Sulfating GLYCAM Residues

This information is out of date and retained here only for historical purposes.  Use the information here at your own risk!

These instructions apply to O-sulfation of residues from GLYCAM06 and later.

The method for adding sulfation to GLYCAM residues is very similar to the method for building branched structures. The only complicated part involves determining the proper charge adjustment for the residue to which the sulfation is added.

1. Make sure you have a recent set of prep files and parameters.
These can be obtained here. The most current sulfate residue is called SO3 and is included in all GLYCAM_06 prep files beginning with version h. The older version of the residue is called SUL and is still available in the file sulfate.prep.

2. Determine the base GLYCAM residue(s) you need to use.
To do this, first determine the total number of attachment points for each sulfated saccharide monomer. For example, if you wish to build a-D-Manp-(1-6)-b-D-Glcp-OH with sulfation on the glucopyranose at positions 2 and 4, then the residues you will need are ROH (the reducing end hydroxyl group), RGB (b-D-Glcp linked at the 2, 4 and 6 positions) and 0MA (non-reducing end terminal alpha-D-Manp).

3. Determine the amount to alter the charge at each sulfation point.
The sulfate residue contains a sulfur and three oxygens. The sum of charges on the sulfate residue (as of this writing) is -0.837. The entire charge on the sulfate group must be -1.000. You might think, at first, that the charge on the oxygen should be adjusted by the difference between -1.000 and -0.837 (-0.163). However, the oxygens in the residue RGB have already had their charges adjusted to compensate for the loss of the hydrogen in preparation for linking. To make GLYCAM residues modular, yet still realistic, the charges are adjusted at each linking anomeric carbon so that they are 0.194. Correspondingly, they are adjusted at each oxygen branch point so that they are -0.194. Since you need each attachment point to account for the extra -0.163 not carried by the SO3 residue, you need to add 0.031 to each oxygen to which a sulfate is attached (assuming the current prep file).

4. Alter the charge at each sulfation point.
The example below shows how to alter the oxygen charges individually using xleap or tleap. If you are comfortable copying and altering the appropriate prep file entries, that is an acceptable alternative.

5. Build up your molecule in a manner similar to any other GLYCAM structure.
The example below should be reasonably explanatory.

Example input for tleap or xleap

 ## Load in the databases
 source leaprc.GLYCAM_06h-2 # or substitute a more recent leaprc
 ## Be sure you have downloaded all files required for your leaprc!
 loadAmberPrep sulfate.prep # as of 20110627, this is the file name
 ## Create a unit containing the basic glycan
 m = sequence { ROH RGB } # stopping here ensures no confusion about linkages
 set m tail m.2.O6 # tell leap explicitly where to link
 m = sequence { m 0MA }
 # finish building the base glycan ##
 ## Set charges on the oxygens
 ## You can use "desc m.2.Ox" to obtain the current linking-O charges
 ## (here x=2 or 4).
 ## Here, we found them by reading the RGB entry in the GLYCAM_06.prep file.
 ## The charges set below are the orignal charges altered by +0.031.
 set m.2.O2 charge -0.445 ## was originally -0.4760
 set m.2.O4 charge -0.437 ## was originally -0.4680
 ## Add sulfates to positions 2 and 4
 set m tail m.2.O2
 m = sequence { m SO3 }
 set m tail m.2.O4
 m = sequence { m SO3 }
 ## Check the charge to make sure it is -2.000 as we expect.
 charge m
 ## Write out files we can use for simulations or to check our structure ##
 saveamberparm m m.rst
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