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

[Anna Marabotti <>]

Dear Modeller caretaker,
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?
Many thanks and best regards
Anna Marabotti

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Anna Marabotti, Ph.D.
Laboratorio di Bioinformatica e Biologia Computazionale
Istituto di Scienze dell'Alimentazione, CNR
Via Roma 52 A/C
83100 Avellino (Italy)
Tel: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: 
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
Coming soon: BBCC2008: http://bioinformatica.isa.cnr.it/BBCC/BBCC2008
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