Repeating sequence in Rosetta de novo protein folding

[Anonymous]

Hi,

I am trying to do a de novo protein folding from a protein sequence with repeating Gly and Arg only.

So the sequence looks like GRGRGRGRGR….. I put the sequence onto Robetta Fragment Server and it gave me this error message:

=======================================================================================

Target:    GR25

Status:    Error

Date Submitted:    02/07/18 01:54:32 AM

Started:    02/07/18 04:29:00 AM

Ended:    02/07/18 05:07:22 AM

Expires:    02/14/18 05:07:22 AM   (6 days 08:41:40)

Sequence:    

GRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGRGR

Length:    50

Exclude Homologues:    no

Error

sam target99 failed! 

=========================================================================================

This might be a dumb question but I was wondering if there are some restrictions on the usage of de novo protein folding in Rosetta when the sequence is repeating…?

Thanks for your help! 

 

Orion

 

[Anonymous]

Fragment prediction is based on finding chunks of PDBs with similar sequences and/or similar predicted secondary structure to the request.  I would guess that nothing looks like this that’s in the PDB, so the system errors out.  I guess try BLASTing this sequence against what’s been crystallized to see if there are any hits.

[Anonymous]

Do you have any reason to believe that your sequence will be folded/structured in vivo?

If you perform disorder prediction by submitting that sequence to DISOPRED3 at bioinf.cs.ucl.ac.uk/psipred/ then you will see that it is predicted to be “disordered state, protein binding”  with a confidence near 1.0.

Warning: If you ask Rosetta to fold a sequence, it will give you the best folded structure it can find. But if that sequence prefers to be unstructured, then your prediction may have little value.

 

[Author]

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