Re: [modeller_usage] [Fwd: modeling crosslinked homodimeric protein]

[Modeller Caretaker <>]

> hello everybody,
> i am tryong to model the structure of enzyme which is crosslinked
> homodimeric protein
> two identical chains of protein are crosslinked in opposite orientation
> to form the two compete active sites.
> that is, both chains contribute fo the foramtion of aech of the active
> site. (there are 64 hydrogen bonds involved in inetaction between two
> chains)
> i tried to model to chains seperatly and superimpossed bsed on template,
> but the orientation of the chains is not giving the proper active site, so
> how i can model the whole protein, i.e. both the chains simultaneously
> so that i can get full active site?
> or is there any way by which seperatly modeled chaines can be put together?
> please suggest any solution for this problem.

It is straightforward to model both chains together - just add a chain 
break (/) to your alignment. See 
http://salilab.org/modeller/9v1/manual/node27.html for an example. (That 
example also constrains the two chains to be symmetrical, but you don't 
have to do that, of course.)

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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