Isoelectric focusing gradients

Isoelectric Focusing. Isoelectric focusing is a technique used for protein separation, by driving proteins to a pH where they have no mobiUty. Resolution depends on the slope of a pH gradient that can be achieved in a gel. 

Isoelectric focusing takes along (from ca 3 to 30 h) time to complete because sample compounds move more and more slowly as they approach the pH in the gel that corresponds to their isoelectric points. Because the gradient ampholytes and the samples stop where they have no mobiHty, the resistivity of the system increases dramatically toward the end of the experiment, and the current decreases dramatically. For this reason, isoelectric focusing is usually mn with constant voltage. Constant current appHcation can lead to overheating of the system. 

In considering the applicability of preparative classical electrophoretic methods to chiral separations, it should be noted that practitioners in the art of classical electrophoresis have been particularly inventive in designing novel separation strategies. For instance, pH, ionic strength and density gradients have all been used. Isoelectric focusing and isotachophoresis are well-established separation modes in classical electrophoresis and are also being implemented in CE separations [7, 8]. These trends are also reflected in the preparative electrophoretic approaches discussed here. 

Figure 4-5. Two-dimensional lEF-SDS-PAGE.The gel was stained with Coomassie blue. A crude bacterial extract was first subjected to isoelectric focusing (lEF) in a pH 3-10 gradient. The lEF gel was then placed horizontally on the top of an SDS gel, and the proteins then further resolved by SDS-PAGE. Notice the greatly improved resolution of distinct polypeptides relative to ordinary SDS-PAGE gel (Figure 4-4).

Fig. 5. Isoelectric focusing (pH gradient 3-10) of Fraction A and Fraction B in ultrathin polyacrylamide layers. 5 pg of fractions were applied. Activity detection with ruthenium red (left) and with Ostazin Brilliant Red/D-galacturonan DP 10 agar print (right).

Fig. 3. Isoelectric focusing in ultrathin polyacrylamide layers (pH gradient 3 -10) of multiple forms of polygalacturonase produced by Candida boidinii under different cultivation conditions a - pectin, pH 3.51 b - pectin, pH 5.49 c -pectin, pH 7.01 d - 20% of D-galactopyranuronic acid in pectin e - pectate. A - Activity detection with print technique on colouress D-galacturonan DP 10 dyed additionally with ruthenium red ( both exo- and polygalacturonases) and B - activity detection with Ostazin Brilliant Red/D-galacturonan DP 10 agar print (polygalacturonases).

Righetti, P. G., Isoelectric focusing of proteins in conventional and immobilized pH gradients, in Protein Structure A Practical Approach, Creighton, T. E., Ed., IRL Press, New York, 1989, 23. 

Another limitation of 2D gels is that membrane proteins are underrepresented. Because membrane proteins account for approximately 30% of total proteins (Wallin and Von Heijne, 1998), this is a serious problem for characterization of the proteome. The relative lack of membrane proteins resolvable on 2D gels can be attributed to thee main factors (i) they are not abundant, and therefore are difficult to detect by standard staining techniques, (ii) they often possess alkaline pi values, which make them difficult to resolve on the pH gradients most often used for isolelectric focusing, and (iii) the most important reason for under representation may be that membrane proteins are poorly soluble in the aqueous media used for isoelectric focusing (Santoni et al., 2000). Membrane proteins are designed to be soluble in lipid bilayers and are therefore difficult to solubilize in water-based solutions. 

Rabilloud, T., Valette, C., and Lawrence, J. J. (1994). Two-dimensional electrophoresis of basic proteins with equilibrium isoelectric focusing in carrier ampholyte-pH gradients. Electrophoresis 15, 1552-1558. 

Ek, K., Bjellqvist, B., Righetti, R G. (1983). preparative isoelectric-focusing in immobilized pH Gradients. 1. General principles and methodology. J. Biochem. Bioph. Meth. 8(2), 135-155. 

Essader, A.S., Cargile, B.J., Bundy, J.L., Stephenson, J.L., Jr. (2005). A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics. Proteomics 5, 24—34. 

Ruchel, R. (1977). Two-dimensional micro-separation technique for proteins and peptides, combining isoelectric focusing and gel gradient electrophoresis. J. Chromatogr. 132, 451 168. 

Norbeck J et al. Two-dimensional electrophoretic separation of yeast proteins using a non-linear wide range (pH 3-10) immobilized pH gradient in the first dimension reproducibility and evidence for isoelectric focusing of alkaline (pi >7) proteins. Yeast 1997 13 1519-1534. 

K. Macounova, C.R. Cabrera, M.R. Holl, and P. Yager, Generation of natural PH gradients in micro fluidic channels for use in isoelectric focusing. Anal. Chem. 72, 3745—3751 (2000). 

Two variations of the basic technique are isoelectric focusing and immuno-electrophoresis. The former offers improved resolution and sharper bands in the separation of weak acids, weak bases and ampholytes through the use of pH and density gradients superimposed along the potential gradient. The latter employs specific antigen-antibody interactions (Chapter 10) to visualize the separated components of serum samples. 

Capillary isoelectric focusing (CIEF) is suitable for the separation of amphoteric analyses in a pH gradient. A continuous pH gradient is built up in the column by using ampholytes under a potential field. Amphoteric analyses migrate to the point where their net charge equal to zero and they form stationary and sharply focused zones. 

Figure 8.9 Isoelectric focusing. The motion of a protein undergoing isoelectric focusing is depicted (circles). The protein is shown near its pi in a pH gradient. Both the pH gradient and the motion of the protein are governed by an applied electric field. At pH values lower than the pi, the protein is positively charged (+) and it is driven toward the cathode as shown by the arrow. Above its pi, the protein is negatively charged (-) and it moves toward the anode. There is no net electrical force on the protein at its pi (0). The protein focuses in a Gaussian distribution centered at the pi.

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