Use circular permutation approach to solve and visualize chiral assemblies of Type IV collagen protomers. The approach provided here is applicable to other domains of interest, not simply biochemistry. Lastly, please note that the code/method here is rough and the code isn't particularly elegant, but it gets the job done and is easy to read.
The biology of collagen
Collagen is the most abundant protein in animals and during its synthesis, three collagen polypeptide strands are assembled in triple-helix quaternary structure. You can ready all about it here. These triple-helix assemblies - effectively trimers - are also called protomers. There are many types of collagens but this page is focused on human Type IV collagen. There are six genes for Type IV Collagen, and their protein products are α1, α2, α3, α4, α5, and α6. These can be mixed into protomers to form functional collagen.
| Subunit | Representation |
|---|---|
| α1 |  |
| α2 |  |
| α3 |  |
| α4 |  |
| α5 |  |
| α6 |  |
However, only a handful of trimer configurations have been discovered to exist in nature: α1-α1-α2, α3-α4-α5, and α5-α5-α6.
Solved as a linear model, there are 432 possible trimers. However, the circular arrangement of these results in the use of circular permutations to address uniqueness. For example, the timer α1-α1-α2 is the same as α1-α2-α1 and the same as α2-α1-α1. Moreover, even when we solve the number of possible trimers, not all of these have been observed in nature.
- Python 2.7
- Processing 2.2
- Use
generate-nonredundant-trimers.pyto solve and generate list of chiral trimer assemblies. - Take output and inject it into one the
simple*scripts in the Processing folder
Use processing/simple/simple.py
Use processing/simple_with_labels/simple_with_labels.
Use processing/simple_with_labels_and_inner_circle/simple_with_labels_and_inner_circle.py
sketch_arc_midpoint.py - calculate and generate arc midpoint
sketch_static.py - image array generator, this was simply a go-between towards final scripts.
