I have the need to dissolve a peptide (pI = 3.3) for some studies. Nature of my peptide is supposed to be highly polar and good dissolution in water should be achieved (based nature of amino acids and some online prediction). I cannot get it to dissolve in water or in my buffer which has relatively high salt (almost 500mM NaCl). Peptide handling literature suggests dissolving the peptide in 0.1M ammonium bicarbonate. Should I go forward with this or would I be encountering problems with interaction between my peptide and protein? Is there any other way to dissolve acidic peptides?
Acidic peptides, if they are not too burdened with hydrophobic side chains, should be soluble in water at some concentration as long as the pH is high enough to deprotonate the acidic side chains. Water will probably not be a good solvent because the pH will be too low. A high-salt buffer is also not the best choice because you could salt-out the peptide. A low-salt buffer of a high enough concentration to neutralize the acidity of the peptide should work. The peptide will probably also dissolve in DMSO. Think about what will be tolerable to your protein when you do the experiment.
If you are planning to do ITC or SPR, it will be extremely important to match the peptide solvent to the protein solvent very closely.
Your peptide must have a lot of hydrophobic residues, which as stated by Adam Shapiro will favor its precipitation at high salt concentrations. What is the concentration of your peptide? Also, the pH of the final solution should be away from the peptide's pI.
The 100 mM ammonium bicarbonate buffer sounds as a good solvent for an acidic peptide. As mentioned by the previous scientists, the aqueous solubility is favored by low salt concentration and high pH. In the most extreme case you may try demi-water with a drop of ammonia, but 100 or 10 mM ammonium bicarbonate buffer will be a safer option.
Assuming your stock peptide solution will be far more concentrated than the final working concentration of your peptide, then de dilution will take care of the basic media and you should be OK for your binding assays. As others have said, bicarbonate is a fine additive.
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