Peptide mapping of proteins in gel bands after partial cleavage with acidic cyanogen bromide vapors

A procedure is described for obtaining peptide maps from microgram quantities of protein in gel bands, after cleavage at the methionyl peptide bonds with vapors of acidic cyanogen bromide (CNBr). Absence of direct contact of the gel pieces with CNBr eliminates the need for extensive equilibration of the gel piece to remove CNBr prior to electrophoresis. The milder conditions lead to partial cleavage of the proteins, yielding larger peptides and thereby reducing the risk of peptide loss during the postelectrophoresis procedures. The "fingerprints" obtained are reproducible and independent of an eightfold change in CNBr concentration.     

Pouring and Running a Protein Gel by reusing Commercial Cassettes

The evaluation of proteins using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is a common technique used by biochemistry and molecular biology researchers^1-4. For laboratories that perform daily analyses of proteins, the cost of commercially available polyacrylamide gels (˜$10/gel) can be considerable over time. To mitigate this cost, some researchers prepare their own polyacrylamide gels. Traditional methods of pouring these gels typically utilize specialized equipment and glass gel plates that can be expensive and preclude pouring many gels and storing them for future use. Furthermore, handling of glass plates during cleaning or gel pouring can result in accidental breakage creating a safety hazard, which may preclude their use in undergraduate laboratory classes. Our protocol demonstrates how to pour multiple protein gels simultaneously by recycling Invitrogen Nupage Novex minigel cassettes, and inexpensive materials purchased at a home improvement store. This economical and streamlined method includes a way to store the gels at 4°C for a few weeks. By re-using the plastic gel cassettes from commercially available gels, labs that run frequent protein gels can save significant costs and help the environment. In addition, plastic gel cassettes are extremely resistant to breakage, which makes them ideal for undergraduate laboratory classrooms.     

Rapid isolation of human plasma anti-alpha-galactoside antibody using sugar-specific binding to guar galactomannan or agarose.

A method of purifying the naturally occurring antibody to alpha-galactoside moiety (anti-alpha-Gal) in human plasma by a single-step affinity chromatography on cross-linked guar galactomannan (CLGG) or agarose (Sepharose 4B) is described. IgG nature of the two preparations, as revealed by agar gel diffusion, as well as their preference for alpha-anomer of galactose, as revealed in inhibition of their agglutination of trypsinized rabbit erythrocytes by sugars, identified them with anti-alpha-Gal. The antibody binding capacity of Sepharose 4B was only a third of that of CLGG. Both gels showed similar dependence on ionic strength for binding. The pH optimum for binding of anti-alpha-Gal to CLGG was 8.0. Significantly anti-alpha-Gal binding to Sepharose was unaffected by CNBr activation and ligand coupling to the gel, thus warning that contaminating plasma could introduce artifacts in agarose-based chromatography of human tissue biomolecules.     

Electroelution of fixed and stained membrane proteins from preparative sodium dodecyl sulfate-polyacrylamide gels into a membrane trap

The membrane trap is a new device for the electroelution of all kinds of charged macromolecules from gels. Instead of dialysis membranes, the membrane trap uses a new membrane. Retention of macromolecules in an electric field by dialysis membranes depends on the presence of sodium dodecyl sulfate (SDS) in the buffer. The new membrane retains all charged macromolecules larger than approximately 5000 Da without adsorbing them, independent of the use of SDS. Here we report the electroelution of five different lipophilic membrane proteins (33 to 193 kDa) of Mycoplasma pneumoniae from preparative SDS-polyacrylamide gels into a 300-microliter recovery volume. After an 8-h elution period, recovery ranged from 80 (193 kDa) to 97% (33 kDa). The "losses" were generally due to proteins still remaining in the gel slice. All of the eluted proteins tested in a dot-blot assay proved to be antigenically active. The advantages of the device described here are easy handling (insertion of membranes, open system), quantitative recovery, and high reproducibility of the elution results.     

A method for preparing proteins and peptides for microsequencing

We present simple methods for the generation and separation of peptides suitable for automated amino acid sequencing using Edman chemistry. We describein-situ CNBr cleavage of proteins electrophoretically separated in polyacrylamide gels. The generated peptides are separated by gel electrophoresis and blotted onto polyvinylidene diflouride membrane. Membranebound peptides are detected by Coomassie Blue staining and directly applied to an automated sequencer.     

Hybridization of DNA to RNA in methylmercuric hydroxide agarose gels

We describe a method for hybridization of cDNA probes to RNA directly in agarose gels which provides a practical alternative to methods involving transfer of the RNA out of the gel. Total cellular RNA is subjected to electrophoresis in agarose gels containing methylmercuric hydroxide as the denaturing agent. After removal of the methylmercuric hydroxide, the gel is dried and 32P-labeled DNA probes are hybridized to the immobilized RNA. This method is more economical in time and expense than methods involving transfer of the RNA out of the gel, while maintaining a level of sensitivity comparable to other procedures.     

Optimization of the method of cyanogen bromide mapping of polypeptides separated by polyacrylamide gel electrophoresis

Two highly efficient methods of CNBr-peptide mapping of polypeptides divided by polyacrylamide gel electrophoresis are described. The first is elaborated on the basis of peptide mapping of collagen proposed by G. Barsh et al. The following three modifications diminish wasting the material essential for the method. 1. CNBr treatment takes place in the absence of CNBr solution outside the gel, excluding the peptides elution from the gel fragments in the process of mapping. 2. After CNBr treatment the solution of CNBr is substituted by the samples buffer before electrophoresis by means of drying and subsequent addition of minimal volumes of the buffer. The latter procedures substitute the gel washing out by the buffer solution. 3. The step of washing the gel fragments by the 70% strong solution of formic acid before CNBr treatment is excluded. The second method of CNBr-peptide mapping is notable for extracting peptides from the gel fragments in the process of CNBr-treatment and permits obtaining of the high quality peptide electrophoregrams.     

Stabilization of Micrococcal Endonuclease by Immobilization on Agarose Gels Highly Activated with CNBr

The attachment of enzymes, through their amino groups, to CNBr activated agarose gels has been tested as an immobilization stabilization system. By using this system, the development of a strategy to immobilize enzymes through multipoint covalent attachment has been studied. We have prepared different staphylococcal nuclease-Agarose derivatives by using Sepharose 2B gels previously activated with CNBr. Activity and stability of the derivatives obtained were very dependent on the degree of activation of the support. The most stable derivatives, prepared with the most activated supports, were 700 fold more stable than the soluble enzyme in irreversible thermal inactivation experiments, at 40d`C. In contrast, a significant loss of catalytic activity (k_cat decreases down to 40%) was associated with the increase in stability. Colorimetric titration of amine groups in the stabilized derivatives suggested that enzyme-support multipoint attachment was the main reason for the observed stabilizing effect.

Index Entries: micrococcal nuclease immobilization enzyme stabilization enzyme-support multipoint attachment     

Iodine stain for detection of peptides after isoelectric focusing

Iodine stain is used for the detection of peptides after isoelectric focusing has been developed. Ultrathin gels (240–360 μm) are cast and, after focusing, dried at 110°C on a filter paper sheet. The paper-pasted gel is then exposed to iodine vapors for a few seconds to a few minutes, depending on the peptide load. White peptide zones are visivle on a brown, uniform background. The reaction is fully reversible and can be used also for small-scale preparative purification of peptides. Better than 80% recoveries of peptide from the gel can be obtained by elution in 80% acetic acid.     

Covalent immobilization of unilamellar liposomes in gel beads for chromatography

For immobilized (proteo)liposome chromatography, unilamellar liposomes were covalently bound within gel beads that had been activated by CNBr, N-hydroxysuccinimide, tresyl, or chloroformate. Liposomes composed of phosphatidylcholine (PC) and 2 mol% of amino-containing lipid (phosphatidylethanolamine-caproylamine) were immobilized in the activated gels at 5-35 micromol lipid/ml gel and yields of 11-70%. The highest immobilized amount was found in chloroformate-activated TSK G6000PW gel, which contains large pore size (>100 nm). Liposomes composed of PC alone could also be attached to the chloroformate-activated gels at 33-42 micromol/ml gel and yields of 58-65%, probably by crosslinking of the phosphate moiety of phospholipid with the active group of the adsorbent. Liposomes prepared by various phospholipids with or without amino-containing lipids can generally be immobilized in the chloroformate-activated gels. The covalently bound liposomes were characterized by their high stability, unilamellarity, permeability of the membranes, and drug-membrane partition properties. A stable membrane phase was constructed for chromatographic experiments to be performed under extreme elution conditions.     

An automated in‐gel digestion/iTRAQ‐labeling workflow for robust quantification of gel‐separated proteins

Simple protein separation by 1DE is a widely used method to reduce sample complexity and to prepare proteins for mass spectrometric identification via in‐gel digestion. While several automated solutions are available for in‐gel digestion particularly of small cylindric gel plugs derived from 2D gels, the processing of larger 1D gel‐derived gel bands with liquid handling work stations is less well established in the field. Here, we introduce a digestion device tailored to this purpose and validate its performance in comparison to manual in‐gel digestion. For relative quantification purposes, we extend the in‐gel digestion procedure by iTRAQ labeling of the tryptic peptides and show that automation of the entire workflow results in robust quantification of proteins from samples of different complexity and dynamic range. We conclude that automation improves accuracy and reproducibility of our iTRAQ workflow as it minimizes the variability in both, digestion and labeling efficiency, the two major causes of irreproducible results in chemical labeling approaches.     

Immobilized Human Plasmins: Preparation and Enzymatic Properties

Plasminogen was immobilized on agarose using either a commercially available substituted gel, or the cyanogen bromide (CNBr) activation procedure as a means of coupling the protein to agarose. Coupling the zymogen to the gel followed by its activation with urokinase yielded an immobilized plasmin. The immobilized enzymes have esterase, amidase and protease activity towards lysine and arginine esters, lysine anilide and casein, respectively. They activate plasminogen by a linear non-autocatalytic process. Both enzyme preparations are stable for extended periods of time in the absence of any stabilizing agents, and are not denatured by high salt concentrations or detergents.     

Automated DNA sequencing: ultrasensitive detection of fluorescent bands during electrophoresis.

A simple system has been designed enabling ultrasensitive on-line detection of fluorescently labelled macromolecules, e.g. nucleic acids, proteins and peptides during electrophoretic separations in gels. An important application is the automated DNA sequence determination without radioactivity. Drying of gels, film exposure and handling are not necessary. A sulphydryl containing M13 sequencing primer has been synthesised and end-labelled in a reaction with fluorescein iodoacetamide. This is then used in the dideoxy reactions. In particular no moving parts or complicated software are required for data collection and analysis. Compared to our first automated device detection sensitivity has been improved by a factor of thirty to about 3 X 10(-18) mol per band. The resolution has increased to about 400 bases in 5 hours, with the possibility to read up to about 500 bases when they are properly labelled. Gels shorter than 20 cm may be used for resolution of about 300 bases. The single gel system may be upgraded for simultaneous running and reading of six or ten sequencing samples.     

A new silver staining apparatus and procedure for matrix-assisted laser desorption/ionization-time of flight analysis of proteins after two-dimensional electrophoresis

We report on a new silver stain especially developed for staining large gels (25 cm x 20 cm) from the Hoefer ISO-DALT system for matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) analysis of proteins. The staining protocol can be summarized as follows: the gels are sensitised in tetrathionate/potassium acetate solution and washed several times in distilled water. After impregnation with silver nitrate, the silver is reduced in the presence of potassium carbonate, thiosulphate and formaldehyde. The staining procedure is stopped with Tris/acetate after which the gels are rinsed and stored in water before spot picking for MALDI-TOF analysis is performed. This protocol has several advantages over existing ones. The gels are stained in a new apparatus that reduces gel handling to a minimum thus also reducing the contamination with keratins to a minimum. The development times in potassium carbonate are very long (up to 40 min) thus improving batch-to-batch reproducibility. Only the surface of the proteins is stained and the silver can be oxidized, thereafter MALDI-TOF can be performed with protein loads as little as 100 micrograms per gel.     

Identification and analysis of the maize P700 chlorophyll a apoproteins PSI-A1 and PSI-A2 by high pressure liquid chromatography analysis and partial sequence determination

We recently described a pair of partially homologous maize chloroplast genes, one of which was shown to code for an apoprotein of the P700 chlorophyll a complex of photosystem I (Fish, L.E., Kück, U., and Bogorad, L. (1985) J. Biol. Chem. 260, 1413-1421). Two chlorophyll-free apoprotein bands from maize chlorophyll-protein complex I (CPI) can be resolved on lithium dodecyl sulfate (LDS)-urea polyacrylamide gels. Proteins in both bands react with antibodies prepared against CPI, but antibodies prepared against two synthetic peptides corresponding to predicted sequences of PSI-A1 react only with the upper band. The presence of products of the two genes, ps1A1 and ps1A2, in CPI was verified by analysis of cyanogen bromide (CNBr) fragments of the lower apoprotein band obtained from LDS-urea polyacrylamide gels by reverse-phase high pressure liquid chromatography. Amino-terminal sequencing of five CNBr fragments indicates that the lower band contains a product of the ps1A2 gene. The possibility of extensive processing was investigated because the apparent molecular masses of the maize CPI proteins are about 58-70 kDa on LDS-polyacrylamide gels rather than the predicted sizes of about 83 kDa. Antibodies against a synthetic peptide corresponding to a predicted sequence in PSI-A1 were used to determine that the amino-terminal end of PSI-A1 is intact beyond about position 52. The amino-terminal CNBr fragment of PSI-A2 was identified by sequencing, indicating that the amino-terminal end of PSI-A2 is not processed. The carboxyl-terminal CNBr fragment of PSI-A2 was also identified by sequencing. These results indicate that the PSI-A1 and PSI-A2 polypeptides are not extensively processed, although some processing at the carboxyl-terminal end has not been ruled out.     

The influence of fibrin(ogen) fragments on the kinetic parameters of the tissue-type plasminogen-activator-mediated activation of different forms of plasminogen

In the present work we have determined Km,app and kcat,app values for tissue-type plasminogen-activator-catalyzed activation of Glu-plasminogen, Lys-plasminogen and mini-plasminogen in the absence and in the presence of fibrinogen-derived fragments. These were CNBr fragment 2, the A alpha chain remnant of CNBr fragment 2 (A alpha 148-207) and plasmin-generated fragment D-EGTA. The time course of plasmin formation from the various types of plasminogen (plg) was measured spectrophotometrically in a coupled assay system where D-valyl-L-leucyl-L-lysine p-nitroanilide served as a plasmin substrate. The kinetic constants are summarized as follows. (Values in parentheses are concentrations at which the minimum Km,app and maximum kcat,app value is reached.) (Table: see text). In conclusion our results show that CNBr fragment 2, A alpha 148-207 and to some extent D-EGTA mimic the accelerating effect of fibrin. The first two of these fragments did not accelerate activation of mini-plasminogen, lacking the kringle structures I-IV. This suggests that the stimulating effects of these two fragments were dependent on the presence of kringles I-IV of the plasminogen molecule.     

Low-cost two-dimensional gel densitometry

A major obstacle to full utilization of the powerful technique of two-dimensional (2-D) gel electrophoresis is the expense and complexity of quantifying the results. Using an analog-to-digital converter already present in the widely available Commodore 64 or Commodore 128 microcomputer, we have developed a 2-D gel densitometer (GELSCAN) which adds only $20.00 to the cost of the Commodore system (currently around $700.00). The system is designed to work with autoradiograms of 2-D gels. Spots of interest are identified visually and then positioned manually over a light source. A pinhole photoelectric sensor mounted in a hand-held, Plexiglas holder, or "mouse," is briefly rubbed over each spot. Maximum density of the spot is determined and its value is converted to counts per minute via an internal calibration curve which corrects for the nonlinear response of film to radiation. Local spot backgrounds can be subtracted and values can be normalized between gels to adjust for variation in amount of radioactivity applied or in exposure time. Reproducibility is excellent and the technique has some practical as well as theoretical advantages over other more complicated approaches to 2-D gel densitometry. In addition, the GELSCAN system can also be used for scanning individual bands in 1-D gels, quantitation of "dot-blot" autoradiograms and other tasks involving transmission densitometry.     

Development and applications of in-gel CNBr/tryptic digestion combined with mass spectrometry for the analysis of membrane proteins

Hydrophobic membrane proteins often have complex functions and are thus of great interest. However, their analysis presents a challenge because they are not readily soluble in polar solvents and often undergo aggregation. We present a sequential CNBr and trypsin in-gel digestion method combined with mass spectrometry for membrane protein analysis. CNBr selectively cleaves methionine residues. But due to the low number of methionines in proteins, CNBr cleavage produces a small number of large peptide fragments with MWs typically >2000, which are difficult to extract from gel pieces. To produce a larger number of smaller peptides than that obtained by using CNBr alone, we demonstrate that trypsin can be used to further digest the sample in gel. The use of n-octyl glucoside (n-OG) to enhance the digestion efficiency and peptide recovery was also studied. We demonstrate that the sensitivity of this membrane protein identification method is in the tens of picomole regime, which is compatible to the Coomassie staining gel-spot visualization method, and is more sensitive than other techniques reported in the literature. This CNBr/trypsin in-gel digestion method is also found to be very reproducible and has been successfully applied for the analysis of complex protein mixtures extracted from biological samples. The results are presented from a study of the analysis of bacteriorhodopsin, nitrate reductase 1 gamma chain, and a complex protein mixture extracted from the endoplasmic recticulum membrane of mouse liver.     

Capillary electrophoresis of peptides and proteins with plug of Pluronic gel

Electromigration capillary methods are promising techniques in proteomics and they are still under research. We used a partial filling approach, i.e. a combination of gel and non-gel separation mechanisms in a single dimension. We tried using an interesting gel, Pluronic F 127, which can be considered as a surfactant capable of self-association both with isotropic and anisotropic gels. The Pluronic was inserted inside the capillary as a plug at the start of the capillary, and it provided separation at the first time. Separation by this gel was achieved according to molecular weight and/or hydrophobicity. The applicability of this method was demonstrated in the separation of real samples-peptides arising from collagen after CNBr or collagenase cleavage and albumin after trypsin cleavage (peptide mapping). Some peptides and proteins were selectively retained by the Pluronic gel. These interactions with the gel did not depended on their molecular weight alone, but they probably depend on a combination of both principles. It was confirmed that capillary electrophoresis with Pluronic plug can give us another new separation option, complementary to free solution capillary electrophoresis. The CE method presented here, consisting of a partial filling approach with combine gel and non-gel separation mechanisms seemed to be a promising method for the separation of complex mixtures of peptides.     

A non-radioactive automated method for DNA sequence determination

A method and instrument for automated DNA sequencing without radioactivity have been developed. In spite of the success with radioactive labels there are drawbacks attached to the technique, such as hazards in the handling, storage and disposal of radioactive materials, and the considerable cost of the radiolabelled nucleoside triphosphates. In addition, there is deterioration of sample quality with time. A sulphydryl containing M13 sequencing primer has been synthesised and subsequently conjugated with tetramethylrhodamine iodoacetamide. The fluorescent primer is used to generate a nested set of fluorescent DNA fragments. The fluorescent bands are excited by a laser and detected in the gel (detection limit about 0.1 fmol per band) during electrophoresis, and sequence data from the four tracks are transferred directly into a computer. Standard gels, 200 mm wide with 20 sample slots have also been used. The device contains no moving parts. At present 250-300 bases can be read in 6 h. The system is capable of single base resolution at a fragment length of at least 400 bases.