I am planning to perform crosslinking studies between two proteins and a peptide using DSS as the crosslinker. Both proteins are currently in SEC buffer, so I attempted buffer exchange into HEPES pH 6.5. However, one of the proteins precipitated immediately upon exchange into HEPES.
I would like to know if there are alternative buffer systems compatible with DSS crosslinking that are also more protein-friendly, especially for preserving solubility and stability during the reaction.
Here is some information on using DSS crosslinker.
https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0011240_DSS_BS3_CrsLnk_UG.pdf
I would suggest that you raise the pH to 7 or higher to favor the crosslinking reaction.
As for maintaining your protein in solution, I doubt the problem is HEPES buffer per se, which is very compatible with proteins. It may help to increase the salt concentration and lower the protein concentration. Changing the pH can also have a significant effect, especially if the pH is close to the isoelectric point of the protein, which is to be avoided if possible.
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