I like to replace arginine with argpyrimidine. It is easy to change the amino acid, but i am not finding a way how to add a new chemical structure in the place of an existing amino acid. Thanks for the help.
(The answer below assumes you are trying to do this with a downloaded pdb in a molecular modelling package to play with molecular docking)
I used to do this using a stand-alone version of WebLabViewerPro (no longer available, but maybe a similar package can be found?). You could build a pyrimidine around the initial arginine, then isolate that tiny modified part with the lasso tool, and try to do a very local molecular minimization - just to get bond angles and distances for the introduced ring correct. You might need to guess at the likely interactions with other residues and set up bump monitors and distance monitors. You may need to move rotatable bonds for the side chain for residue manually - guessing at the desired conformation and intramolecular interactions. Then maybe do a slightly larger side chain minimization for just this residue. Each time getting ready to hit the "go back" button if the minimized structure is too goofy.
All of this would be very highly speculative, because the residue modification might locally or regionally induce new conformations to the protein. (Especially in this case, since you've just capped off the arginine base).
Good luck!
Yes Michael, you are right. Argpyrimidine is one of advanced glycosylation end products formed in diabetes by coupling of glucose with arginines on proteins. Once formed it locally changes protein structure. Such studies only tell about gross changes in protein structure by CD or FTIR. So need to run simulation the way you suggested.
Thank you Michael J Malaska for your kind help. I will try to do that. Thank you Madhav Joglekar for your suggestions.
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