protein peptide complex scattering profile

Calculation of SAXS and SANS profiles (CRYSOL, CRYSON), superposition of models (SUPCOMB, DAMAVER, DAMCLUST), database DARA
Post Reply
Message
Author
zhuwenkai
Active member
Posts: 17
Joined: 2016.09.27 19:06

protein peptide complex scattering profile

#1 Post by zhuwenkai » 2016.09.27 19:29

Hi,
I am dealing with a protein-peptide complex. when i compared my experimental curves with theoretical curve computed by crysol,i was wondering what contrast should i substract, buffer vs buffer with peptide.?
the atoms of the peptide are also included in the pdb file, would the crysol take the contribution of the peptide into
consideration?

ckerr
Active member
Posts: 86
Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: protein peptide complex scattering profile

#2 Post by ckerr » 2016.09.28 08:49

You should aim to subtract what is left in the buffer after [some of] the peptide has bound to the protein. If the concentration ratio is 1:1 then there is no free peptide left after binding, so you should subtract the buffer without peptide. If you have a large excess of peptide then the concentration in the buffer is almost the same as before binding, so you should subtract the buffer with peptide.

CRYSOL will by default use all ATOM and HETATM records in a PDB file which are not waters, explicit hydrogens, or rotamer alternatives of atoms which have already been read. So if the peptide is in the PDB file it will be included in the calculated scattering.

zhuwenkai
Active member
Posts: 17
Joined: 2016.09.27 19:06

Re: protein peptide complex scattering profile

#3 Post by zhuwenkai » 2016.09.28 09:32

thank you for your quick reply, i got it.It depends on the affinity of the complex, i think i know what to substract.

ckerr
Active member
Posts: 86
Joined: 2015.03.25 09:03
Location: EMBL Hamburg

Re: protein peptide complex scattering profile

#4 Post by ckerr » 2016.09.28 12:03

ckerr wrote:CRYSOL will by default use all ATOM and HETATM records in a PDB file which are not waters, explicit hydrogens, or rotamer alternatives of atoms which have already been read. So if the peptide is in the PDB file it will be included in the calculated scattering.
Sorry, I was looking at the development version when I wrote that. Skipping of rotamer alternatives is not in any of the currently available CRYSOL versions, but will be in the next release (2.8.0). However, that doesn't affect this issue.

Post Reply