Which program to use to model protein modified by DNA?

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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kurinji
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Which program to use to model protein modified by DNA?

#1 Post by kurinji » 2017.11.29 18:01

Hi,
I have SAXS data from a protein which has been modified by double stranded DNA of a known sequence(22 base pairs) by covalently attaching the DNA to the surface accessible amines on the protein. I also have SAXS data from the unmodified protein and a rough estimate of the number of DNA strands attached to each protein. I was wondering which ATSAS program would be the most appropriate to model my system?

Thank you :)

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AL
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Re: Which program to use to model protein modified by DNA?

#2 Post by AL » 2017.12.13 13:33

(It's not clear if your protein is partially unfolded. I'll assume it is well folded.)

If you have a model of the protein - start with comparing fitting it to your "unmodified protein" SAXS data with CRYSOL. You may try to improve the fit with SREFLEX.
If you have a model of the DNA you may model the protein:DNA complex with SASREF. You may want to break the protein model into several rigid bodies with PARCOOR.

If you don't have any atomistic models you may try your luck with DARA to see if there is a protein:nucleic acid model in PDB that fits your data and consists of a DNA and a protein of the sizes you expect.
You may model your protein:DNA complex ab initio with MONSA. The protein alone can be modelled with DAMMIF, DAMMIN or GASBOR.

All these programs you can run from a web interface.

kurinji
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Re: Which program to use to model protein modified by DNA?

#3 Post by kurinji » 2017.12.13 19:36

My protein is folded and I have managed to fit the experimental SAXS data from the unmodified protein to the scattering envelope produced from the corresponding PDB file using CRYSOL. However, I do not have an atomistic model for the DNA - so I will attempt to use DARA or MONSA as you suggested. Thank you for your suggestions! :)

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