[Chimera-users] Model protein with coenzyme

[Elaine Meng]

Hello Xinxin,
Depends what you mean by "model" -- if you mean view and analyze structures of proteins with ligands and cofactors, the answer is yes.  If you mean that you have a structure of a protein but it does not have the coenzyme, the answer is maybe... It depends what information you have already about the protein, and whether there are known structures of similar proteins that include the cofactor molecule.

If there is a known structure of a similar protein (e.g. same fold) that already includes the cofactor molecule in it, then if you are willing to assume that your protein binds it the same way, you can superimpose the two proteins and then just use that position of the coenzyme after deleting the protein part.  Superimposing structures, for example with Matchmaker:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

That will give you two models, one with your protein, and one with just the coenzyme.  Depending on what you  need this cofactor-enzyme structure for, you may need to combine them into a single model with the "copy/combine" button on the  
right side of the Model Panel (Favorites... Model Panel) or with the  
"combine" command.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>

If you don't have a similar protein with cofactor included in the structure, then it depends what you know about your protein.  You could try to put the cofactor molecule in "manually" which would include moving it with the mouse and rotating bonds to change the conformation of the cofactor and possibly also parts of the protein like sidechains. However, this can be very, very difficult. 
Moving models separately: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>
Rotating bonds:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

 Instead, you may need to use a separate molecular docking program (not Chimera but a totally different program, e.g. DOCK, SwissDock, Autodock Vina, etc.).

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> From: Xinxin <zhuxinxin17 at mails.ucas.edu.cn>
> Date: January 22, 2022 at 4:36:13 AM PST
> 
> Description
> I want ask a question, could the Chimera model protein with coenzyme? And how to perform?
> Thank you very much.