How to use CORAL model a dimerized protein?

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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jameshsu
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How to use CORAL model a dimerized protein?

#1 Post by jameshsu » 2016.07.12 23:39

I am new to use CORAL model a dimerized protein.

In my case, this protein has three major domains. I named domain 1, 2 and 3.

The third domain is determined to form the dimerization region.

I attached the pdb files for all three domains. The third one contains the dimer.

My question is how to setup the input files to run CORAL to determine the rigid body modeling? especially the sequence file.

How can I specify these are two chains and fix the dimerization interface? Because I always get an error says "check the sequence and the domains"

Thanks,
Attachments
SrrB.dat
(22.16 KiB) Downloaded 74 times
SrrB_sequence.txt
(381 Bytes) Downloaded 75 times
3d.pdb
(245.61 KiB) Downloaded 74 times
2.pdb
(56.25 KiB) Downloaded 76 times
1.pdb
(30.06 KiB) Downloaded 73 times

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AL
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Re: How to use CORAL model a dimerized protein?

#2 Post by AL » 2016.07.19 11:24

You have to position your dimer to the center of coordinates such that the symmetry axis is aligned with the z-axis (use ALPRAXIN and/or PyMOL). Then remove one monomer from the pdb file.
You don't need the sequence file for CORAL, just figure out how long the linkers between the domains are (and the length of missing N-terminal and C-terminal if any).
Then go to CORAL online and choose:

Experimental data: SrrB.dat
Angular units: 1/A
Overall symmetry: P2
Number of domains: 3
Domain 1: 1.pdb [free] [linker]
Domain 2: 2.pdb [free] [linker]
Domain 3: 3m.pdb [fixed] [C-terminal]

The point is: CORAL should rebuild your dimer from the monomer and leave it intact during the modelling.

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