Hi, Dr. Kirschner,
Thank you so much for your help!
Wei Chen
ÒýÓÃ kkirschn.hamilton.edu:
> Hi Wei,
> Tough question. It depends...using GLYCAM...
>
> 1) If you have a pdb structure that contains the coordinates of the
> protein and the polysaccharide, it is a relatively straight forward
> exercise. Essentially you have to rename the residues to match the
> Glycam residue name, which can be found in the manual (including the
> N-linked amino acid to NLN). Now, if the polysaccharide is branched,
> then you have to modify the input pdb to terminate each linear
> carbohydrate sequence with "TER". After you have done this you will
> have to create a bond between the linear sequence to create the
> branched scacharide using leap and the bond command. You may have to
> create a bond between the polysaccharide and the protein as well.
> Please see the manual for help on this (Section 2.7.3 and Ch. 3) and
> the correction for the carbohydrate example on the website (http://
> amber.scripps.edu/doc8/man9_example.html).
>
> 2) Now if you are trying to create a polysaccharide chain and add to
> your protein of interest, this takes a little more effort. I would
> suggest that you "grow" the carbohydrate one residue at a time by
> renaming the atom label within the NLN amino acid residue that will
> be the C1 atom on the first attached carbohydrate(I think it is a
> hydrogen) to C1 atom type. (Make sure you renumber the residue number
> as well.) Execute leap and it will add the missing atoms (ie all but
> C1), and thus it will put the carbohydrate in for you based on its
> internal coordinate present in the prep file. Visually check to see
> if there are any poor contacts between the carbohydrate and protein,
> correct them by using the impose command in leap (or using the edit
> command in xleap to display it graphically and manipulate it from
> there). Grow the second carbohydrate by renaming the appropriate
> hydrogen on the previous carbohydrate to C1 for the next carbohydrate
> (again, make sure you rename the residue number). Run leap to add
> the missing atoms, and visualize the output to ensure proper contacts
> again. Repeat until the terminal carbohydrate is achieved. A sander
> minimization on the NLN-polysaccharide will remove any erroneously
> short bond distances or close contacts. This is by no means a
> trivial task but it gives the most control over the formation of the
> polysaccharide with respect to the protein structure.
>
> I am sure that there is probably better methodologies out there, but
> this is how my mind works out the problem. If you are having trouble
> and you keep getting errors - start small by making sure you
> understand how to create a polysaccharide (linear and branched) using
> leap (see manual/Amber8 web page); then add your manufactured
> polysaccharide to a capped NLN molecule. If you can achieve and
> understand these small goals then proceed to your larger system.
>
> Good luck,
> Karl
> ____________________________________
> Karl N. Kirschner, Ph.D.
> Visiting Assistant Professor of Chemistry
> Hamilton College, Clinton NY 13323
> ____________________________________
>
> On Aug 17, 2005, at 2:25 PM, Wei Chen wrote:
> > Dear Amber users,
> > I want to attach a sugar chain to a protein, e.g. N-glycan. Does
> > anybody know how I can do this?
> > Thanks,
> > Wei Chen
>
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Received on Wed Aug 17 2005 - 23:53:00 PDT
