Nondenaturing

FIGURE 8.12 Effect of pore diameter on SEC of standards (nondenaturin > mobile phase). Nondenaturing" refers to the effect on the stationary phase. Most iarge proteins were in fact denatured by this mobile phase (which was optimized for use with peptides, not proteins). Accordingly, it was necessary to use polyacrylamide to demonstrate the approximate range and position of Vo under these conditions. The polyacryiamide standards both eiuted at V with the 300-A coiumn (not shown). Columns and flow rate Same as in Fig. 8.11. Mobile phase Same as in Fig. 8.1. Sample key (B) Ovalbumin (43,000 Da) 0) polyacrylamide (1,000,000 Da) (K) polyacrylamide (400,000 IDa) (L) low molecular weight impurity in the polyacrylamide standards. Other samples as in Fig. 8.11. 

FIGURE 6. Gel electrophoresis of purified E. coli Met(0)-peptide reductase. (A) 15% polyacrylamide containing 0.1% NaDodSO. (B) 13% polyacrylamide (pH8.8) nondenaturing. Reproduced by permission of Academic Press from Brot and coworkers112. 

The purification strategy for CBPs is conceptually simple. Proteins from carotenoid-rich tissues are separated under nondenaturing and relatively aqueous conditions where carotenoids are expected to remain bound to the CBPs. CBPs are then detected by the color of the carotenoids. 

B. Characterization of Proteins That Are Unstructured under Nondenaturing Conditions... 

Bai, Y W., Chung, J., Dyson, H. J., and Wright, P. E. (2001). Structural and dynamic characterization of an unfolded state of poplar apo-plastocyanin formed under nondenaturing conditions. Protein Sci. 10, 1056-1066. 

Protein applications are extremely sensitive to solvent pH, salt concentration, and small molecular weight additives such as trifluoroacetic acid (TFA), which affect solute equilibria. These effects are known and depending on the specific application, proteins are often run under denaturing conditions, which offer vastly different retention conditions than nondenaturing conditions. 

An interesting twist to the story is provided by studies on N. brasiliensis, which secretes three distinct isoforms of AChE, designated A, B and C (Ogilvie et al, 1973). These enzymes can be easily separated by nondenaturing electrophoresis due to their distinct pis, and this is illustrated in Fig. 11.1, which also shows the distinct electrophoretic properties of the amphiphilic enzyme (arrowed) found only in somatic extracts and therefore presumably associated with neuromuscular function. The overall amount of AChE produced by this parasite increases dramatically following establishment in the jejunum, and a switch in isoform expression occurs,... 

Dissolve the antibody to be conjugated in 0.1M sodium phosphate, 0.15 M NaCl, pH 7.5, at a concentration of lOmg/ml. If the antibody contains oligomers (as evidenced by nondenaturing electrophoresis or HPLC gel filtration analysis), then the monomeric IgG... 

SDS-PAGE is a denaturing technique in which proteins are broken down to their constituent polypeptide chains. Nondenaturing procedures are also available... 

IFF is a high-resolution technique that can routinely resolve proteins differing in pi by less than 0.05 pH unit. Under nondenaturing conditions, antibodies, antigens, and enzymes can retain their activities during IEF. The proper choice of ampholyte or IPG range is very important to the success of a fractionation. 

Fusion protein pull-down assays involve the overexpression of bait and/or fusion proteins in bacteria. Often, the expressed fusion proteins are localized in occlusion bodies and not readily soluble under nondenaturing conditions. The expressed proteins can be extracted using urea, sonication, sodium dodecyl sulfate (SDS), or a combination of all the three. The net result is the denaturation of the recombinant protein and it may need to be refolded if the interaction domain is conformationally dependent. A major advantage of the pull-down assay is that high concentrations of proteins can be easily generated thus favoring protein association for a reversible equilibrium between two proteins. 

---