Assembly a multi-domain protein from available mono-domain?

Interactive modelling (MASSHA, SASpy) and global minimization programs (SASREF, BUNCH, CORAL, GLOBSYMM)
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Sidamo
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Assembly a multi-domain protein from available mono-domain?

#1 Post by Sidamo » 2018.11.06 10:33

Hello :)

I am new to SAXS, this is the first time of my atomic modeling, so maybe the questions I asked are really naive :oops: .
I'm trying to assembly a two domain proteins, which have available structure of each two domains, and I've collected the SAXS data of full-length protein.
But now, I'm not really sure which software to use.
According to https://bmcstructbiol.biomedcentral.com ... 6807-12-17
the BUNCH program is designed specifically for the multi-domain assembly task, so I tried to use it but it didn't work. ( I'm not sure the reason, but I've put the .pdb or .seq file in the bin folder, but the pre-bunch answered me "not exist" and crash.

In the other hand, I tried to use FoXSDock and fitted two mono-domain in SAXS data to build full-length atomic model, but the SAXS X score is too high....(higher than 30...)

Please give me some ideas, or is there any protocol or practicing about assembling a multi-domain proteins from available mono-domain?

Thank you very much.

Sidamo
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Re: Assembly a multi-domain protein from available mono-domain?

#2 Post by Sidamo » 2018.11.08 07:41

This is the product of FoXSDock, and I'm wondering why the X score is so high....and how to fix it, and also it seems normal in c1 c2.

Image

this is a two domain protein, and I got full-length SAXS experimental data.
One of these domains is available crystal structure from PDB, the other one is from swiss homologous modeling and I use UCSF chimera to build missing residues.
So the molecular weight is equal to the SAXS experimental sample which I used.

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AL
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try SASREF online

#3 Post by AL » 2018.11.08 12:17

Try SASREF online.

Step 1
Experimental data: SAXS (X-ray) only, standard
Number of curves: 1
Number of subunits: 2
Overall symmetry: P1

Step 2
Provide your experimental SAXS data and the two subunits.
Check 'Provide contact conditions'.

Step 3
Provide one contact condition by choosing the last residue of the first subunit and the first residue of the second subunit. It is possible to provide a range of residues, to specify one residue you have to choose the same residue twice.

Sidamo
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Re: Assembly a multi-domain protein from available mono-domain?

#4 Post by Sidamo » 2018.11.22 05:51

It's embarrassed about the result. :oops: :oops:
I've tried several times, but the fitting is still terrible...
Image

the distance constrain seems like it doesn't work or something wrong.
or maybe something wrong in my setting of parameter. :?
Image
Image

SaxsMax
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wrong angular units

#5 Post by SaxsMax » 2018.12.03 14:49

It seems that the experimental data are in inverse angstroems,
but 1/nm is given as the input. Try to rerun with proper units.

Sidamo
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Re: Assembly a multi-domain protein from available mono-domain?

#6 Post by Sidamo » 2018.12.06 07:56

Thank you for your reply!
but, I fit the units into volumetric map,
their fitting are not really bad like that.
Image

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