Efficient way to check pdb enzyme protein models with certain mutations if the active site still works?

Question

[skim]

Hello. I have an original pdb file of each of some enzyme proteins. I also have pdb files that I have built using homology modelling after making some mutations with the fasta sequrnces. I would like to check if the mutated enzymes still do their functions on their active sites using a computer program. Programs like TM-Score and etc show very similar scores even if there are a substancial amount of mutations. How should I do this efficiently and with a mininum amount of error? This is only for prediction before actually doing wet lab, but it should be efficient enough.

Thank you very much in advance.

Answer 1

[Joe]

I think this would most likely be quite difficult, and it's probably not guaranteed to work 100%.

Your TM scores are similar because they compare the structural similarity of the models in 3D space. Changing a single base here and there may, but is unlikely to, change the overall gross structure very much. There may be one or two very key residues (e.g. If you disrupted a disulphide bridge), but I'm guessing you used an approach like Phyre2 or ITASSER, which both use threading, and so they will coerce the structure to look very similar to the known templates anyway.

The only way I can think that you could try this would be to use something like AutoDock Vina to try simulated ligand docking of the known enzyme substrates. This should give you values for the binding strength and so on. If these numbers get worse for your attenuated sequences, that would be a reasonable bet that they are likely going to make a non functioning or lower functioning protein.

Docking approaches can be tricky and often give spurious results though, so be careful.

[skim]

Thank you for the recommendation. Is it possible to automate the process using for example python subprocess module with vina?

[Joe]

I don't see why not. I have never done it myself so can't give you specifics, but I believe it has a commandline interface. You need not even necessarily appeal to Python to do it. Some simple shell scripting should allow you to launch several docking jobs at once if that is all you want to do.

Alternatively, UCSF Chimera is written mostly in python, and has a Docking module you could make use of. Their documentation is extensive, so I won't even attempt to delve in to detail here.