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