Modeling a larger protein with multiple templates
Hello I have sent this query before, but noone replied so I will send it again, hoping for some assistance. I am wondering if anyone can help me with this problem I have. I am modeling a large protein and I am using five different templates on different regions of the protein. Let's say the alignment looks like this: MMMMMMMMSMMMMMMMMMMSMMMMMMMMMMMMMMMMMMMSMMMMMMMSMMMMMMMMMSMMMMSMMMM Model AAAAAA----------------AAAAAAAAAAAAAA-------------AAAAAAAASAA------- core template ----BBBBSBBBBBBB--------------------------------------------------- template2 ----------CCCCCCCCCSCCCCC------------------------------------------ template3 ----------------------------------DDDDDSDDDDDDDSDDDDDD------------- template4 ----------------------------------------------------------EEEESEEEE template5 sulfur bridge sulfur bridge sulfur bridge
Overlaps and sequences are of course much longer. The problem is getting the different templates in the same frame of reference, since the alignment is created manually and not by Modeller. The model sequence has very high identity to the core template so what i would like to do is first model with only the core template and then remodel the three large "inserts" with the other four templates and still maintain the sulfur bridges.
Any other suggestions are of course also welcome in trying to solve this problem.
Thank you
On 2/8/10 4:31 AM, nornik wrote: > I am modeling a large protein and I am using five different > templates on different regions of the protein. ... > The problem is getting the different templates in the same frame of > reference, since the alignment is created manually and not by > Modeller.
It doesn't make any difference how you created your alignment - the restraints for modeling are all internal distances in individual templates, so templates do not need to be structurally aligned with each other (I'm assuming that's what you mean by "same frame of reference"). A Modeller-created alignment is no different in this regard from one you make yourself. But this does mean that you need some overlap between your templates so that the distances in the overlap regions are restrained.
> The model sequence has very high identity to the core template so > what i would like to do is first model with only the core template > and then remodel the three large "inserts" with the other four > templates and still maintain the sulfur bridges.
The alignment you posted seems to have reasonable overlap, so it seems like you should be able to do a regular modeling run, selecting all 5 templates as your 'knowns', and everything will just work. But you could certainly build a model, then use the resulting model as a template for a further run, if you really wanted to - you may just lose some accuracy.
Ben Webb, Modeller Caretaker
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nornik