Dear Modellers, I am looking for some insight into modeling a heterodimeric complex in a single species. The original crystal structure was solved with Chain A and Chain B from two different species.
Chain A is from humans and Chain B is from mice. I would like to model the whole complex in the mouse form. Chain A is about 77% conserved between mice and humans. Here's my basic protocol.
1) I edited my sequences to contain only the portions modeled in the PDB. 2) I used align2d to create my PIR and PAP files 3) I used automodel and subclassed it to only select chain A for modeling
The final structure looks ok visually. The DOPE score per residue actually decreased by about .01 for a few regions between the crystallographically solved structure and final homology model. Otherwise is looks about the same.
Does this protocol sound correct? Is there anything else I should have done? or other potential problems I should look out for? My main concern is that the dimer interface be as close to the real deal as possible.
I ran one of the models through PDBsum and a couple of Gamma turns were lost. One turn had the same sequence in both human and mouse, but no did not show up as having the secondary structure.
Any help would be greatly appreciated.
Best regards, Kit
Kit Fuhrman IDP Graduate Student Department of Pathology, Immunology and Laboratory Medicine University of Florida College of Medicine kit.fuhrman@pathology.ufl.edu