that the molecule is synthesized towards the core of the structure. The procedure to make this elimination is to discard the growth of any chain with a distance between its end and the centre of the molecule that is less than the distance of another chain belonging to two preceding tiers. This method generates a molecule with a more circular shape.
To make it easier to visualise, the software does not allow for chains to cross paths on the same plane, which does reduce the number of valid tiers compared to a three dimensional model. If there is more than one possible valid chain then the software will randomly select which valid chain to build.
Glyco2D Predictions
Glyco2D produces three structural predictions.
Unmodified Structure
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam
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.
Modified Structure
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam
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.
Restricted Growth Structure
Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam.
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.
