Estimation of molecular weight by polyacrylamide gel electrophoresis using heat stable fluorophors

Protein Stains and Applications

Staining of proteins separated on gels provides the basis for determination of the critical properties of these biopolymers, such as their molecular weight and/or charge. Detection of proteins on gels and blots require stains. These stains vary in sensitivity, ease of use, color, stability, versatility, and specificity. This review discusses different stains and applications with details on how to use the stains, and advantages and disadvantages of each stain. It also compiles some important points to be considered in imaging and evaluation. Commonly used colorimetric and fluorescent dyes for general protein staining, and stains that detect posttranslational modification-specific detection methods are also discussed.

Protein stains and applications

Staining of proteins separated on gels provides the basis for determination of the critical properties of these biopolymers, such as their molecular weight and/or charge. Detection of proteins on gels and blots require stains. These stains vary in sensitivity, ease of use, color, stability, versatility, and specificity. This review discusses different stains and applications with details on how to use the advantages and disadvantages of each stain. It also compiles some important points to be considered in imaging and evaluation. Commonly used colorimetric and fluorescent dyes for general protein staining, and posttranslational modification-specific detection methods are also discussed.

Quantitative proteomics: assessing the spectrum of in-gel protein detection methods

Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.

Carboxyl BODIPY dyes from bicarboxylic anhydrides: one-pot preparation, spectral properties, photostability, and biolabeling

New fluorescent dyes based on 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) and functionalized with a free carboxyl group have been conveniently synthesized from pyrroles and dicarboxylic anhydrides in one-pot reactions. Their spectral properties in different solvents showed little effect of solvatochromism (<10 nm). The methyl groups on the BODIPY skeleton benefit the fluorescence quantum yields (Phi(f) up to 0.80 in water) but affect the photostability of the dyes. Photooxidation and photodegradation experiments suggest that dyes 1a and 2a exhibit excellent photostability, especially in water, and several factors were taken into account to elucidate the experimental phenomena. Dyes 1c and 2c, derived from 1a and 2a via the esterification of NHS (N-hydroxysuccinimidyl ester), can be easily acquired in high yields (>90%). Single crystal X-ray structures of dyes 2c and 3a are also obtained and discussed. The fluorescence labeling of BSA and followed prestaining method for gel electrophoresis of BSA demonstrate that the protein can be directly observed by naked eyes at as low as 2 ng level under a normal UV fluorescence electrophorogram gel image system.

SDS-PAGE of proteins using a chameleon-type of fluorescent prestain

A new prestaining method for protein SDS-PAGE was developed using the fluorogenic amino-reactive label Py-1. This resulted in one of the fastest, most sensitive, and environmentally friendly protocols available. It is mainly due to the unique optical properties of Py-1, which is blue and virtually nonfluorescent but turns to red and becomes much more strongly fluorescent once it is conjugated to the amino group of a protein. Staining times of 30 min are adequate to visualize subnanogram quantities of proteins because pre-electrophoretic labeling Py-1 does not require the time-consuming steps of washing or fixation of gels. LODs as low as 16 pg of protein are found which is better than the best (commercial) poststains and comparable to the best (commercial) prestains. In addition, prestaining requires marginal amounts of staining solution. The change in electrophoretic mobility and band broadening is at a low level because Py-1 causes a mass shift of 288 Da per bound molecule only. By virtue of the small mass shift it causes, this stain is compatible with mass spectrometric protein analysis even though it acts as a covalent label.

A mechanism for the fluorogenic reaction of amino groups with fluorescamine and MDPF

Fluorescamine and 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) react with primary amines at alkaline pH to yield highly fluorescent products, claimed to be diaryl-2-hydroxy-pyrrolinones. However, it seems to have been overlooked that these products appear as the pseudobase of coplanar and cationic diarylpyrrolones. Horse blood smears subjected to fluorogenic MDPF and fluorescamine reactions showed eosinophil granules with bright blue-white fluorescence, which required washing at neutral pH and was dependent on the presence of amino groups. The fluorescence of MDPF-butylamine product was abolished at alkaline pH and by bisulphite, suggesting that nucleophilic attacks to the pyrrolone ring (with formation of carbinol (pseudobase) and sulfonate derivatives, respectively), destroy the planarity and conjugation of the whole molecule, thus abolishing the emission at long wavelength. Analysis of the correlation between the largest conjugated fragment (LCF) values and the emission peaks of several fluorophores (fluorescamine- and MDPF-butylamino products, non-rigid fluorochromes) showed the best-fit when the cationic pyrrolones were considered. Although the pseudobases of fluorescamine- and MDPF-amino derivatives are formed at alkaline pH, a full conjugated, coplanar and cationic molecule is suggested to be the true fluorescent product.

Protein stains for proteomic applications: which, when, why?

This review recollects literature data on sensitivity and dynamic range for the most commonly used colorimetric and fluorescent dyes for general protein staining, and summarizes procedures for the most common PTM-specific detection methods. It also compiles some important points to be considered in imaging and evaluation. In addition to theoretical considerations, examples are provided to illustrate differential staining of specific proteins with different detection methods. This includes a large body of original data on the comparative evaluation of several pre- and post-electrophoresis stains used in parallel on a single specimen, horse serum run in 2-DE (IPG-DALT). A number of proteins/protein spots are found to be over- or under-revealed with some of the staining procedures.

Visible fluorescent detection of proteins in polyacrylamide gels without staining

2,2,2-Trichloroethanol (TCE) incorporated into polyacrylamide gels before polymerization provides fluorescent visible detection of proteins in less than 5min of total processing time. The tryptophans in proteins undergo an ultraviolet light-induced reaction with trihalocompounds to produce fluorescence in the visible range so that the protein bands can be visualized on a 300-nm transilluminator. In a previous study trichloroacetic acid or chloroform was used to stain polyacrylamide gel electrophoresis (PAGE) gels for protein visualization. This study shows that placing TCE in the gel before electrophoresis can eliminate the staining step. The gel is removed from the electrophoresis apparatus and placed on a transilluminator and then the protein bands develop their fluorescence in less than 5min. In addition to being rapid this visualization method provides detection of 0.2microg of typical globular proteins, which for some proteins is slightly more sensitive than the standard Coomassie brilliant blue (CBB) method. Integral membrane proteins, which do not stain well with CBB, are visualized well with the TCE in-gel method. After TCE in-gel visualization the same gel can then be CBB stained, allowing for complementary detection of proteins. In addition, visualization with TCE in the gel is compatible with two-dimensional PAGE, native PAGE, Western blotting, and autoradiography.

A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics

As proteomics evolves into a high-throughput technology for the study of global protein regulation, new demands are continually being placed upon protein visualization and quantitation methods. Chief among these are increased detection sensitivity, broad linear dynamic range and compatibility with modern methods of microchemical analyses. The limitations of conventional protein staining techniques are increasingly being encountered as high sensitivity electrophoresis methods are interfaced with automated gel stainers, image analysis workstations, robotic spot excision instruments, protein digestion work stations, and mass spectrometers. Three approaches to fluorescence detection of proteins in two-dimensional (2-D) gels are currently practiced: covalent derivatization of proteins with fluorophores, intercalation of fluorophores into the sodium dodecyl sulfate (SDS) micelle, and direct electrostatic interaction with proteins by a Coomassie Brilliant Blue-type mechanism. This review discusses problems encountered in the analysis of proteins visualized with conventional stains and addresses advances in fluorescence protein detection, including immunoblotting, as well as the use of charge-coupled device (CCD) camera-based and laser-scanner-based image acquisition devices in proteomics.

Staining methods in gel electrophoresis, including the use of multiple detection methods

Polyacrylamide gel electrophoresis is a reliable and widely used technique for the separation, identification and characterization of proteins and protein mixtures. With the introduction of high resolution two-dimensional polyacrylamide gel electrophoresis in 1975 upward to 2000 individual polypeptides spots are easily separated on a single electrophoretic gel thereby necessitating the availability of highly sensitive protein detection methods. Although a plethora of protein-staining and -visualization protocols have been described utilizing both radioactive and non-radioactive reagents, many times the use of mono-dimensional detection procedures is insufficient to address the experimental questions asked. The present review highlights the utilization of combined protein-labeling and -staining methodologies in gel electrophoresis including selected applications in polyacrylamide gels and solid membrane matrixes.

Polyhydroxy and polyethyleneglycol (meth)acrylate polymers: physical properties and general studies for their use as electrophoresis matrices

A new series of materials have been tested for their suitability as electrophoresis matrices. The mechanical and optical properties of gels composed of polyethyleneglycol (meth)acrylate esters or polyhydroxy (meth)acrylate esters in water and in various concentrations of organic solvents are described. Several crosslinkers including polyethyleneglycol and polyhydroxy di(meth)acrylates, piperazine diacrylate, and bisacrylamide were used in these studies. Electrophoretic migration and separation of a series of protein standards through polyethyleneglycol methacrylate (PEGM) 200, PEGM 400, and glyceryl methacrylate is demonstrated. Further, copolymerization of all of the monomers with acrylamide was performed and the distribution of monomer incorporation into the polymer network calculated. All monomers and copolymers that were examined by IR spectroscopy showed greater than 99% polymerization. These results justify their further study for biomolecule separations.

Electrophoresis of proteins and nucleic acids: I--Theory

Images

Rapid imaging, using a cooled charge-coupled-device, of fluorescent two-dimensional polyacrylamide gels produced by labelling proteins in the first-dimensional isoelectric focusing gel with the fluorophore 2-methoxy-2,4-diphenyl-3(2H)furanone

A new method for visualising proteins in two-dimensional polyacrylamide gels was developed. Proteins were labelled with the fluorophore 2-methoxy-2,4-diphenyl-3(2H)furanone (MDPF) while present in the first-dimensional gel after isoelectric focusing and subsequently electrophoresed into the second-dimensional gel. High resolution spot patterns were produced and compared with other methods of visualisation. A new rapid imaging system based on a cooled charge-coupled-device was used to view the two-dimensional fluorescent protein spot patterns. The method allows the immediate and rapid imaging of two-dimensional gels at the end of electrophoresis with no further processing.

Two-dimensional gel electrophoresis of proteins

The high-resolution capacity of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) makes it an excellent tool for the analysis and characterisation of complex protein mixtures. The evolution of two-dimensional electrophoresis is briefly described. The various steps involved in 2-D PAGE, the identification and characterization of proteins separated by 2-D PAGE and the quantitative and qualitative analysis of 2-D patterns are discussed in detail and some new approaches are described. In the final section a brief outline of some of the biomedical applications of 2-D PAGE to screening of body fluids, genetic diseases, inborn errors of metabolism, cancer and neoplastic transformation are discussed.

Fluorescent labeling of cysteinyl residues to facilitate electrophoretic isolation of proteins suitable for amino-terminal sequence analysis

A protein labeling procedure which enables detection of subpicomole quantities of proteins on sodium dodecyl sulfate (SDS)-polyacrylamide gels is described. Proteins are rendered fluorescent by reduction of disulfide bonds with dithiothreitol followed by alkylation with 5-N-[(iodoacetamidoethyl)amino]naphthalene-1-sulfonic acid (5-I-AEDANS) or 5-iodoacetamido-fluorescein. Labeling is performed prior to electrophoresis, thus eliminating the need for staining with dyes and destaining after electrophoresis. As little as 375 fmol (25 ng) of prelabeled bovine serum albumin can be readily visualized after electrophoresis. Bands are still visible after electrophoretic transfer to nitrocellulose. Simultaneous labeling of proteins in complex mixtures is possible using this technique. This includes cysteine containing proteins of disrupted Newcastle disease virus. The magnitudes of the molecular weight increases which occur upon labeling reflect the cysteine contents of proteins. The mode of chemical modification for the prelabeling procedure was chosen because of its compatibility with analytical techniques, such as amino acid analysis, peptide mapping, or sequence analysis, which may be applied to the protein after electroelution from SDS-acrylamide gels. It replaces the need for reduction and carboxymethylation prior to these analytical procedures. Protein-sequence analysis of prelabeled bovine serum albumin, including samples electroeluted from SDS-acrylamide gels, has justified the choice of this method to facilitate isolation of proteins for sequence analysis. Equivalent sequence data were obtained with reduced bovine serum albumin S-alkylated with iodoacetic acid or 5-I-AEDANS.

A fluorescent screening assay for collagenase using collagen labeled with 2-methoxy-2,4-diphenyl-3(2H)-furanone

This report describes the use of the compound 2-methoxy-2,4-diphenyl-3(2H)-furanone to label collagen as a substrate for the detection of mammalian collagenase in a fluorescent assay which is suitable for screening large numbers of samples. The compound 2-methoxy-2,4-diphenyl-3(2H)-furanone presents distinct advantages over other fluorophores, since both the unbound reagent and its hydrolysis products are nonfluorescent. The labeling procedure uses commercially available collagen, is fast and simple, and gives a 90% yield of labeled substrate. The fluorescent collagen substrate is stable and retains fluorescence over a wide range of pH. The assay detects, reproducibly, metal-dependent collagenase activity in microliter volumes of conditioned media from cultured neoplastic cells or in chromatographic fractions from such media.

Synthesis of the large subunit of ribulose-1,5-bisphosphate carboxylase in anin vitro partially definedE. coli system

Thein vitro DNA- or RNA-directed synthesis of the large subunit (LS) of spinach chloroplast ribulose-1,5-biphosphate carboxylase (RuP2C) has been examined in a highly definedE. coli transcription-translation system. Spinach chloroplast DNA, RNA and recombinant plasmids containing the spinach chloroplast LS gene (rbcL) have been used as templates in thein vitro system and a quantitative assay has been developed to measure LS formation. Thein vitro formed product contains formylmethionine at the N-terminal position and sediments primarily as a monomer. There is no detectable enzymatic activity associated with thein vitro product. To determine where theE. coli RNA polymerase used in these systems initiates, we have examined the transcripts produced by this enzymein vitro. Measurements of run-off transcripts indicate thatE. coli RNA polymerase initiates at the same position on the gene as is seenin vivo. In addition, the complete nucleotide sequence of therbcL gene including previously unsequenced 3' and 5' flanking regions has been determined. The sequence agrees, except at two nucleotide positions, with previously published sequencing data for this gene (Zurawski, G, Perrot, B, Bottomley, W, Whitfeld, PR, 1981. Nucleic Acids Res. 9:3251-3270).

Advantages of preelectrophoretic conjugation of polypeptides with fluorescent dyes

A rapid simple procedure is described for the conjugation of proteins, glycoproteins, and peptides with the fluorescent dye fluorescein isothiocyanate during the time required to polymerize a polyacrylamide gel. Such conjugation does not perturb the electrophoretic mobility of the polypeptides in detergent containing gels. The location of polypeptide . dye conjugate is evident by inspection immediately upon removal of a gel from an electrophoresis cabinet avoiding the time required for postelectrophoretic staining and destaining procedures. The sensitivity of detection of polypeptide . fluorescein conjugates is at least equivalent to that obtained using Coomassie blue.

Isolation and properties of the rabbit skeletal muscle protein inhibitor of adenosine 3',5'-monophosphate dependent protein kinases

The heat-stable protein inhibitor (Walsh, D. A., et al. (1971), J. Biol. Chem. 246, 1977--1985) of the cyclic adenosine 3',5'-monophosphate dependent protein kinase has been isolated in pure form from rabbit skeletal muscle after a 430 000-fold purification with a 47% yield. The four-step procedure involves sequentially a heat treatment, batchwise anion and cation exchange, and affinity chromatography on protein kinase catalytic subunit covalently coupled to Sepharose 4B. The inhibitor is an acidic protein (pI = 4.24) of molecular weight 11 300. It contains 98 amino acid residues none of which contains sulfur and only 2 (phenylalanine and tyrosine) are aromatic. The NH2-terminus is blocked. The muscle content is ca. 0.6 mg of inhibitor per L of intracellular water. The inhibitor is tightly bound to the catalytic subunit of protein kinase (Ki congruent to 2 X 10(-9) M) and acts competitively with respect to the protein substrates. Protein kinase recognizes a short stretch of the inhibitor sequence, in which arginyl side chains play a crucial role. A study of various competitive inhibitors of the kinase confirms the importance of guanidino groups and hydrophobic side chains in the specific interaction with the substrate binding site.