Ion exchange chromatography can be used to separate proteins because they contain charged functional groups. The ions of interest (in this case charged proteins) are exchanged for another ions (usually H) on a charged solid support. The solutes are most commonly in a liquid phase, which tends to be water. Take for example proteins in water, which would be a liquid phase that is passed through a column. The column is commonly known as the solid phase since it is filled with porous synthetic particles that are of a particular charge. These porous particles are also referred to as beads, may be aminated (containing amino groups) or have metal ions in order to have a charge. The column can be prepared using porous polymers, for macromolecules of a mass of over 100 000 Da, the optimum size of the porous particle is about 1 μm. This is because slow diffusion of the solutes within the pores does not restrict the separation quality. The beads containing positively charged groups, which attract the negatively charged proteins, are commonly referred to as anion exchange resins. The amino acids that have negatively charged side chains at pH 7 (pH of water) are glutamate and aspartate. The beads that are negatively charged are called cation exchange resins, as positively charged proteins will be attracted. The amino acids that have positively charged side chains at pH 7 are lysine, histidine and arginine.
The isoelectric point is the pH at which a compound - in this case a protein - has no net charge. A protein's isoelectric point or PI can be determined using the pKa of the side chains, if the amino (positive chain) is able to cancel out the carboxyl (negative) chain, the protein would be at its PI. Using buffers instead of water for proteins that do not have a charge at pH 7, is a good idea as it enables the manipulation of pH to alter ionic interactions between the proteins and the beads. Weakly acidic or basic side chains are able to have a charge if the pH is high or low enough respectively. Separation can be achieved based on the natural isoelectric point of the protein. Alternatively a peptide tag can be genetically added to the protein to give the protein an isoelectric point away from most natural proteins (e.g., 6 arginines for binding to a cation-exchange resin or 6 glutamates for binding to an anion-exchange resin such as DEAE-Sepharose).
Elution by increasing ionic strength of the mobile phase is more subtle. It works because ions from the mobile phase interact with the immobilized ions on the stationary phase, thus "shielding" the stationary phase from the protein, and letting the protein elute.
Elution from ion-exchange columns can be sensitive to changes of a single charge- chromatofocusing. Ion-exchange chromatography is also useful in the isolation of specific multimeric protein assemblies, allowing purification of specific complexes according to both the number and the position of charged peptide tags.