Alkylation of a protein with iodoacetamide or iodoacetic acid
generates protons. If the solution is not well buffered the pH will change
dramatically. So it is a normal observation, especially when you add SH to
consume all of the remaining reagent. In the old days when we alkylated
large amounts of protein (> 100 mg), we used a pH STAT that constantly
adjusted the pH by infusion of NaOH.
Check out chapter 15 in Current Protocols in Protein Science for
alkylation protocols.
Greg
Gregory A. Grant
ggrant@pharmdec.wustl.edu