Proteins residue-specific method

Fushman, D. and D. Cowburn, Nuclear magnetic resonance relaxation in determination of residue-specific 1SN chemical shift tensors in proteins in solution protein dynamics, structure, and applications of transverse relaxation optimized spectroscopy, in Methods Enzymol. T. James, U. Schmitz, and V. Doetsch, Editors. 2001. p.109-126. 

A variety of methods are available to detect proteins separated by electrophoresis or to measure the concentration of total protein in a solution. These methods are normally based on the binding of a dye to one of the amino acids in protein, or a color reaction with an amino acid side chain. The most commonly used stains for protein detection on gels are Coomassie Brilliant Blue (98) and silver stain (99,100). These methods detect any protein residues, either in solution or on an electrophoresis gel. Their main requirement is sensitivity, not specificity. New, more sensitive dyes are being developed for the proteomic analysis of protein structure and sequence, for example Ruby Red (101). 

In principle, it should be possible to sequence an entire protein by using the Edman method. In practice, the peptides cannot be much longer than about 50 residues. This is so because the reactions of the Edman method, especially the release step, are not 100% efficient, and so not all peptides in the reaction mixture release the amino acid derivative at each step. For instance, if the efficiency of release for each round were 98%, the proportion of "correct" amino acid released after 60 rounds would be (0.98 0), or 0.3—a hopelessly impure mix. This obstacle can be circumvented by cleaving the original protein at specific amino acids into smaller peptides that can be sequenced. In essence, the strategy is to divide and conquer. 

The Soy Protein Residue Assay is a double-antibody (sandwich) ELISA using specific anti-soy tripsyn inhibitor and other soy protein antibodies coated onto microwells. After addition of the sample, the enzyme conjugate, and the TMB substrate, a positive reaction (indicating the presence of soy protein), produces a blue color. Addition of the stop solution ends the assay and turns blue to yellow. The result may be read visually (in the qualitative method) or with an ELISA reader (in the qualitative or quantitative method). Quantification can be obtained by mnning positive control standards (2.5-5-10-25 ppm) together with the samples. A standard curve is then plotted using the optical density (OD) values of the control standards (OD vs. concentration). 

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