Proteins Can Be Separated and Purified

A pure preparation is essential before a protein's properties and activities can be determined. Given that cells contain thousands of different kinds of proteins, how can one protein be purified? Methods for separating proteins take advantage of properties that vary from one protein to the next, including size, charge, and binding properties.

The source of a protein is generally tissue or mi-crobial cells. The first step in any protein purification procedure is to break open these cells, releasing their proteins into a solution called a crude extract. If necessary, differential centrifugation can be used to pre-

lix is a part of the tertiary structure of the folded polypeptide, which is itself one of the subunits that make up the quaternary structure of the multisubunit protein, in this case hemoglobin.

pare subcellular fractions or to isolate specific organelles (see Fig. 1-8).

Once the extract or organelle preparation is ready, various methods are available for purifying one or more of the proteins it contains. Commonly, the extract is subjected to treatments that separate the proteins into different fractions based on a property such as size or charge, a process referred to as fractionation. Early fractionation steps in a purification utilize differences in protein solubility, which is a complex function of pH, temperature, salt concentration, and other factors. The solubility of proteins is generally lowered at high salt concentrations, an effect called "salting out." The addition of a salt in the right amount can selectively precipitate some proteins, while others remain in solution. Ammonium sulfate ((NH4)2SO4) is often used for this purpose because of its high solubility in water.

A solution containing the protein of interest often must be further altered before subsequent purification steps are possible. For example, dialysis is a procedure that separates proteins from solvents by taking advantage of the proteins' larger size. The partially purified extract is placed in a bag or tube made of a semipermeable membrane. When this is suspended in a much larger volume of buffered solution of appropriate ionic strength, the membrane allows the exchange of salt and buffer but not proteins. Thus dialysis retains large proteins within the membranous bag or tube while allowing the concentration of other solutes in the protein preparation to change until they come into equilibrium with the solution outside the membrane. Dialysis might be used, for example, to remove ammonium sulfate from the protein preparation.

The most powerful methods for fractionating proteins make use of column chromatography, which takes advantage of differences in protein charge, size, binding affinity, and other properties (Fig. 3-17). A porous solid material with appropriate chemical properties (the stationary phase) is held in a column, and a buffered solution (the mobile phase) percolates through it. The protein-containing solution, layered on the top of the column, percolates through the solid matrix as an ever-expanding band within the larger mobile phase (Fig. 3-17). Individual proteins migrate faster or more slowly through the column depending on their properties. For example, in cation-exchange chromatography (Fig. 3-18a), the solid matrix has negatively charged groups. In the mobile phase, proteins with a net positive charge migrate through the matrix more slowly than those with a net negative charge, because the migration of the former is retarded more by interaction with the stationary phase. The two types of protein can separate into two distinct bands. The expansion of the protein band in the mobile phase (the protein solution) is caused both by separation of proteins with different properties and by diffusional spreading. As the length of the column increases, the resolution of two types of protein with different net charges generally improves. However, the rate at which the protein solution can flow through the column usually decreases with column

Reservoir

Protein sample (mobile phase)

Solid porous matrix (stationary phase)

Porous support

Effluent

Reservoir

Effluent

Column Reservoir
Proteins A

length. And as the length of time spent on the column increases, the resolution can decline as a result of dif-fusional spreading within each protein band.

Figure 3-18 shows two other variations of column chromatography in addition to ion exchange. Size-exclusion chromatography separates proteins according to size. In this method, large proteins emerge from the column sooner than small ones—a somewhat counterintuitive result. The solid phase consists of beads with engineered pores or cavities of a particular size. Large proteins cannot enter the cavities, and so take a short (and rapid) path through the column, around the beads. Small proteins enter the cavities, and migrate through the column more slowly as a result (Fig. 3-18b). Affinity chromatography is based on the binding affinity of a protein. The beads in the column have a covalently attached chemical group. A protein with affinity for this particular chemical group will bind to the beads in the column, and its migration will be retarded as a result (Fig. 3-18c).

A modern refinement in chromatographic methods is HPLC, or high-performance liquid chromatogra-phy. HPLC makes use of high-pressure pumps that speed the movement of the protein molecules down the column, as well as higher-quality chromatographic materials that can withstand the crushing force of the pressurized flow. By reducing the transit time on the column, HPLC can limit diffusional spreading of protein bands and thus greatly improve resolution.

The approach to purification of a protein that has not previously been isolated is guided both by established precedents and by common sense. In most cases, several different methods must be used sequentially to purify a protein completely. The choice of method is

FIGURE 3-17 Column chromatography. The standard elements of a chromatographic column include a solid, porous material supported inside a column, generally made of plastic or glass. The solid material (matrix) makes up the stationary phase through which flows a solution, the mobile phase. The solution that passes out of the column at the bottom (the effluent) is constantly replaced by solution supplied from a reservoir at the top. The protein solution to be separated is layered on top of the column and allowed to percolate into the solid matrix. Additional solution is added on top. The protein solution forms a band within the mobile phase that is initially the depth of the protein solution applied to the column. As proteins migrate through the column, they are retarded to different degrees by their different interactions with the matrix material. The overall protein band thus widens as it moves through the column. Individual types of proteins (such as A, B, and C, shown in blue, red, and green) gradually separate from each other, forming bands within the broader protein band. Separation improves (resolution increases) as the length of the column increases. However, each individual protein band also broadens with time due to diffusional spreading, a process that decreases resolution. In this example, protein A is well separated from B and C, but diffusional spreading prevents complete separation of B and C under these conditions.

• Large net positive charge O Net positive charge

O Net negative charge

• Large net negative charge

• Large net positive charge O Net positive charge

O Net negative charge

• Large net negative charge

Negatively Charged Protein

Polymer beads with negatively charged functional groups

Protein mixture is added to column containing cation exchangers.

Polymer beads with negatively charged functional groups

Protein mixture is added to column containing cation exchangers.

1 2 3 4 5 6 Proteins move through the column at rates determined by their net charge at the pH

being used. With cation exchangers, proteins with a more negative net charge move faster and elute earlier.

FIGURE 3-18 Three chromatographic methods used in protein purification. (a) Ion-exchange chromatography exploits differences in the sign and magnitude of the net electric charges of proteins at a given pH. The column matrix is a synthetic polymer containing bound charged groups; those with bound anionic groups are called cation exchangers, and those with bound cationic groups are called anion exchangers. Ion-exchange chromatography on a cation exchanger is shown here. The affinity of each protein for the charged groups on the column is affected by the pH (which determines the ionization state of the molecule) and the concentration of competing free salt ions in the surrounding solution. Separation can be optimized by gradually changing the pH and/or salt concentration of the mobile phase so as to create a pH or salt gradient. (b) Size-exclusion chromatography, also called gel filtration, separates proteins according to size. The column matrix is a cross-linked polymer with pores of selected size. Larger proteins migrate faster than smaller ones, because they are too large to enter the pores in the beads and hence take a more direct route through the column. The smaller proteins enter the pores and are slowed by their more labyrinthine path through the column. (c) Affinity chromatography separates proteins by their binding specificities. The proteins retained on the column are those that bind specifically to a ligand cross-linked to the beads. (In biochemistry, the term "ligand" is used to refer to a group or molecule that binds to a macromolecule such as a protein.) After proteins that do not bind to the ligand are washed through the column, the bound protein of particular interest is eluted (washed out of the column) by a solution containing free ligand.

Protein mixture is added to column containing cross-linked polymer.

Sec Column Fractions Size
Porous polymer beads

Protein mixture is added to column containing cross-linked polymer.

Protein molecules separate by size; larger molecules pass more freely, appearing in the earlier fractions. T ~2 4 16

Porous Beads
Mixture of proteins

Protein mixture is added to column containing a polymer-bound ligand specific for protein of interest.

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