I'm studying a transmembrane ion channel (protein 1). There are structures of protein 1 in a closed conformation, and I am interested in the open conformation. There is a very similar protein in an open conformation (protein 2). So I am trying to thread the sequence of protein 1 onto the atomic model of protein 2. I know the template.
I tried robetta and swiss prot for this. How should I do things with modeller? Could someone point me to a tutorial? The sequences are quite similar, except for some insertions. I know my protein very well and am looking for a protein modelling approach where I can have low level control, and manual manipulation at the sequence alignment and structure level. I don't need something that does everything automagically.
-- Geoffrey Woollard, MSc PhD student Department of Medical Biophysics, University of Toronto Princess Margaret Cancer Centre, University Health Network
On 6/10/20 5:45 AM, Geoffrey Woollard via modeller_usage wrote: > I'm studying a transmembrane ion channel (protein 1). There are > structures of protein 1 in a closed conformation, and I am interested in > the open conformation. There is a very similar protein in an open > conformation (protein 2). So I am trying to thread the sequence of > protein 1 onto the atomic model of protein 2. I know the template.
This should be very straightforward to do with Modeller. See the simple example at https://salilab.org/modeller/9.24/manual/node16.html
Ben Webb, Modeller Caretaker
Thanks! As a proof of concept, I modelled the full length sequence onto the structure (ie I filled in the missing densities from loops etc).
I did this proof of concept with one protomer. However the channel is a homotetramer with C4 symmetry.
The structure of the tetramer is known (ie chains ABCD, with C4 symmetry). However, I can't just duplicate the protomer and align it with the each chain in the tetramer because some of the new modelled density clashes with where the tetramer contacts are. This included the ion pore, which interests me, and which I want to get right.
Can I do the modelling in the context of the tetramer? Otherwise I would have to just do it with the protomer, and then delete out parts that were clashing.
Are there options for applying symmetry during modelling? Or at least telling modeller that other density is present and to avoid clashing (in this case the new density of one protomer might clash with the missing density of the rest of the tetramer).
On Wed, Jun 10, 2020 at 1:34 PM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 6/10/20 5:45 AM, Geoffrey Woollard via modeller_usage wrote: > > I'm studying a transmembrane ion channel (protein 1). There are > > structures of protein 1 in a closed conformation, and I am interested in > > the open conformation. There is a very similar protein in an open > > conformation (protein 2). So I am trying to thread the sequence of > > protein 1 onto the atomic model of protein 2. I know the template. > > This should be very straightforward to do with Modeller. See the simple > example at https://salilab.org/modeller/9.24/manual/node16.html > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Geoffrey Woollard -
Modeller Caretaker