-------- Original Message -------- Subject: modeling crosslinked homodimeric protein Date: Mon, 26 Mar 2007 10:29:24 +0530 From: Archana Chavan archananiper@gmail.com To: modeller-care@salilab.org
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.
Thanks in advance.
> 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