Hi,
I am trying to model a fusion protein construct that is designed using two proteins connected by a linker. Since the structures of the two individual proteins (cyclinD-CDK4) associating with each other is known, I was expecting that the 2 subunits in fusion construct will be associating in a similar fashion. These are the results of my job: http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S226571/
The fusion is designed as His tag-cyclinD-linker(GGGGSGGGGSGGGGS)-CDK4-Strep tag. I noticed that the alignment program has only picked up the CDK4 portion of the fusion as the closest match and the Cyclin portion is completely ignored. As a result when I compared the alignments of the predicted models with reference Pdb: 2W96 in PyMOL, RMSD values were widely variable with predicted model 4 and 5 having the least RMSD values of 14 and 15 respectively. I am not every confident of these predicted models. So can someone please help me in the correct use of iTASSER for modeling multimeric proteins based on known structures of individual subunits?
Thank you.