Unfortunately, the solubility of a peptide in water cannot be predicted just by studying the structure. However, a few clues can be deduced from the sequence: a relatively short peptide containing Lys and Arg residues will be soluble in aqueous buffers, as most basic functionalities will be protonated in peptides sold as trifluoroacetate salts. The guanidine function of Arg is a strong base, whereas the ε-amino group of Lys is a moderately strong base. By contrast, “acidic” peptides containing a large proportion of Asp and Glu tend to be insoluble in water, but they are readily dissolved by diluted ammonia, and by basic buffers. The side-chain carboxy functions are rather weak acids, they are considerably less acidic than the C-terminal carboxyl group.
Degassed buffers have to be used for reconstituting Cys- and Met-containing peptides. Contrary to sulfoxide formation, the oxidation of the thiol moiety is pH-dependent. Peptides containing free cysteines should be dissolved in acidic buffers.