CORAL - spacing between proteins in protein complex

Global minimization programs: SASREF, CORAL, BUNCH, GLOBSYMM
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BD
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CORAL - spacing between proteins in protein complex

#1 Post by BD » 2022.01.13 17:55

Dear all,

I collected SAXS data on a protein complex that consists of a dimeric protein A bound to two copies of protein B.
From other experiments I know that it is the intrinsically disordered C-terminus of protein B that interacts with protein A.
High-resolution structures are available of the dimeric protein A and of protein B, but in the latter structure the intrinsically disordered C-terminus (50 amino acids long) is missing.
I tried to use CORAL to model the complex between protein A and B, using the input parameters in attachment on the online web interface.

However, in the resulting model, one copy of protein B is always moved very far away from the other copy of protein B and the dimeric protein A. Moreover, I always receive following message:
“Warning: truncating input data to length: 2048”

Does anyone know what this means and if there is anything I can change in the input settings to overcome this problem (I added the .log file in attachment)?

Thank you very much in advance.

BD
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try3_4.log
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Input parameters
Input parameters
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Re: Warning: truncating input data to length: 2048

#2 Post by biosaxs.com » 2022.01.14 10:31

BD wrote: 2022.01.13 17:55... Moreover, I always receive following message:
“Warning: truncating input data to length: 2048”
This means your experimental data contains more points than CORAL can handle and only the first 2048 points are taken for fitting.

Does the molecular weight estimated from your SAXS data correspond to the molecular weight of your protein complex?
Do you know what residue of protein A interacts with the intrinsically disordered C-terminus of protein B?

BD
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Re: CORAL - spacing between proteins in protein complex

#3 Post by BD » 2022.01.17 13:28

Hi,

Thank you for your reply.
The estimated molecular weight indeed corresponds to the expected molecular weight of my complex.
I do know what residue of protein A interacts with the disordered C-terminus. Can I impose this contact condition even though the C-terminus is not part of the crystal structure of protein B?

Best regards,

BD

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CORAL contact conditions file

#4 Post by biosaxs.com » 2022.03.25 15:54

BD wrote: 2022.01.17 13:28I do know what residue of protein A interacts with the disordered C-terminus. Can I impose this contact condition even though the C-terminus is not part of the crystal structure of protein B?
Yes, you can run CORAL on your PC and specify the contact in a contact conditions file.

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