Electronic Western blot of matrix-assisted laser desorption/ionization mass spectrometric-identified polypeptides from parallel processed gel-separated proteins

Identification of proteins previously separated by one-dimensional (1-D) or two-dimensional gel electrophoresis requires significant manipulations to digest the proteins into their respective peptides and to extract them from the gel prior to mass analysis. This article describes the simultaneous transfer and digestion of proteins directly from 1-D gels onto a membrane ready for matrix-assisted laser desorption/ionization (MALDI) mass spectrometric (MS) analysis. Protein transfer and digestion efficiencies are estimated to be more than 95%. The effectiveness of this procedure is demonstrated by identifying 110 unique proteins derived from a lysate of Escherichia coli and 149 proteins derived from a mouse liver homogenate separated by 1-D sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using crude mouse liver homogenates, four distinct glutathione S-transferase classes, ranging from 23 to 27 kDa, are identified from a separating gel, indicating the discriminating potential for this method. A Visual Basic program allowed visualization of the identified proteins according to their respective positions on the 1-D gels. In many cases, two or more proteins could be identified within a single band of the SDS gel. The “digital” images generated resemble Western blots without the use of antibodies or signal amplification techniques.     

Isolation of outer membrane proteins of Escherichia coli and their characterization on polyacrylamide gel

Proteins from the outer membrane of Escherichia coli were studied on a ureadodecyl sulfate polyacrylamide gel by electrophoresis. A polyacrylamide gel containing sodium dodecyl sulfate and urea gave an excellent resolution of outer membrane proteins. Seventeen protein bands were reproducibly observed on a gel. By use of Sephadex G-200, DEAE-cellulose and polyacrylamide gel, eight proteins were purified to near homogeneity. Five of them were found to be heat-modifiable proteins. The behavior of these purified proteins was studied on a polyacrylamide gel under three different electrophoretic conditions, which had been used for the analysis of cell envelope proteins. Thus correspondence was made between these purified proteins and envelope proteins reported by other investigators.     

Identification of the 7S globulin with β-conglycinin in soybean seeds

The 7S globulin, a major ultracentrifugal component with the 11S globulin, was identical with β-conglycinin one of four antigenic components in the reserve proteins of soybean seeds (Glycine max). Double gel immunodiffusion and immunoelectrophoresis in agar gel were used for their identification. In addition, some characteristic properties on ultracentrifugation and in carbohydrate content agreed well between the proteins. Their MWs were ca 180000.     

Gel permeation chromatography of asymmetric proteins

The gel permeation chromatographic behavior of three asymmetric proteins—collagen, fibrinogen, and the prolate ellipsoid lysozyme—was investigated using a variety of gel and high-performance liquid chromatographic media of various pore sizes and a wide range of flow rates. The time dependency of the elution patterns for columns and the partitioning of proteins between solvent and gel phases in batch experiments show that the “anomalous” behavior of asymmetric proteins is explicable by the mechanism proposed by Y. Nozaki, N. M. Schechter, J. A. Reynolds, and C. Tanford (1976, Biochemistry15, 3884); i.e., that these proteins penetrate pores of a size comparable to the minor semiaxis of the protein by end-on insertion. Thus, native type I collagen behaves as if it were a spherical protein of radius 8.2 Å, fibrinogen has an apparent radius of 32.4 Å, and lysozyme has an apparent radius of 14.6 Å. The rate at which asymmetric proteins penetrate the gel interior, however, is slow compared to the rate of gel penetration by globular proteins. The end-on insertion mechanism predicts that given infinite time, asymmetric proteins will be included into that portion of the internal volume of the gel which their smallest projectional cross sections allow them to penetrate. A method is presented for extrapolating the elution volume of asymmetric proteins to infinitely slow flow rate; from this extrapolation, one can calculate the minor semiaxis of the protein.     

Light-induced Changes in the Pattern of Protein Synthesis during the Early Stages of Greening of Etiolated Maize Leaves

The effect of light on protein synthesis during the early stages of greening of etiolated maize (Zea mays) leaves was studied using double labeling with leucine and fractionation of proteins by gel filtration and acrylamide gel electrophoresis. The incorporation of labeled leucine into a relatively small number of plastid proteins is effected within the first 30 to 60 minutes of illumination. These proteins do not accumulate with time. When illumination is prolonged, additional proteins are effected.     

A simplified and efficient system for separating proteins by preparative polyacrylamide electrophoresis. With notes on horse heart myoglobin

A simplified but effective method for preparative polyacrylamide gel electrophoresis is presented, suitable for single runs of ∼15 mg of protein, which allows: (1) a gel casting shaped and cooled so that proteins do not assume curvature as they migrate down the column; (2) direct contact of the bottom of the gel with buffer; (3) use of reduced electrical field since anode and cathode are spaced only 9.5 cm apart; (4) increased stability of the anodal face of the gel, by employing a dilute running buffer and consequently a still lower current (7 to 8 mA at 150 V); (5) obtaining successive effluents in separate Visking sacs, at appropriate time intervals, and removal of proteins in absence of an electrical field; (6) rinsing of the column between collections; (7) advance planning of the actual times of collection, calculated from the rates of migration of proteins of interest relative to the time of passage of (yellow) “myoglobin standard” determined in analytical columns run under the same conditions.     

Activity assay for nisin-like acidic bacteriocins using an optimal pH-conditioned gel matrix

A new zymography for detecting nisin-like acidic bacteriocins was developed using a tricine-sodium dodecyl sulfate (SDS) gel and an acidic gel matrix (pH 4.0). After electrophoresis, proteins in the tricine gel were electrotransferred to an optimal pH-conditioned gel matrix (OP-CGM). The OP-CGM was overlaid with indicator cells (Bacillus cereus) embedded in nutrient broth soft agar (0.8%, w/v). Antibacterial activity shown as a growth inhibition using B. cereus was detected at approximately 3.8 kDa. Because nisin is unstable in buffers at pH values over 6.0, the common electrophoretic systems, SDS-polyacrylamide gel electrophoresis and tricine gel, are not suitable for detection of nisin-like acidic bacteriocins.     

Comparative Electrophoretic Analyses of Soluble Proteins from Heterodera glycines Races 1-4 and Three Other Heterodera Species

Modified polyacrylamide gel and SDS-polyacrylamide gel electrophoretic systems using a low molarity tris-HCl buffer and equal pH of homogenizing buffer and stacking gel provided improved stacking for separation of soluble proteins from Heterodera schachtii, H. trifolii, H. lespedezae, and H. glycines races 1, 2, 3, and 4, compared with previous studies with cyst nematodes, The four Heterodera species were easily distinguished using the polyacrylamide gel system, but H. trifolii and H. lespedezae had similar protein patterns. H. glycines races were not separable by that system. The SDS-polyacrylamide gel system produced different protein patterns for all four Heterodera species although H. trifolii and H. lespedezae differed by only a single band, suggesting that these two may be subspecifically related. A protein band unique to H. glycines races 3 and 4 was not detected in SDS-polyacrylamide gel profiles from races 1 and 2. Molecular weight determinations were 55,000 for distinctive proteins in profiles of H. trifolii and 75,000 for H. glycines races 3 and 4.     

A simple preparative polyacrylamide disc gel electrophoresis apparatus: purification of three branched-chain amino acid binding proteins from Escherichia coli

The equipment used for preparative polyacrylamide gel electrophoresis has been either difficult to construct or costly if purchased commercially. An inexpensive preparative acrylamide gel apparatus and peristaltic pump are described in this paper which are easy to use and may be constructed from readily available materials. The construction of the preparative gel apparatus requires no special machining or glass blowing.This report describes the use of the disc gel apparatus in the final purification step of three binding proteins which appear to be involved in the transport of the branched-chain amino acids in Escherichia coli. Two of these proteins have been described previously (1–4). The apparatus has also been successfully used in a number of other laboratories for the purification of a variety of other proteins (5–9).     

Thiol group determination in proteins by flameless atomic absorption spectrometry of mercury.

The flameless atomic absorption procedure for determination of minute amount of mercury has been adapted for measuring thiol-groups in native and denatured proteins. The excess ofp-hydroxymercuribenzoate is removed by gel filtration after its reaction with the protein. The protein-p-hydroxymercuribenzoate complex is digested and the mercury is determined in an atomic absorption spectrophotometer. The sensitivity of the method allows measurement of 0.05 μg protein-bound mercury with the equipment used, but can be further increased. Results are presented for five different proteins.     

Identification of S-RNase and peroxidase in petunia nectar

Previous SDS PAGE gel analysis of the floral nectars from petunia and tobacco plants revealed significant differences in the protein patterns. Petunia floral nectar was shown to contain a number of RNase activities by in gel RNase activity assay. To identify these proteins in more detail, the bands with RNase activity were excised from gel and subjected to trypsin digestion followed by LC-MS/MS analysis. This analysis revealed that S-RNases accumulate in nectar from Petunia hybrida, where they should carry out a biological function different from self-pollen rejection. In addition, other proteins were identified by the LC-MS/MS analysis. These proteins include a peroxidase, an endochitinase, and a putative fructokinase. Each of these proteins contained a secretory signal sequence that marked them as potential nectar proteins. We developed RT-PCR assays for each of these five proteins and demonstrated that each of these proteins was expressed in the petunia floral nectary. A discussion of the role of these proteins in antimicrobial activity in nectar is presented.     

Biochemical Identification of the Two Races of Radopholus similis by Polyacrylamide Gel Electrophoresis

Analysis of proteins of the banana and citrus race of Radopholus similis was carried out by several different types of polyacrylamide gel electrophoresis. These included standard slab gel, SDS slab gel, gradient slab gel, and two-ditnensional slab gel electrophoresis. A major band difference was detected between the two races by slab gel electrophoresis. However, several other poorly resolved but consistent hands of high molecular weight proteins near the gel origin also were considered as diagnostic. Resolution of protein bands was greatly improved by SDS and gradient slab gel electrophoresis, but no differences could be detected among the proteins resolved between the two rares with these techniques. Two-dimensional gels revealed a large number of proteins, but background staining obscured them hindering interpretation. When nematode races were reared on three different host plants, no differences in protein patterns were detected between them, indicating host preferences does not play a role in determining the types proteins occurring in these nematodes.     

Identification of proteins according to biological activity following separation by two-dimensional isoelectric focusing/sodium dodecyl sulfate gel electrophoresis: analysis of human exocrine pancreatic proteins

A novel procedure is described whereby proteins can be identified according to their biological activity after their separation in two dimensions using isoelectric focusing and polyacrylamide gel electrophoresis in sodium dodecyl sulfate (G. Scheele, 1975, J. Biol. Chem., 250, 5375–5385). This procedure includes an optimal staining method for the visualization of two-dimensional gel spots, which avoids the use of chemical fixatives, and a one-step method for elution and renaturation of proteins. Fifteen out of the twenty discrete proteins separated from human pancreatic juice by the two-dimensional gel method were successfully identified by this procedure.     

Isolation,purification, and properties of mammalian and avian liver and yeast fatty acid synthetase acyl carrier proteins

Acyl carrier proteins were isolated from rat, human, pigeon, and chicken liver and yeast fatty acid synthetase complexes. These proteins were separated from the other proteins of subunit I of each complex by ultrafiltration after dialysis of subunit I for 3 h against low ionic strength buffer [Qureshi et al. (1974) Biochem. Biophys. Res. Commun.60, 158–165]. Subunit I of each fatty acid synthetase was previously separated from subunit II by affinity chromatography on Sepharose ?-aminocaproyl pantetheine and subsequent sucrose density gradient centrifugation. The separated acyl carrier proteins were then subjected to gel filtration on a Sephadex G-50 column. The proteins obtained from each fatty acid synthetase were homogeneous with respect to size and charge on gel filtration, paper and disc gel electrophoresis, and chromatography on diethylaminoethyl-cellulose. The physical properties and the ability to accept acetyl and malonyl groups from acetyl- and malonyl-CoA in the presence of transacylase were similar to those of Escherichia coli acyl carrier protein. These proteins ranged in molecular weight from 7500 to 10,000. Each of the acyl carrier proteins showed the presence of β-alanine and each yielded acetyl- and malonyl-A₁ and A₂ peptic peptides, thus indicating the presence of a 4′-phosphopantetheine prosthetic group in each. They differed somewhat from each other in amino acid composition, but each had a high number of negatively charged (aspartate and glutamate) amino acid residues.     

Phosphorylation of Chromatin-associated Proteins in Lemna and Hordeum

Sterile embryos of barley (Hordeum vulgare) and cultures of Lemna perpusilla have been labeled with ³²Pi and the chromatin proteins prepared and separated by acid-urea and sodium dodecyl sulfate gel electrophoresis. Under these conditions chromatin proteins became labeled and the gel radioactivity profiles which were complex indicated a probable minimum of 15 to 20 proteins phosphorylated with molecular weights ranging from 10⁴ to 10⁵. The majority of the radioactivity, 80 to 90% of the total, is found in the acidic protein fraction and this can be recovered as serine phosphate after partial acid hydrolysis.     

Sequence determination of three cuticular proteins and isoforms from the migratory locust,Locusta migratoria,using a combination of Edman degradation and mass spectrometric techniques

The cuticle (exoskeleton) is a characteristic structure of insects and other arthropods. It is an extracellular layer which surrounds and protects the insect, and it is composed of proteins, lipids, water molecules, phenolic materials and chitin. Four proteins isolated from the thorax and femur cuticle of pharate adult migratory locust, Locusta migratoria, have been purified by ion-exchange chromatography and reversed-phase high performance liquid chromatography (RP-HPLC). Their amino acid sequences were determined by combined use of mass spectrometry and automated Edman degradation. The cuticular extract was also separated by two-dimensional gel electrophoresis. In order to localize and identify the position of the proteins in the gel, a number of gel spots were excised and the proteins electroeluted. The molecular mass of some of the electroeluted proteins was determined by means of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) as well as by electrospray mass spectrometry (ESI-MS). Two of the sequenced proteins exist as pairs of closely related isoforms; one of the pairs contains the conserved 68-residue RR-2 motif, common for proteins from solid cuticles, and the other proteins contain the short motif Ala-Ala-Pro-Ala/Val repeatedly throughout the sequence.     

Two-Dimensional Polyacrylamide Gel Electrophoresis of Envelope Proteins of Escherichia coli

A method of separating envelope proteins by two-dimensional polyacrylamide gel electrophoresis is described. Escherichia coli envelopes (inner and outer membranes) were prepared by French pressing and washed by repeated centrifugation. Membrane proteins were solubilized with guanidine thiocyanate and were dialyzed against urea prior to two-dimensional electrophoretic analysis. The slab gel apparatus and conditions were similar to the technique developed by Metz and Bogorad (1974) for the separation of ribosomal proteins. This separation occurs in 8 M urea for the first dimension and in 0.2% sodium dodecyl sulfate for the second dimension. The technique separates about 70 different membrane proteins in a highly reproducible fashion according to both intrinsic charge and molecular weight. Some examples of alterations in the membrane protein pattern are demonstrated. These alterations are caused by a mutation affecting a sugar transport system and by growth in the presence of D-fucose, inducer of the transport system. A further example of membrane protein changes introduced by growth at the nonpermissive temperature of a temperature-sensitive cell division mutant is shown. Finally, it is demonstrated that the major outer membrane component of Escherichia coli K-12 contains more than four proteins of similar molecular weight.     

Selective separation procedure for determination of ribosomal proteins L7 and L12.

An electrophoretic procedure for the selective separation and determination of the closely similar ribosomal proteins L7 and L12 (which are specifically involved in the GTPase reactions of the ribosome) from the total protein mixture extracted from unwashed ribosomes is described. In this procedure, which takes advantage of their unusually low isoelectric points. L7 and L12 (and a few other acidic proteins) migrate into gel asanions, while the bulk of ribosomal proteins which are basic remain behind. The positions of L7 and L12 were determined with authentic, pure proteins. It was further determined by means of 2-dimensional gel electrophoresis that no other protein components present in unwashed ribosomes comigrate with the bands of L7 and L12.     

Developmental staging of maize microspores reveals a transition in developing microspore proteins

A method for the preparation of developmentally staged microspores and young pollen from maize (Zea mays) has been devised. The preparations are of sufficient purity and quantity for biochemical analysis, including the analysis of steady-state protein and RNA populations associated with each stage. A major transition in protein populations occurs during the developmental period that encompasses microspore mitosis, the asymmetric nuclear division producing the vegetative and generative nuclei. Several differences between early and late stage proteins can be detected by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Two-dimensional gel electrophoresis of proteins reveals that over half of the steady-state proteins differ between the younger and older stages, either quantitative or qualitative. One protein that increases in relative abundance about fourfold is actin. In vitro translation of RNA isolated from staged microspores demonstrates changes in microspore gene expression during the same developmental period.