Section 9.2 Quantitation and Selective Purification of Proteins in SolutionSeveral colorimetric methods have been described for quantitating proteins in solution, including the widely used Bradford Quant-iT Protein Assay KitThe Quant-iT family of assay kits provides state-of-the-art reagents for sensitive and selective quantitation of protein (Table 9.1), DNA or RNA (Table 8.12) samples using a standard fluorescence microplate reader. These kits have been specially formulated with ready-to-use buffers, prediluted standards and easy-to-follow instructions, making quantitation both accurate and extremely easy (Figure 8.52). Each Quant-iT assay is:
Because the fluorescent dye in each Quant-iT Kit matches common fluorescence excitation and emission filter sets in microplate readers, these assay kits are ideal for high-throughput environments, as well as for small numbers of samples. The Quant-iT Protein Assay Kit (Q33210) simplifies protein quantitation without sacrificing sensitivity. This protein assay exhibits a detection range between 0.25 and 5 µg protein (Figure 9.3), and the response curve is sigmoidal (pseudolinear from 0.5 to 4 µg) with little protein-to-protein difference in signal intensity. Common contaminants, including salts, solvents, 2-mercaptoethanol, amino acids and DNA, are well tolerated in this assay; however, it is not compatible with detergents. Each Quant-iT Protein Assay Kit contains:
Sufficient reagents are provided to perform 1000 assays, based on a 200 µL assay volume in a 96-well microplate format; this assay can also be adapted for use in cuvettes or 384-well microplates. The fluorescence signal exhibits excitation/emission maxima of 470/570 nm and is stable for three hours at room temperature. The Quant-iT protein reagent is a new formulation of Molecular Probes' NanoOrange reagent, which is described below. NanoOrange Protein Quantitation KitOur Patented NanoOrange Protein Quantitation Kit (N6666) provides an ultrasensitive assay for measuring the concentration of proteins in solution.
Our NanoOrange protein quantitation reagent, with an excitation/emission maxima of 470/570 nm when bound to proteins, is suitable for use with a variety of instrumentation. Fluorescence is typically measured using instrument settings or filters that provide excitation/emission at ~485/590 nm, which are commonly available for both spectrofluorometers and microplate readers. A spectrofluorometer either a standard fluorometer or a minifluorometer offers the greatest effective range and lowest detection limits for this assay. With fluorescence microplate readers, the NanoOrange assay is useful over a somewhat narrower range from 100 ng/mL to 10 µg/mL in final protein concentration. The NanoOrange Protein Quantitation Kit (N6666) supplies:
The amount of dye supplied in this kit is sufficient for ~200 assays using a 2 mL assay volume and a standard fluorometer or minifluorometer, or ~2000 assays using a 200 µL assay volume and a fluorescence microplate reader. The NanoOrange reagent is ideal for quantitating protein samples before gel electrophoresis CBQCA Protein Quantitation Kit The ATTO-TAG CBQCA reagent was originally developed as a chromatographic derivatization reagent for amines Each CBQCA Protein Quantitation Kit (C6667) contains:
The CBQCA Protein Quantitation Kit provides sufficient reagents for 300800 assays using a standard fluorometer, minifluorometer or fluorescence microplate reader. EZQ Protein Quantitation KitThe EZQ Protein Quantitation Kit (R33200) provides a fast and easy high-throughput assay for proteins in solution. Because detergents, reducing agents, urea and tracking dyes do not interfere, this fluorescence-based protein quantitation assay is ideal for determining the protein concentration of samples prior to polyacrylamide gel electrophoresis. This convenient kit can also provide a quick assessment of protein content during protein purification schemes and fractionation procedures. The EZQ assay requires only 1 µL of a sample per spot, and up to 96 samples, including standards, can be assayed in one session. The protein samples are simply spotted onto one of the provided assay papers, fixed with methanol and then stained with our proprietary EZQ protein quantitation reagent. This assay paper is then clamped into the specially designed 96-well microplate for quick analysis in a top- or bottom-reading fluorescence microplate reader (Figure 9.11). For added versatility, the solid-phase assay format and provided 96-well microplate are also compatible with laser scanners equipped with 450, 473 or 488 nm lasers and with UV illuminators in combination with photographic or CCD cameras for image documentation and analysis. Once the samples are spotted, the assay protocol can be completed in about 1 hour. The protein concentration is determined from a standard curve, and the effective range for the assay is generally 0.055 mg/mL or 0.055 µg per spot (Figure 9.12). Protein-to-protein sensitivity differences in the assay are minimal the observed coefficient of variation is typically ~16% (Figure 9.13). The EZQ Protein Quantitation Kit is extremely useful for estimating the concentration of chromatographically separated protein fractions. Each EZQ Protein Quantitation Kit contains:
Sufficient reagent and assay paper are provided for ~2000 protein quantitation assays. Other Reagents for Protein Quantitation in Solution Other than our premier protein quantitation products described above, most other fluorogenic reagents for general protein quantitation in solution detect accessible primary amines. The sensitivity of assays based on these reagents therefore depends on the number of amines available a function of both the protein's three-dimensional structure and its amino acid composition. For example, horseradish peroxidase (MW ~40,000 daltons), which has only six lysine residues, Certain dyes that detect primary aliphatic amines, including ATTO-TAG CBQCA (A6222), fluorescamine (F2332; FluoroPure Grade, F20261) and o-phthaldialdehyde (OPA, P2331MP), have been the predominant reagents for fluorometric determination of proteins in solution (Table 9.1). These same reagents, and others such as naphthalene-2,3-dicarboxaldehyde Fluorescamine Fluorescamine (F2332; FluoroPure Grade, F20261) is intrinsically nonfluorescent but reacts in milliseconds with primary aliphatic amines, including peptides and proteins, to yield a fluorescent derivative o-Phthaldialdehyde The combination of o-phthaldialdehyde (OPA, P2331MP) and 2-mercaptoethanol provides a rapid and simple method of determining protein concentrations in the range of 0.2 µg/mL to 25 µg/mL SYPRO Red and SYPRO Orange Protein Gel StainsAn assay has been reported that uses the SYPRO Red protein gel stain (S6653, S6654; Section 9.3) for quantitating total protein content of bacterial cells by flow cytometry. Selective Protein Quantitation in SolutionEZQ Phosphoprotein Quantitation KitThe EZQ Phosphoprotein Quantitation Kit (E33201) provides a fast and simple assay for phosphoproteins in solution. No radioactivity or antibodies are required, and sample analysis can typically be completed within 60 minutes. The EZQ phosphoprotein quantitation assay shows high selectivity for phosphoproteins over nonphosphorylated proteins (Figure 9.14) and is compatible with samples containing detergents, reducing agents and urea buffers with up to 1% carrier ampholytes. Furthermore, this assay requires only 1 µL of sample, and up to 96 samples, including standards, can be assayed simultaneously. This kit is ideal for analyzing protein kinase or phosphatase activities, as well as for monitoring relative phosphoprotein concentrations during chromatography or after IEF fractionation of protein samples. In this assay, the phosphoprotein samples are spotted onto specially prepared assay paper, fixed onto the paper with methanol and then stained with our proprietary EZQ phosphoprotein quantitation reagent. Relative phosphate content is determined from a standard curve of ovalbumin or any standard phosphoprotein of interest. As little as 20 ng of ovalbumin that contains 2 phosphate residues per ovalbumin can be selectively detected, and the ovalbumin standard curve has an overall dynamic range of 250-fold, from 0.4 to 120 picomoles. The Z-factor for this assay is in the "excellent" range at greater than 0.8, with N = 8. For normalizing the phosphoprotein signal to the total protein levels, total protein quantitation can be easily performed after phosphoprotein analysis on the same paper using the EZQ Protein Quantitation Kit (R33200) described above. Each EZQ Phosphoprotein Quantitation Kit contains:
Sufficient materials are provided for 2000 microplate-well assays. The EZQ Phosphoprotein Quantitation Kit is designed for high-throughput analysis. The solid-phase format and special 96-well microplate can be used with readily available fluorescence-based detection instruments, including either top- or bottom-reading microplate readers and laser scanners equipped with 532560 nm lasers, as well as UV illuminators in combination with photographic or CCD cameras for image documentation and analysis (with lower sensitivity). EZQ Phosphopeptide Quantitation KitThe EZQ Phosphopeptide Quantitation Kit (E33202) permits accurate quantitation of phosphopeptides in solution, in the presence of standard buffer components. As with the EZQ Phosphoprotein Quantitation Kit described above, no radioactivity or antibodies are required, and sample analysis can typically be completed within 60 minutes. This phosphopeptide assay requires only 1 µL of sample, and up to 96 samples, including standards, can be assayed simultaneously. This kit is ideal for analyzing phosphatase and kinase activities, as well as for monitoring relative phosphopeptide concentrations before and after analysis by liquid chromatography, mass spectrometry or other separation technique. In the EZQ phosphopeptide quantitation assay, the phosphopeptide samples are spotted onto specially prepared assay paper, fixed onto the paper with methanol and then stained with our proprietary EZQ phosphopeptide quantitation reagent. Relative phosphate content is determined from a standard curve of control phosphopeptide pT1721 or any standard phosphopeptide of interest. Subpicomole amounts of most monophosphorylated peptides can be detected; for peptides that we have tested, the overall dynamic range of detection is over 500-fold, from 0.20.8 picomole at the lower end to about 400 picomoles, depending on the peptide. The Z-factor for this assay is in the "excellent" range at greater than 0.8, with N = 8. Each EZQ Phosphopeptide Quantitation Kit contains:
Sufficient materials are provided for 1000 microplate-well assays. The EZQ Phosphopeptide Quantitation Kit is designed for high-throughput analysis. The solid-phase format and special 96-well microplate can be used with readily available fluorescence-based detection instruments, including either top- or bottom-reading microplate readers and laser scanners equipped with 532560 nm lasers, as well as UV illuminators in combination with photographic or CCD cameras for image documentation and analysis (with somewhat lower sensitivity). Pro-Q Diamond LC Phosphopeptide Detection KitThe Pro-Q Diamond LC Phosphopeptide Detection Kit (P33203) provides sensitive and selective fluorescence-based detection of phosphorylated peptides during liquid chromatography separations. The Pro-Q Diamond LC phosphopeptide detection reagent interacts selectively with phosphoserine-, phosphothreonine- and phosphotyrosine-containing peptides to form unique, highly fluorescent dyephosphopeptide complexes that elute from an HPLC column with altered retention times, allowing identification and purification of phosphopeptides prior to analysis by mass spectrometry. This kit is ideal for isolating phosphopeptides from chromatographic fractions of semi-complex peptide mixtures or from complex peptide mixtures such as the tryptic digest of a phosphoprotein. The Pro-Q Diamond LC Phosphopeptide Detection Kit provides:
Sufficient reagents are provided for 20 HPLC separations; a single separation will selectively detect 20 picomoles or less of a monophosphorylated peptide using a standard microbore C18 HPLC column. Phosphopeptide Standard MixtureFormulated especially for MALDI-MS, the phosphopeptide standard mixture (P33357) contains equimolar amounts of three unphosphorylated and four phosphorylated peptides, ranging in mass from 1047 to 2192 and representing phosphoserine (pS), phosphothreonine (pT) and phosphotyrosine (pY) monophosphopeptides, as well as a peptide containing both pT and pY. This mixture is ideal for use as an internal or external control for LC/MS, MALDI analysis or β-elimination reactions. MBDS: A Fluorogenic Reagent for Serum Albumins 4-Amino-4'-benzamidostilbene-2,2'-disulfonic acid (MBDS, A11760) is a reagent with properties similar to a commonly used probe for hydrophobic sites in proteins, 1-anilinonaphthalene-8-sulfonic acid (1,8-ANS, A47; Section 13.5; Figure 9.15). Like 1,8-ANS (Product Highlight: Monitoring Protein-Folding Processes with Anilinonaphthalenesulfonate Dyes), MBDS is virtually nonfluorescent in water (quantum yield <0.01); however, upon binding to the hydrophobic pocket of serum albumins and some other proteins, it undergoes an almost 100-fold increase in its fluorescence. Anti-Dinitrophenyl Antibody: A Reagent for Measuring Protein CarbonylsOxidative injury can be monitored by following the formation of protein-derived aldehydes and ketones. Traditionally, protein-derived aldehydes and ketones have been quantitated using a colorimetric assay based on their reaction with 2,4-dinitrophenylhydrazine to yield protein-bound dinitrophenyl moieties (DNP). A much more sensitive ELISA method has been developed that detects the protein-bound DNP using unlabeled or biotin-labeled anti-DNP antibodies EnzChek and Amplex Red Assay KitsMolecular Probes prepares numerous chromogenic and fluorogenic substrates that are useful for quantitating enzymes and enzymatic activity in experimental samples. In addition, we have developed several EnzChek Assay Kits, DQ Assay Kits and Amplex Red Assay Kits especially designed for detecting a wide variety of enzymes and their substrates. Most of these products are described in Chapter 10. Selective Protein PurificationGlutathione Agarose and AntiGlutathione S-Transferase Antibody for GST Fusion Protein Identification and Purification In protein fusion techniques, the coding sequence of one protein is fused in-frame with another so that the expressed hybrid protein possesses desirable properties of both parent proteins. One common partner in these engineered products is glutathione S-transferase (GST), a protein with natural binding specificity that can be exploited to facilitate its purification. Molecular Probes also offers a highly purified rabbit polyclonal anti-GST antibody (A5800, Labeled and Unlabeled Anti-Glutathione S-Transferase Antibodies) that can be used to purify GST fusion proteins by immunoprecipitation. Our Glutathione Transferase Fusion Protein Purification Kit (G21801) facilitates isolation and characterization of GST fusion proteins. This kit, which contains sufficient materials for five isolations, contains:
Following purification, the fusion protein can serve as an immunogen for antibody production Streptavidin Agarose and CaptAvidin AgaroseMolecular Probes prepares both streptavidin and CaptAvidin biotin-binding protein conjugated to 4% beaded crosslinked agarose (S951, C21386) matrices that can be used to isolate biotinylated peptides, proteins, hybridization probes, haptens and other molecules. CaptAvidin agarose has been specially designed to allow easier dissociation of the avidinbiotin complex (Figure 7.96). Avidin and biotin form a very strong noncovalent bond with a Ka of ~1015 M-1. Although this high affinity is advantageous for many histochemical applications, it is a major drawback for affinity chromatography. The conditions needed to dissociate the avidinbiotin complex (8 M guanidine hydrochloride, pH 1.5) are usually too harsh for proteins and prevent the use of avidin for purifying biotinylated molecules. To address this problem, the tyrosine residues in the four biotin-binding sites of CaptAvidin biotin-binding protein (C21385, CaptAvidin Biotin-Binding Protein) are nitrated, considerably reducing its affinity for biotinylated molecules above pH 9. At pH 4.0, CaptAvidin biotin-binding protein binds biotin tightly, with a Ka of 109 M-1. At pH 10, however, this association is reversed, allowing complete dissociation of the avidinbiotin complex. Researchers have used CaptAvidin agarose affinity chromatography to purify immunoglobulins from whole rabbit serum and to isolate anti-transferrin antibody directly from rabbit IgG fractions. Streptavidin Acrylamide, CaptAvidin Acrylamide and Reactive Acrylamide DerivativesStreptavidin acrylamide (S21379, Agarose and Acrylamide Conjugates), which is prepared from the succinimidyl ester of 6-((acryloyl)amino)hexanoic acid (acryloyl-X, SE, A20770), may be useful for the preparation of biosensors. |