Hi, I am trying to model circular permutation in my protein which is a beta barrel and I modeled it the following way-- AAAA-----BBB--------CCC------- A and B comprise the two halves of beta barrel and ---- refers to a cut in the loop region of beta barrel where the other domain has to be attached ... I generated some 20 models but none of them was satisfactory as the beta-barrel gets distorted in each of those models.. Can any body tell how can I achieve good models for modeling circular permutation ???
---------- Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
E-mail : monu46010@yahoo.com
On 2/16/11 5:23 AM, bharat lal wrote: > I am trying to model circular permutation in my protein which is a beta > barrel and I modeled it the following way-- > > AAAA-----BBB > --------CCC-------
If this is really your alignment, Modeller will try to use structural information from both B and C for two residues (and nothing at all for the linker between A and B). That's probably not going to work. You might want to manually perform the mutation first in one of your template PDB files, and give Modeller that modified template.
Ben Webb, Modeller Caretaker
participants (2)
-
bharat lal -
Modeller Caretaker