CORAL and contact region between 2 proteins

Global minimization programs: SASREF, CORAL, BUNCH, GLOBSYMM
Post Reply
Message
Author
giachin
Guest
Posts: 1
Joined: 2020.10.26 09:22

CORAL and contact region between 2 proteins

#1 Post by giachin » 2020.10.26 09:51

Dear SaxieR community,

I am a stuck with rigid body modelling of a complex of two proteins for which I have recently collected SAXS data on the complex only (i.e. 38.9 kDa monomeric protein A + 23 kDa monomeric protein B). Here some more info to let you know better my questions.

I have the X-ray crystallographic structure that covers 95% of protein A sequence, while I have only a homology model that covers approximately 60% of the protein B C-terminal sequence. 40% of protein B is predicted to be partially unfolded. Contact regions between A and B are known from literature. Modelling A + B without missing segment is duable but the fitting is quite bad (Chi square around 3.5), therefore I have added "dummy atoms" on B N-terminal region using CORAL on-line. Here I haven't added the contact region yet, but I see that the fitting is much better (Chi square around 1).

My questions are the following:

(1) Is there the possibility to add contact region on CORAL on-line?
(2) I have tried to run CORAL locally, but I am stuck where to add the contact region information. Should I add them in the configuration ".con" file? If yes, how and where?
(3) Does EOM allow to add contact region? As far as I see no....
(4) finally, does SASREF allow to add missing segments?

Many many thanks for your attention. Any suggestion is welcomed.

Gabriele

Post Reply