Hello,
A few days ago I asked on the amber list about how to modify a neutral
lysine in order to make another bond.
The system that I study is something like this:
O O
|| ||
protein - Lys - N(NZ) - C - linker - C - N(NZ) - Lys - protein
| |
H H
Basically the NZ atom of the lysine residue has one hydrogen attached to it
and enters in a peptidic bond with the CO group of the linker.
I've managed to get all the bonds in xleap, but now comes the big problem.
First I was interested in determining the charge for the lysine residues,
but since I've removed an hydrogen they are now -1. Unfortunately I don't
have access to the JCC paper where the procedure of getting charges for
amino acids is described (for example CYX).
It would help me alot if someone could suggest a way on how to derive the
charges for a charged amino acid and secoundly, should I constrain the
charges on the CO moieties of the linker (I've seen that for almost all
amino acids the atoms that enter a peptidic group have constrained charges).
Thank you
Marius
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Received on Sun Apr 05 2009 - 01:15:22 PDT
