The refolding buffer (50mM MES) I tried for my protein has pH 6.0, pI of protein is also 6.2. Next step is I want to purify it through Ni-NTA resin. Should I maintain same buffer MES and pH 6.0 for washing and elution?
You can but it is not appropriate. pH has to be at least 7 for imac thus you need to use another buffering molecule. I do not understand the refolding part, could you elaborate in the whole process you are running.
Ideally working pH should be at least 1 unit away from pI. For IMAC, imidazole of histidines has to be deprotonated therefore working pH should be at least 7.