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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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage