Team:NRP-UEA-Norwich/Modeling/3D
3D Modelling Overview
We built 3D models to see how changing parameters such as branching degree and the number of tiers affect the overall structure of the molecule in a chemically accurate way.
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Glycogen
Glycogen is the glucose storage molecule in animals, bacteria and fungi. It is a polysaccharide composed of monosaccharide glucose units linked by alpha-1,4 glycosidic bonds. Each linear chain contains approximately 13 glucose residues and a number of alpha-1,6 glycosidic bonds, which allow branching, that are 3–4 residues apart. Glycogen is the analogue of starch in plants but is more extensively branched and compact.
This simple model - created for our wiki by the SWEET software1 - shows a small section of a glycogen molecule consisting of 91 glucose units which are contained within 7 branches and 3 tiers. The 1,4 linked sections can be seen to coil into a helical shape, and the 1,6 linkages form helical branches away from the centre of the molecule.
You can interact with the model using your mouse.
3D Printing
Our knowledge of developments in 3D printing suggested that we could take advantage of this to generate physical models of the molecules we are interested in. This would be helpful in explaining the chemical structure of these molecules because the models would be truly interactive.
The process of creating a model that is valid to be 3D printed from a PDB file, which is a textual file format describing the three-dimensional structures of molecules, turned out to be very challenging. After what seemed like an impossible task and a number of failed attempts, we managed to successful create a valid 3D model that could be printed. The print itself took just over 28 hours.
You can see some the pictures from our 3D printing adventure in our 3D printing gallery!
References
1. SWEET - a program for constructing 3D models of saccharides from their sequences using standard nomenclature. http://glycosciences.de/modeling/sweet2/doc/index.php
