[modeller_usage] R: question for a (putative?) disulfide bridge

[Anna Marabotti <>]

Dear Ben,
thank you for your message, and sorry to bother you again. I tried to use model.patch() to add the disulfide
bridge to my model, but I have a supplementary problem. In fact, my protein is a homodimer and the disulfide
bridge should link two Cys residues in the two different subunits. I tried to indicate "A" and "B" in the
script in this way:
# Create the disulfide bond:
def patches(mdl):
    mdl.patch(residue_type='DISU', residues=(mdl.residues['55:A.'],
                                             		mdl.residues['180:B']))

but it doesn't work. What is the correct way to include this supplementary information about the chains?
Many thanks again and best regards
Anna


-----Messaggio originale-----
Da: Modeller Caretaker [">mailto:] 
Inviato: giovedì 20 novembre 2008 18.58
A: Anna Marabotti
Cc: 
Oggetto: Re: [modeller_usage] question for a (putative?) disulfide bridge

Anna Marabotti wrote:
> using mutate_model I replaced a residue in a protein with Cys.
> Looking at the mutant protein, I saw that this new Cys residue is
> near to another Cys residue that was previously in the protein. The
> two sulphur moieties are not facing each others as in a disulfide
> bridge, but are rotated away. However, manually rotating the side 
> chains, they can approach their sulphur moieties until less than 3A
> of distance, so in my opinion a disulfide bridge could be formed. At
> present I have not experimental data to confirm if a disulfide bridge
> is forming or not in this mutant. How can I check with MODELLER if
> this newly introduced mutation is really able to form a new disulfide
> bridge into my protein? How can I model this new disulfide bridge?

You can use model.patch() to add a disulfide bridge (see
http://salilab.org/modeller/9v5/manual/node24.html) and build a model in
the usual fashion (you could use your original model prior to
mutate_model as your template, and use the mutated sequence as your
target, or you could use the output from mutate_model as your template
and use a 1:1 alignment). The standard assessment scores will give you
an idea whether the resulting model is native-like, but you can't be
sure that means a disulfide bridge exists.

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