Question: Modelling a region between 2 domains
0
gravatar for Misty
3.3 years ago by
Misty0
Canada
Misty0 wrote:

Hello,

 

 

I want to predict the 3D structure for my adaptor protein which contains 2 domains (both have multiple homologous PDB structures that I used as templates) and a central "region" between the 2 domains with no good hits (tried PSI-BLAST to no avail). With modeller (Chimera), I got reasonable structures where the 2 domains are but a ridiculously long loop for the central region. I-Tasser, on the other hand, gave a decent looking structure but not exactly what I had hoped for (c-score = -0.73, TM-score = 0.62 and est. RMSD = 9.5 A!). Is there a way to model this region separately with a higher accuracy and then merge them all into one final structure? I eventually want to investigate protein-protein interactions but can't model the protein domain-wise because both domains are required simultaneously (one binds to a kinase and the other recruits effector proteins) and there are multiple tyrosines in the "region" that also play an important role in recruitment of other proteins. I am new to this field and can't code much... so any suggestions regarding different approaches are highly appreciated!

Thanks!

 

 

 

 

 

ADD COMMENTlink written 3.3 years ago by Misty0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1081 users visited in the last hour