AC media separate proteins on the basis of a reversible interaction between a protein (or a group of proteins) and a speciﬁc ligand attached to a chromatographic matrix. The technique is well-suited for a capture or as an intermediate puriﬁcation step and can be used whenever a suitable ligand is available for the protein(s) of interest. AC offers high selectivity and usually high capacity. It is frequently used as the ﬁrst step (capture step) of a two-step puriﬁcation protocol, followed by a second chromatographic step (polishing step) to remove remaining impurities.
The target protein(s) is/are speciﬁcally and reversibly bound by a complementary binding substance (ligand). The sample is applied under conditions that favor speciﬁc binding to the ligand. Unbound material is washed away, and bound target protein is recovered by changing conditions to those favoring elution. Elution is performed speciﬁcally, using a competitive ligand, or nonspeciﬁcally, by changing the pH, ionic strength, or polarity. Samples are concentrated during binding, and the target protein is collected in puriﬁed and concentrated form. The key stages in an AC separation are shown in Figure A11.1. AC is also used to remove speciﬁc contaminants; for example, Benzamidine Sepharose 4 Fast Flow (high sub) removes serine proteases.
Figure A11.1.Typical affinity purification
IEX media separate proteins based on differences in surface charge, generating high-resolution separations with high sample loading capacity. The separation is based on the reversible interaction between a charged protein and an oppositely charged chromatography medium. Proteins bind as they are loaded onto a column. Conditions are then altered so that bound substances are eluted differentially. Elution is usually performed by increasing salt concentration or changing pH. Changes are made stepwise or with a continuous linear gradient. Most commonly, samples are eluted with salt (NaCl), using a gradient elution (Figure A11.2). Target proteins are concentrated during binding and collected in a puriﬁed, concentrated form.
Figure A11.2. Typical IEX gradient elution. Blue line = absorbance; red line = conductivity (salt concentration).
The net surface charge of proteins varies according to the surrounding pH. Typically, when above its isoelectric point (pI) a protein will bind to an anion exchanger (e.g., Q Sepharose); when below its pI a protein will bind to a cation exchanger (e.g., SP Sepharose). However, it should be noted that binding depends on charge and that surface charges may thus be sufﬁcient for binding even on the other side of the pI. Typically IEX is used to bind the target molecule, but it can also be used to bind impurities if required. IEX can be repeated at different pH values to separate several proteins that have distinctly different charge properties, as shown in Figure A11.3.
Figure A11.3. Effect of pH on protein elution patterns. V = volume.
To reduce separation times and buffer consumption, transfer to a step elution after method optimization as shown in Figure A11.4.
Figure A11.4. Step elution. Blue line = absorbance; red line = conductivity (salt concentration).
HIC media separate proteins with differences in hydrophobicity. The technique is well-suited for the capture or intermediate steps in a puriﬁcation protocol. Separation is based on the reversible interaction between a protein and the hydrophobic surface of a chromatography medium. This interaction is enhanced by high ionic strength buffer, which makes HIC an excellent “next step” after precipitation with ammonium sulfate or elution in high salt during IEX. Samples in high ionic strength solution (e.g., 1.5 M ammonium sulfate) bind as they are loaded onto a column. Conditions are then altered so that the bound substances are eluted differentially.
Elution is usually performed by decreases in salt concentration (Figure A11.5). Changes are made stepwise or with a continuous decreasing salt gradient. Most commonly, samples are eluted with a decreasing gradient of ammonium sulfate. Target proteins are concentrated during binding and collected in a puriﬁed and concentrated form. Other elution procedures include reducing eluent polarity (ethylene glycol gradient up to 50%), adding chaotropic species (urea, Gua HCl), or detergents, changing pH or temperature.
Figure A11.5. Typical HIC gradient elution. Blue line = absorbance; red line = conductivity (salt concentration).
To reduce separation times and buffer consumption, transfer to a step elution after method optimization, as shown in Figure A11.6.
Figure A11.6. Step elution. Blue line = absorbance; red line = conductivity (salt concentration).
SEC media separate proteins with differences in molecular size and shape. The technique is well-suited for the ﬁnal polishing steps in puriﬁcation when sample volumes have been reduced (sample volume signiﬁcantly inﬂuences speed and resolution in SEC). Samples are eluted isocratically (single buffer, no gradient, Figure A11.7). Buffer conditions can be varied to suit the sample type or the requirements for further puriﬁcation, analysis, or storage, because buffer composition usually does not have major effects on resolution. Proteins are collected in puriﬁed form in the chosen buffer.
Figure A11.7. Typical SEC elution.
RPC media separate proteins and peptides with differing hydrophobicity based on their reversible interaction with the hydrophobic surface of a chromatographic medium. Proteins bind as they are loaded onto a column. Conditions are then altered so that the bound substances are eluted differentially. Due to the nature of the reversed phase matrices, binding is usually very strong. Binding may be modulated by the use of organic solvents and other additives (ion pairing agents). Elution is usually performed by increases in organic solvent concentration, most commonly acetonitrile. Samples that are concentrated during the binding and separation process are collected in a puriﬁed, concentrated form. The key stages in a separation are shown in Figure A11.8.
Figure A11.8. Typical RPC gradient elution. Blue line = absorbance; red line = % elution buffer.
RPC is often used in the ﬁnal polishing of oligonucleotides and peptides and is well-suited for analytical separations, such as peptide mapping.
RPC is generally not recommended for protein puriﬁcation if recovery of activity and return to a correct tertiary structure are required, because many proteins are denatured in the presence of organic solvents. Exceptions exist.