Thanks for this, the second link is particularly useful. I guess I wanted to model it because it would be cool to make use of alphafold, and the pretty pictures might help convince my supervisor that this is possible.
It's also not a perfect straight line between both termini (minor deviation around the outside required). I'm also concerned that too long a linker will allow multimerisation in the opposite direction (i.e. clockwise vs anticlockwise), as is seen for concatenated cys-loop receptors. For now I'll probably start with a long linker and validate experimentally before optimising. I'll let you guys know if I manage to model the dimer.
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What are the errors you are getting for the failed Gly linked trimer? What step is failing? Are you potentially running out of memory in the GPU you are using?
Potentially trying to use one of the larger GPUs could alleviate the issue, something like a V100 or A100 if it is a memory error.
You could also try running the analysis as a homodimer first to check the effect of different length linkers. That said, the first multimers were created using this concept, and this is why AF2-Multimer was developed. To my knowledge the non-linker multimer structures are better predicted.
Thanks, that's good idea to run the dimer first (kinda obvious now that I think of it). The structures are just messy combinations, whereas the actual protein complex has substantial intersubunit contacts with threading loops and threefold symmetry.
I should have added that I'm running this through the Cosmic website. On Google colab I run out of free GPU time before I can get a homotrimer. I suspect that running a linked dimer/trimer on multimeter mode would help (option on Google colab alphafold, not sure on Cosmic). I should just pay for Google colab I guess, the cost is negligible compared to the kits and time needed to clone these constructs.
Given that there's already a cryo structure of this, is there any way to force it onto a template? I'm just trying to get a rough idea of necessary linker length (the termini already have a few flexible AAs).
I'm new to this so I'm also struggling to get my head around the parameters such as suitable # of models vs recycles.
Yeah, I suspect you're exceeding the limits of free allowances and that's the reason it's failing.
Setting up GCP and colabfold is pretty easy and for a single complex it'll be cheap if you use the cost-efficient T4s. You usually can get some free credits too so may not even have to pay for this project. I think the length limit is ~2500 AAs at the moment.
From experience, I doubt you'll manage to get a good resolution of such a complex interaction. We couldn't replicate the interaction between Roq1 and XopQ for example. And whilst it's close and general orientation is correct, there are a lot of fine scale differences. This is especially true for unstructured looping regions in my work. Good luck!