An Introduction to Protein Purification Methods - Promega Corporation

Medium- to Large-Scale Purification of Polyhistidine-Tagged Proteins In Column or Batch Formats

The two most common support materials for resin-based, affinity-tagged protein purification are agarose and silica gel. As a chromatographic support, silica is advantageous because it has a rigid mechanical structure that is not vulnerable to swelling and can withstand large changes in pressure and flow rate without disintegrating or deforming. Silica is available in a wide range of pore and particle sizes including macroporous silica, which provides a higher capacity for large biomolecules such as proteins. However, two of the drawbacks of silica as a solid support for affinity purification are the limited reagent chemistry that is available and the relatively low efficiency of surface modification.

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The HisLink™ Protein Purification Resin (Cat.# V, V) overcomes these limitations by using a new modification process for silica surfaces that provides a tetradentate metal-chelated solid support with a high binding capacity and concomitantly eliminates the nonspecific binding that is characteristic of unmodified silica. HisLink™ Resin is a macroporous silica resin modified to contain a high level of tetradentate-chelated nickel (>20mmol Ni/ml settled resin). Figure 3 shows a schematic diagram of HisLink™ Resin and polyhistidine tag interaction. The HisLink™ Resin has a pore size that results in binding capacities as high as 35mg of polyhistidine-tagged protein per milliliter of resin.

The HisLink™ Resin enables efficient capture and purification of bacterially expressed polyhistidine-tagged proteins. This resin also may be used for general applications that require an immobilized metal affinity chromatography (IMAC) matrix (Porath et al. ; Lonnerdal and Keen, ). HisLink™ Resin may be used in either column or batch purification formats. For a detailed protocol, see Technical Bulletin #TB327.

Column-Based Purification using HisLink™ Resin

The HisLink™ Resin provides a conventional means to purify polyhistidine-tagged proteins and requires only a column that can be packed to the appropriate bed volume. When packed to 1ml under gravity-driven flow, HisLink™ Resin shows an average flow rate of approximately 1ml/minute. In general a flow rate of 1–2ml/minute per milliliter of resin is optimal for efficient capture of polyhistidine-tagged protein. Gravity flow of a cleared lysate over a HisLink™ column will result in complete capture and efficient elution of polyhistidine-tagged proteins; however, the resin also may be used with vacuum filtration devices (e.g., Vac-Man® Vacuum Manifold, Cat.# A) to allow simultaneous processing of multiple columns. HisLink™ Resin is also an excellent choice for affinity purification using low- to medium-pressure liquid chromatography systems such as fast performance liquid chromatography (FPLC).

Example Protocol Using the HisLink™ Resin to Purify Proteins from Cleared Lysate by Gravity-Flow Column Chromatography

Materials Required:

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• HisLink™ Protein Purification Resin (Cat.# V) and protocol
• HEPES buffer (pH 7.5)
• imidazole
• HisLink™ Binding Buffer
• HisLink™ Wash Buffer
• HisLink™ Elution Buffer
• column 

Cell Lysis: Cells may be lysed using any number of methods including sonication, French press, bead milling, treatment with lytic enzymes (e.g., lysozyme) or use of a commercially available cell lysis reagent such as the FastBreak™ Cell Lysis Reagent (Cat.# V). If lysozyme is used to prepare a lysate, add salt (>300mM NaCl) to the binding and wash buffers to prevent lysozyme binding to the resin. Adding protease inhibitors such as 1mM PMSF to cell lysates does not inhibit binding or elution of polyhistidine-tagged proteins with the HisLink™ Resin and is highly recommended to prevent degradation of the protein of interest by endogenous proteases. When preparing cell lysates from high-density cultures, adding DNase and RNase (concentrations up to 20μg/ml) will reduce the lysate viscosity and aid purification.

1. Prepare the HisLink™ Binding, Wash and Elution Buffers
   Note: Polyhistidine-tagged proteins can be eluted using 250–1,000mM imidazole. Polyhistidine tags containing less than six histidines typically require less imidazole for elution, while polyhistidine proteins containing more than six polyhistidines may require higher levels of imidazole.
2. Determine the column volume required to purify the protein of interest. In most cases 1ml of settled resin is sufficient to purify the amount of protein typically found in up to 1 liter of culture (cell density of O.D.600 < 6.0). In cases of very high expression levels (e.g., 50mg protein/liter), up to 2ml of resin per liter of culture may be needed.
3. Once you have determined the volume of settled resin required, precalibrate this amount directly in the column by pipetting the equivalent volume of water into the column and marking the column to indicate the top of the water. This mark indicates the top of the settled resin bed. Remove the water before adding resin to the column.
4. Make sure that the resin is fully suspended; fill the column with resin to the line marked on the column by transferring the resin with a pipette. Allow the resin to settle, and adjust the level of the resin by adding or removing resin as necessary.
   Note: If the resin is not pipetted within 10–15 seconds of mixing, significant settling will occur, and the resin will need to be resuspended. Alternatively, a magnetic stir bar may be used to keep the resin in suspension during transfer. To avoid fracturing the resin, do not leave the resin stirring any longer than the time required to pipet and transfer the resin.
5. Allow the column to drain, and equilibrate the resin with five column volumes of binding buffer, allowing the buffer to completely enter the resin bed.
6. Gently add the cleared lysate to the resin until the lysate has completely entered the column. The rate of flow through the column should not exceed 1–2ml/minute for every 1ml of column volume. Under normal gravity flow conditions the rate is typically about 1ml/minute. The actual flow rate will depend on the type of column used and the extent to which the lysate was cleared and filtered. Do not let the resin dry out after you have applied the lysate to the column.
7. Wash unbound proteins from the resin using at least 10–20 column volumes of wash buffer. Divide the total volume of wash buffer into two or three aliquots, and allow each aliquot to completely enter the resin bed before adding the next aliquot.
8. Once the wash buffer has completely entered the resin bed, add elution buffer and begin collecting fractions (0.5–5ml fractions). Elution profiles are protein-dependent, but polyhistidine-tagged proteins will generally elute in the first 1ml. Elution is usually complete after 3–5ml of buffer is collected per 1.0ml of settled resin, provided the imidazole concentration is high enough to efficiently elute the protein of interest.

Batch Protein Purification Using HisLink™ Resin

One of the primary advantages of the HisLink™ Resin is its use in batch purification. In batch mode, the protein of interest is bound to the resin by mixing lysate with the resin for approximately 30 minutes at a temperature range of 4–22°C. Once bound with protein, the resin is allowed to settle to the bottom of the container, and the spent lysate is removed. Washing requires only resuspension of the resin in an appropriate wash buffer followed by a brief period to allow the resin to settle. The wash buffer is then carefully poured off. This process is repeated as many times as desired. Final elution is best achieved by transferring the HisLink™ Resin to a column to elute the protein in fractions. The advantages of batch purification are: 1) less time is required to perform the purification; 2) large amounts of lysate can be processed; and 3) clearing the lysate prior to purification is not required.

Purification of Polyhistidine-Tagged Proteins by FPLC

The rigid particle structure of the silica base used in the HisLink™ Resin make this material an excellent choice for applications that require applied pressure to load the lysate, wash or elute protein from the resin. These applications involve both manual and automated systems that operate under positive or negative pressure (e.g., FPLC and vacuum systems, respectively). To demonstrate the use of HisLink™ Resin on an automated platform we used an AKTA explorer from GE Healthcare to purify milligram quantities of polyhistidine-tagged protein from 1 liter of culture. The culture was lysed in 20ml of binding/wash buffer and loaded onto a column containing 1ml of HisLink™ Resin. We estimate the total amount of protein recovered to be 75–90% of the protein expressed in the original lysate.

Protein purification under denaturing conditions: Proteins that are expressed as an inclusion body and have been solubilized with chaotrophic agents such as guanidine-HCl or urea can be purified by modifying the protocol to include the appropriate amount of denaturant (up to 6M guanidine-HCl or up to 8M urea) in the binding, wash and elution buffers.

Bio-Rad offers numerous chromatography products for the purification and characterization of biomolecules such as proteins, peptides, and nucleic acids. A resin manufacturer for over 50 years, Bio-Rad has expertise in investigating and manipulating pore structure, bead rigidity, mass transfer rate, ligand structures, and ligand density. These parameters are adjusted so that our chromatography beads provide optimal performance in the purification of biopharmaceuticals. Such characteristics are modulated for the production of both analytical grade and process-scale resins. Process-scale resins provide excellent flow rates when packed in columns of diameters up to 2 m and stability over many CIP cycles. The selectivity provided by the process-scale resins is also useful for laboratory separations with the best resolution often provided by the smaller bead/analytical grade resin.

Contact us to discuss your requirements of Protein Purification Resins​. Our experienced sales team can help you identify the options that best suit your needs.