Comparative modeling of metalloproteins

[Anonymous]

Hi,

Hope everybody is doing well. 

I’m just getting used to using Rosetta and would appreciate some pointers with regards to comparative modeling of metalloproteins. 

I have a protein (155 amino acids) that binds to Zn. I know exactly which amino acids the zn atoms interacts with and I have 2 homologs for templates with homology in the 65% region. I’ve been reading this tutorial

https://www.rosettacommons.org/demos/latest/tutorials/rosetta_cm/rosetta_cm_tutorial

and I can’t tell if Rosetta will account for the Zn because they are in my templates or do I have to specify there are Zn atoms in certain positions separately?

Thanks!,

Chi 

[Anonymous]

hello,

I believe Rosetta will account for the Zn atoms. so long as they are at the end of the each of the template pdb files.

However — watchout for protonation states! Rosetta will not by default remove protons or setup proper tetrahedral geometries.

I would suggest running rosettaCM as best as you can, and If you do not like the results and wish to model the Zn ions better, you can email me at {myname} @ uw.edu. I have some unpublished methods that can help you — but you will need to write a little bit of python code.

~Dan

[Anonymous]

Hi Dan,

Thanks for your reply. 

I’ll have a go at the modeling as best I can and see where it takes me. Will get back to you if my model goes pear-sharped! 

Have a good day!,

Chi

[Anonymous]

Hi everyone,

Just wanted to drop an update on this thread. 

Had another go at modeling my awesome metalloprotein and it looks like Rosetta removed the zinc atoms from my templates at the threading stage (2b, thread target sequences in the above tutorial link) so when it outputs the my_protein.pdb.pdb file the zincs have disappeared. I tried putting them back into the pdb manually and then run hybridize but Rosetta then errors out – not entirely sure what the error message was trying to tell me but think it was something along the lines of it wasn’t able to find or align my last atom to something else. 

Dan I’ve sent you an email about borrowing your code. 

If anyone knows any other tricks do shout! 

Have a good day!,

Chi 

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