Quantification of Proteins

Protein quantification in a solution is an extremely important problem no specific activity can be reported without employing both an activity assay and a protein quantification assay. The outcome of a protein quantification assay is a measure of total protein in a sample solution, routinely reported in mg mlT1 or mg L-1. Compared to an ideal assay, which should be accurate, very sensitive, reliable, fast, and easy to perform, all commonly employed assays for total protein suffer several shortcomings. 

The most frequently used protein assay is based on a method after Bradford (Bradford, 1976), which combines a fast and easily performed procedure with reliable results. However, the Bradford assay has sensitivity limitations and its accuracy depends on comparison of the protein to be analyzed with a standard curve using a protein of known concentration, commonly bovine serum albumin (BSA). Many commercially available protein assays such as those from Pierce or BioRad rely on the Bradford method. The assay is based on the immediate absorbance shift from 465 nm (brownish-green) to 595 nm (blue) that occurs when the dye Coomassie Brilliant Blue G-250 binds to proteins in an acidic solution. Coomassie dye-based assays are known for their non-linear response over a wide range of protein concentrations, requiring comparison with a standard. The dye is assumed to bind to protein via an electrostatic attraction of the dye s sulfonic groups, principally to arginine, histidine, and lysine residues. It also binds weakly to the aromatic amino acids, tyrosine, tryptophan, and phenylalanine via van der Waals forces and hydrophobic interactions. 

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To quantitate proteins from staining, a densitometer aided by computer software is used to evaluate band areas of samples compared to band areas of a standard curve. Amido black, Coomassie Brilliant Blue, and silver stains are all appHcable for use in quantification of proteins. 

QconCAT for the absolute quantification of protein samples. This new technology was developed for the identification and absolute quantification in proteomics. Examples of applications may be the analysis of expression levels across a set of samples, the protein expression tracking during development, and the individual members identification in protein families. A concatamer (artificial protein) is... 

Instruments). The antibody panel will be selected to include ubiquitous cytoplasmic, nuclear, and surface markers. Accurate biochemical quantification of proteins in the cell/tissue model will be undertaken for validation of the IHC findings. 

However, IHC as a practical method continues to evolve with increasing demands for standardization, and for true quantification of protein analytes by weight, in the context of their cellular microenvironment. Further studies combining proteomics by mass spectrometry and IHC are likely to lead to the refinement of both methods in the analysis of FFPE tissues. The end result may be the creation of a broader field that defines and quantifies protein expression at a cellular level, incorporating the advantages of the wide spectrum of proteins demonstrable by mass spectrometry and the precise localization offered by IHC. 

The side chains of the aromatic amino acids (Phe, Tyr and Trp) are not particularly reactive chemically, but they all absorb ultraviolet (UV) light. Tyr and Trp in particular absorb strongly at 280 nm, allowing detection and quantification of proteins in solution by measuring the absorbance at this wavelength. 

Detection and quantification of protein by measuring absorbency at 280 nm is perhaps the simplest such method. This approach is based on the fact that the side chains of the amino acids tyrosine and tryptophan absorb at this wavelength. The method is popular, as it is fast, easy to perform and is non-destructive to the sample. However, it is a relatively insensitive technique, and identical concentrations of different proteins will yield different absorbance values if their content of tyrosine and tryptophan vary to any significant extent. Hence, this method is rarely used to determine the protein concentration of the final product, but it is routinely used during downstream processing to detect protein elution off chromatographic columns, and hence track the purification process. 

The most common methods used to determine protein concentration are the dye-binding procedure using Coomassie brilliant blue, and the bicinchonic-acid-based procedure. Various dyes are known to bind quantitatively to proteins, resulting in an alteration of the characteristic absorption spectrum of the dye. Coomassie brilliant blue G-250, for example, becomes protonated when dissolved in phosphoric acid, and has an absorbance maximum at 450 nm. Binding of the dye to a protein (via ionic interactions) results in a shift in the dye s absorbance spectrum, with a new major peak (at 595 nm) being observed. Quantification of proteins in this case can thus be undertaken by measuring absorbance at 595 nm. The method is sensitive, easy and rapid to undertake. Also, it exhibits little quantitative variation between different proteins. 

SDS polyacrylamide gel electrophoresis (SDS-PAGE) represents the most commonly used analytical technique in the assessment of final product purity (Figure 7.1). This technique is well established and easy to perform. It provides high-resolution separation of polypeptides on the basis of their molecular mass. Bands containing as little as 100 ng of protein can be visualized by staining the gel with dyes such as Coomassie blue. Subsequent gel analysis by scanning laser densitometry allows quantitative determination of the protein content of each band (thus allowing quantification of protein impurities in the product). 

For quantitative analysis of protein concentration the colorimetric Bradford-assay [147] is most commonly used. Here another Coomassie dye, Brilliant Blue G-250, binds in acidic solutions to basic and aromatic side chains of proteins. Binding is detected via a shift in the absorption maximum of the dye from 465 nm to 595 nm. Mostly calibration is performed with standard proteins like bovine serum albumin (BSA). Due to the varying contents of basic and aromatic side chains in proteins, systematic errors in the quantification of proteins may occur. 

A related approach is realized in filter binding assays. Here the reaction solution is filtered, e.g., through nitrocellulose where proteins are absorbed, while small molecules can pass. One example of this technique is the quantification of protein bound and free nucleotides (with radioactive labeled ligands). 

Affinity capture-release electrospray ionization mass spectrometry (ACESIMS) is another recently introduced technique for quantification of proteins, and to date has most often been applied to clinical enzymology.60 The product conjugates of the enzymatic reaction between the synthetic substrate and targeted enzyme are captured by immobilized affinity reagents, purified, released into solution, and analyzed by ESI-MS. 

Bader AN, Hofrnan EG, Voortman J, en Flenegouwen PM, Gerritsen HC (2009) Homo-ERET imaging enables quantification of protein cluster sizes with subcellular resolution. Biophys J 97 2613-22... 

M. M. Zhu, R. Chitta, M. L. Gross PLIMSTEX a novel mass spectrometric method for the quantification of protein-ligand interactions in solution. Int. J. Mass Spectrom. 2005, 240, 213—220. 

M. L. Gross Quantification of protein—ligand interactions by mass spectrometry, titration, and H/D exchange PLIMSTEX./. Am. Chem. Soc. 2003, 125, 5252-5253. 

Breuker, K. New mass spectrometric methods for the quantification of protein-ligand binding in solution. Angew. Chem. Int. Ed. 2004, 43,... 

Quantification of Protein-Ligand Interactions in Solution by Hydrogen/Deuterium Exchange (PLIMSTEX)... 

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