Hi Rohit
Since you are saying the C terminus in crystal structure is not
end of your protein in crystal, and you are worried about its charge status, is
in't a good idea to model few residues beyond the C terminus you see in crystal
structure using weak electron density and crystal packing as guide and then do
the electrostatic calculation. Even if you are modeling it as COOH, it's not
going to be true end anyway. Two or three extra residues should be sufficient
as ionic interaction is going to be quite weak beyond 8-10 A.
Dhiraj
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of rohit kumar
<rohit...@gmail.com>
Sent: Wednesday, September 22, 2021 4:29 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: [External] [ccp4bb] Protein's C-terminal neutral
Hello Everyone,
Is there any way that I could make my protein's C-terminal neutral using Coot?
Actually, I have a protein-peptide complex structure and my peptide is bound at
the C-terminal end. While making a surface charge diagram it is negatively
charged (because of the CO group at the end, which is not the end residue of my
purified protein) and I want to make it neutral (possibly a peptide bond in
solution).
Please let me know if I am clear enough with my question.
Thank you
--
Regards
Dr. Rohit Kumar Singh
Postdoctoral fellow
Aurora CO USA
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