Today I released a tutorial about how to use Molecular Maya’s Modeling Kit to fill in a missing region from protein data, based on the illustration I shared in my previous post. You can learn more about Molecular Maya and the modeling add-on kit here (https://clarafi.com/tools/mmaya/), but even if you don’t have the kit, there’s still a number of points about structural data and how to understand PDB reports that may be helpful.
The protein up for demonstration here is a eukaryotic translation initiation factor (English: It helps get messenger RNA to the ribosome so proteins can be made). The challenging thing about this protein is it has a long flexible “disordered” tail that is not included in the x-ray crystallography data, because flexible poorly-structured regions just don’t crystallize well, so this is a very typical scenario when trying to use Protein Data Bank (PDB) files.
Fortunately, we do know the amino acid sequence of this tail, and we can use features of the mMaya modeling kit to synthesize and simulate the missing region, allowing us to complete our protein model.
I hope this tutorial is interesting and useful. If you have questions or if you’d like to see a tutorial on another aspect of building molecular models, you can ask me in the YouTube comments, or DM me on Twitter, or any number of ways!
Thanks for reading (and watching)!
Stuart