Protein purification

Why it matters

To study a protein's structure, kinetics or binding, you first need it pure: a sample where your protein is the main component and contaminants will not confuse the measurement. Purified proteins are also products, from research reagents to insulin and monoclonal antibodies. Planning a purification scheme, and judging it with a purification table, is a core biochemistry skill and a frequent interview question for research associate roles.

Where the protein comes from

Most research proteins are recombinant: the gene is cloned into an expression host (often E. coli, yeast, insect or mammalian cells), usually with an added affinity tagAn extra sequence added to a recombinant protein, such as a His-tag, so it can be captured by a specific resin. to make purification easier. The cells are harvested and broken open (lysis) by sonication, high-pressure homogenisation or detergents, and the debris is removed by centrifugation to give a clarified lysate. All of this is done in a lab under supervision, following institutional biosafety rules for the organisms involved.

Separating by properties

Each chromatography method separates proteins by a different property, so a good scheme combines methods that work on different properties:

• Affinity chromatography uses a specific binding partner. A His-tag (six or more histidines) binds nickel or cobalt ions on the resin (IMAC, immobilised metal affinity chromatography); you wash away other proteins and elute with imidazole. GST tags bind glutathione; antibodies bind Protein A. Affinity steps can give large purification in one step.
• Ion exchangeChromatography that separates proteins by charge, eluted with a salt gradient. (IEX) separates by charge. Below its isoelectric point (pI) a protein is positively charged and binds a cation exchanger; above it, it binds an anion exchanger. Elution uses a salt gradient.
• Size exclusion chromatographyChromatography that separates by size and shape, with large molecules coming out first; often the final polishing step. (SEC, gel filtration) separates by size and shape. Large molecules come out first. It is usually the last "polishing" step, because it also removes aggregates and swaps the protein into its final buffer.
• Hydrophobic interaction chromatography (HIC) separates by surface hydrophobicity, binding at high salt.

A classic order is capture → intermediate → polish: for example IMAC, then ion exchange, then SEC. Between steps you may need to change buffer (dialysis or desalting) because, for instance, the high salt or imidazole from one step will stop binding in the next.

Checking each step

• SDS-PAGE shows which fractions contain a band at the expected molecular weight and how many contaminant bands remain.
• Protein concentration by A280 (using the protein's extinction coefficient) or a dye assay such as Bradford or BCA.
• Activity assay (for an enzyme) measures how much functional protein you kept.

The purification table

The table tracks every step. For an enzyme:

• Total protein (mg).
• Total activity (units, U; for example µmol of product per minute).
• Specific activityTotal activity divided by total protein (U/mg); it rises as the sample gets purer. = total activity / total protein (U/mg). It rises as the sample gets purer.
• YieldThe total activity at a step as a percentage of the total activity in the lysate. = total activity at this step / total activity in the lysate × 100 %.
• Fold purificationThe specific activity at a step divided by the specific activity of the lysate. = specific activity at this step / specific activity of the lysate.

Worked example:

step            total protein (mg)   total activity (U)   specific (U/mg)   yield   fold
lysate          2000                 10000                5                 100 %   1
IMAC            40                   7000                 175               70 %    35
ion exchange    12                   5600                 467               56 %    93
SEC             8                    4800                 600               48 %    120

Each step loses some protein, so yield falls while purity rises. A step that raises fold purification very little but costs a lot of yield is a candidate for removal.

Planning trade-offs

• Stability: keep the protein cold, at a pH and salt it tolerates, and add protease inhibitors to the lysis buffer. Some proteins need reducing agents or cofactors.
• Tag removal: a protease site between tag and protein lets you cut the tag off, then a second IMAC pass ("reverse IMAC") collects the tag and uncut protein, while your untagged protein flows through.
• Scale and purpose: a crystallography sample needs high purity and homogeneity; an antibody for a quick Western blot may need only one step. Therapeutic proteins are purified under GMP with validated processes.

Common mistakes

• Using two steps that separate by the same property (such as two anion-exchange columns at the same pH).
• Forgetting buffer compatibility between steps.
• Reporting purity without activity. A clean band on a gel can still be inactive or aggregated.
• Calculating yield from protein instead of activity. Yield is about the target, so track the target's activity (or a specific measure such as a Western blot).

Safety and real-world practice

This lesson is awareness level. Real purification uses biological materials, solvents and equipment such as centrifuges and high-pressure systems, and requires training and supervision in your institution's lab. The activity below is a paper exercise only.

Recap

• Combine methods that separate by different properties: affinity, charge, size, hydrophobicity.
• Capture, intermediate, polish; check each step by SDS-PAGE and activity.
• Specific activity, yield and fold purification tell you whether a scheme works.

Try it

On the Do tab, plan a purification scheme on paper and fill in a purification table.