Modelling and Software

While we were bringing all the parts together in the lab, a lot of unanswered questions started to raised: How does glycogen and starch look like in real life? How will GlgX and GlgB expression affect the glycogen global structure? How this branching and debranching process take place? And, how will the acyltransferases add the acyl group into the glycogen/starch molecule and in which position? Will this addition affect the functionality of the molecule?

Thanks to computers, software and maths, we were able to predict the outcome of all this processes to help us understanding what was going to happen in the lab.

Software: Glyco2D

We used glycogen as a model system to gain a better understanding of the parameters involved in carbohydrate structure, branching and modification.

We built Glyco2D based on the mathematical model that described the structural properties of glycogen based on different parameters such as chain length, branching degree and the number of tiers₁.

Then we used the software 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 colons of rats ₂.

You can learn more by clicking on the image to the right.

3D models

We build 3D models of carbohydrates (glycogen and the 2 components of starch -amylopectine and amylose-) to get a better understanding of the effect of branching degree and chain length on the real structure. We used the SWEET software to build them.

We developed a pipeline to 3D print these molecules. After several attempts, we managed to have our own 3D printed glycogen!

You can learn more by clicking on the image on the right.