Silver staining of high molecular weight proteins on large-pore polyacrylamide gels

A large-pore gel for electrophoresis in the presence of sodium dodecyl sulfate, composed of 2.55% polyacrylamide crosslinked with 2.75% methylenebisacrylamide, is described. This gel has a resolving power for very high molecular weight proteins and can be stained with silver. The gel is suitable for fractionation of factor VIII/von Willebrand factor directly from plasma samples. Visualization by silver staining revealed a series of covalently bound multimers with molecular weights of up to 8 X 10(6). The procedure described should be useful also for studies on other very high molecular weight proteins and nucleic acids.     

Method for rapid removal of sodium dodecyl sulfate from polyacrylamide gels

A method is described for the isolation of hepatic microsomes by polyethylene glycol 6000 fractionation of the postmitochondrial fraction of liver homogenate. The procedure is simple and rapid requiring two centrifugation steps at 8000g for 10 min. The preparation has peptide patterns and levels of drug metabolic and other enzymatic activity similar to those of the microsomal fraction isolated by high-speed centrifugation and is referred to as polyethylene glycol 6000 microsomes. It is clarified with detergents and can serve as the starting material for the purification of microsomal proteins.     

Visualization of protein-SDS complexes in polyacrylamide gels by chilling

A method is described which gives direct visualization of protein bands in sodium dodecyl sulfate electrophoresis gels. The procedure consists of chilling the gels to 0–4°C and observing the white opaque bands which correspond to the stained protein bands. Ovalbumin can be detected by this method at a minimum concentration of 0.2 μg per mm² of gel surface area.     

Simultaneous staining of proteins during polyacrylamide gel electrophoresis in acidic gels by countermigration of Coomassie brilliant blue R-250

A method for the simultaneous staining of proteins during polyacrylamide gel electrophoresis with Coomassie brilliant blue R-250 at pH 2.5 is described. Calf thymus whole histone and cytochrome c were stained by this method and the results obtained were similar to that obtained by staining after electrophoresis.     

The effect of removal or replacement with proflavine of the Y base in the anticodon loop of yeast tRNAPhe on binding into the acceptor or donor sites of reticulocyte ribosomes

Phe-tRNA from yeast has a highly modified nucleoside, called Y, adjacent to the 3′ side of its anticodon, that can be removed or replaced with proflavine. In a protein-synthesizing system from rabbit reticulocytes, poly (U)-directed binding and polyphenylalanine synthesis are low with these modified Phe-tRNA species relative to the corresponding values with unmodified Phe-tRNA. However, polymerization can be increased with relatively large amounts of elongation factor I. The modified Phe-tRNA species bound to the ribosomes with poly(U) either in the presence or absence of elongation factor I and GTP is immediately reactive in the peptidyl transferase reaction measured by the formation of diphenylalanine or phenylalanyl-puromycin. It appears to have been bound directly into the donor ribosomal site by either the nonenzymatic mechanism involving Mg²⁺ or by the enzymatic mechanism involving EF-I and GTP.     

Cu2+ probe of metal-ion binding sites in melanin using electron paramagnetic resonance spectroscopy. I. Synthetic melanins

The isotope ⁶³Cu²⁺ has been used to probe the metal-ion binding sites of synthetic (autoxidized) catechol and 3,4-dihydroxyphenylalanine melanins using electron paramagnetic resonance spectroscopy. Samples were in aqueous media over a wide range of pH values. Assignments of the structures of the melanin-copper complexes are based in part on model studies of the complexes formed with melanin precursors, catechol and 3,4-dihydroxyphenylalanine, and with phenanthroline. Nearly all complexes involve just one or two ligands from melanin. In catechol melanin below pH 5.0, complexes with carboxyl groups are formed; above 6.0, Cu²⁺ forms complexes with phenolic hydroxyl groups. These same complexes were found in 3,4-dihydroxyphenylalanine melanin and binding of Cu²⁺ at amino acid type sites also was detected. After partial reduction of copper ions bound to 3,4-dihydroxyphenylalanine melanin, a weak signal of copper with four melanin ligands (oxygen and nitrogen in various combinations) was observed.     

Purification of reticulocyte ribosomes using polyuridylic acid: sepharose chromatography.

Deoxycholate-KCl washed reticulocyte ribosomes are purified by affinity chromatography using Sepharose columns to which polyuridylic acid has been covalently bound. Upon passage through the column under nonenzymic conditions (high Mg²⁺:K⁺ ratio) approximately 10% of the ribosomes are retained. These ribosomes are then eluted with a buffer containing a high K⁺:Mg²⁺ ratio and are assayed for activity in various steps of the elongation process of protein synthesis. Approximately a 3- to 4-fold increase in the various activities compared with control ribosomes is obtained.     

Changes in properties of the inner mitochondrial membrane during mitochondrial biogenesis in aging sweet potato tissue slices in relation to the development of cyanide-insensitive respiration.

Protein and phospholipid of the inner mitochondrial membrane in sweet potato root tissue increased after a lag phase during aging of the sliced tissue. The protein, but not the phospholipid, from aged slices was more insoluble in a solution containing sodium deoxycholate and sodium cholate than that from fresh tissue. There were differences in polypeptide composition between deoxycholate-cholate-soluble and -insoluble fractions as determined by polyacrylamide-gel electorophoresis of membrane fragments in the presence of sodium dodecyl sulfate. However, no difference was observed between mitochondrial membranes from fresh and aged slices. When disrupted mitochondrial membrane was subjected to equilibrium density centrifugation, two bands were obtained from aged slices but only one band from fresh tissue. The lighter band from aged slices was indentical to the single band from fresh tissue. The denser band was very poor in phospholipid, and the protein was very insoluble in deoxycholate-cholate solution. The denser membrane fragments possessed a cyanide-insensitive respiratory chain whereas the lighter did not. It is proposed that the development of the cyanide-insensitive respiration in aging slices is related to the formation of phospholipid-deficient mitochondrial membrane.     

The production of oxyluciferin during the firefly luciferase light reaction.

The luciferase-product complex (E · P) was isolated from the reaction mixture after light emission had occurred. The spectral properties of the product in the E · P complex are similar to those of oxyluciferin, with a broad absorption at 385 nm. The enzyme from the complex regains full activity upon the addition of substrates. The product is not covalently bound to the enzyme and readily dissociates in the presence of 6 m urea. The isolated E · P complex was found to have 1 mol of oxyluciferin per 100,000 daltons of luciferase. No AMP could be detected in the E·P complex unless inorganic pyrophosphatase was present during the reaction. In that case 1 mol of AMP per 100,000 daltons was found.Stopped flow studies showed that an increase in 385 nm absorption occurred concomitant with light emission. Measurement of the initial rate of product formation and the rate of photon emission showed they were identical, suggesting that oxyluciferin is indeed the light-emitting product. In the initial burst of the reaction two oxyluciferin moles per 100,000 daltons of luciferase are formed. A plot of the log of the initial rate of product formation was biphasic, indicating that the first mole of product is formed at a faster rate than the second. These results are consistent with previous experiments. However, they do not resolve the question of the molecular weight of the catalytically active species.     

Cu2+ probe of metal-ion binding sites in melanin using electron paramagentic resonance spectroscopy. II. Natural melanin

The isotope ⁶³Cu²⁺ has been used to probe the metal-ion binding sites of natural melanin from the choroid of bovine eyes using electron paramagnetic spectroscopy. Samples were in aqueous media over a wide range of pH values. At pH < 7, binding is to monodentate carboxyl complexes and to bidentate nitrogen-carboxyl complexes just as in synthetic melanin. At pH > 7 binding is to phenolic hydroxyl groups, but the number of such sites is much less than in synthetic melanin and there are indications of a superimposed spectrum of another site. At high pH, a signal unlike any found in synthetic melanin was observed with either three or four nitrogen ligands. A number of experiments indicate that natural melanin is 50% protein by weight. Metal-ion binding sites are the same with and without protein although with some differences in relative populations.     

Ultrasensitive silver-stain method for the detection of proteins in polyacrylamide gels and immunoprecipitates on agarose gels

The highly sensitive silver-stain procedure for the detection of proteins in polyacrylamide gels has been revised and simplified using a single-step silver ion reduction after suitable treatment of proteins with bifunctional aldehyde. Washing steps were eliminated and excellent reproducibility of results was achieved. Sensitivity obtained using this procedure was at least equal to that obtained with the original one. Use of the present silver-staining methods has been extended to the quantitative analysis of immunoprecipitates on agarose gels, with a good increase of sensitivity and excellent increase of resolution when compared to the Coomassie blue stain.     

Cell mass concentration variance resulting from fluctuations in the incoming nutrient concentration to a chemostat

The cellular response in terms of steady-state variance of cell mass concentration to fluctuations in incoming nutrient concentration to a chemostat has been examined. A white noise process is assumed to describe incoming nutrient concentration fluctuations and the variance of cell mass concentration has been found to depend on cell yield (a lumped measure of nutrient concentration fluctuation magnitude and lifetime) and two system time constants.     

Experimentally improved reliability of ultrasensitive silver staining of protein in polyacrylamide gels

Variations of the ultrasensitive silver staining method of B. R. Oakley, D. R. Kirsch, and N. R. Morris (Anal. Biochem.105, 361–363 (1980)) have been tested. It was established that the reliability of the method was greatly improved if (i) free silver was carefully washed out before reduction with formaldehyde; (ii) the extent of development was controlled by using methylamine to inactivate the formaldehyde; and (iii) the optimum quantity of ammonia, which was found to be 4 mol/mol of silver was used (this quantity was defined as that which titrates a particular amount of 1 n HCl). The time of preparation of the formaldehyde reducer was found not to be highly critical. In our hands the method can detect down to 0.1 ng of protein/5-mm slot.     

Detection of subnanogram amounts of RNA in polyacrylamide gels in the presence and absence of protein by staining with silver

The new ultrasensitive photochemically derived silver stain described for polypeptides in polyacrylamide gels (Merril et al., Science211, 1437–1438 (1981)) also stains nucleic acid in polyacrylamide gels. Reovirus genome double-stranded (ds) RNA segments were clearly detected in gels at about 0.03 ng/mm² with the silver staining technique when either purified virions or isolated, purified dsRNA was analyzed. The silver stain was about 10 to 30 times more sensitive than ethidium bromide for detecting reovirus dsRNA.     

Direct visualization of collagens and procollagens in polyacrylamide gels.

This report describes a procedure that results in the rapid visual identification of collagens and procollagens in polyacrylamide gels. The technique results in a pink stain for collagenous proteins and a blue stain for all other proteins. The color difference has been evaluated spectrophotometrically. The absorbance maxima for collagen-Coomassie blue R250 complexes in gels is 520–535 nm, and the maxima for all other protein-Coomassie blue R250 complexes that we tested is 550–560 nm. This technique will facilitate the identification of collagenous proteins in complex mixtures of proteins derived from cell membranes, whole cell extracts, conditioned media, and extracellular matrices. We use the technique to detect procollagens in human diploid fibroblast conditioned media. The technique is simple, relatively rapid, has utility for proteins extracted by a variety of methods, and is applicable to all polyacrylamide gel systems in general use.     

Staining for protease activity on polyacrylamide gels

A high-performance liquid chromatographic procedure has been developed for the detailed analysis of amino acids and related compounds in 10-μl samples of perilymph from the guinea pig cochlea (inner ear). The procedure employs an Aminco amino acid analyzer and combines the use of a single chromatographic column, lithium citrate buffers for elution, a change of column temperature, and fluorometric detection of o-phthaldialdehyde/2-mercaptoethanol adducts of primary amines. Sensitivity is about 0.2 pmol referenced to leucine. Fifty-four primary amine components are detectable in perilymph collected in relative silence. Twentynine compounds have been identified, and six are putative amino acid neurotransmitters. The present method provides new information about the chemical composition of perilymph and is suitable for the analysis of physiological fluids available only in volumes of several microliters.     

RNA synthesis in permeable HeLa cells

The equilibria and kinetics are reported for the partial reactions of the catalytic cycle of the Ca²⁺ ionophore X537A in phospholipid vesicles. The analysis is based on the study of the behavior of the ionophore's intrinsic fluorescence in fluorescence lifetime, stopped-flow, temperature, and conventional steady-state fluorescence experiments. Binding to dimyristoyl phosphatidylcholine vesicles gives rise to an enhancement of the fluorescence. At the pH of study (7.4) this involves the singly negatively charged form (X^?). Complexation of the membrane-bound form (X_m^?) by monovalent (M⁺) or divalent (M²⁺) cations to give 1:1 (M-X)_m and (M-X)_m⁺ complexes, respectively, gives rise to a further fluorescence enhancement. No evidence could be found for stoichiometries other than 1:1 in the equilibrium experiments. The fluorescence of X537A in the presence of phosphatidic acid vesicles or phosphatidylcholine/ phosphatidylethanolamine or phosphatidylcholine/cholesterol mixtures is much smaller than for pure phosphatidylcholine. Fluorescence lifetime experiments show that this is due to a reduction in binding rather than a reduction of the quantum yield of the bound species. Fluorescence decay profiles from the above-mentioned membranes showed two exponential components indicating that there were two fluorescent species. The shorter-lived species had a lifetime of 3–5 ns and accounted for 80–90% of the membrane-bound ionophore. The longerlived species (9–13 ns) was estimated to account for the remaining 10–20%. This species enjoys a higher degree of hydrophobic shielding than the shorter-lived species. Possible interpretations in terms of the ionophore orientation in the membrane are discussed. Temperature-jump experiments show that the binding rate of the ionophore is fast. The binding and dissociation rate constants were ca. 2 × 10⁷m (PC)^?1 s^?1 and 2 × 10³ s^?1, respectively. Stopped-flow experiments gave evidence for a slower “insertion” process with a ca. 10-ms half-time. Analysis shows that this process is capable of transport of (K-X) across the membrane with a rate constant ≤ 69^?1. In the presence of divalent cations a slower process involving transport of M²⁺-ionophore complexes across the membrane can be observed. The dependence of the rate on the total ionophore concentration indicates that the transported species is a neutral (M-X₂) complex. The lower limit for the rate constant for transport of the (Ca-X₂) complex is 35 s^?1. The divalent cation specificity of the overall reaction was shown to be Mg²⁺ ? Ca² < Sr²⁺ < Ba²⁺. The rates of the overall transport at low ionophore concentration are limited by the equilibrium constant for formation of the (M-X₂)_m complex from the (M-X)_m⁺ complex.     

On the mechanism of production of superoxide radical by reaction mixtures containing NADH, phenazine methosulfate, and nitroblue tetrazolium

In aerobic reaction mixtures containing NADH, phenazine methosulfate, and nitroblue tetrazolium, O2- production is mediated by the tetrazolium, not the phenazine. Thus, superoxide dismutase inhibited reduction of the tetrazolium, but when ferricytochrome c was substituted for the tetrazolium its reduction was not affected by this enzyme. Furthermore, NADH plus the phenazine did not accelerate the oxidation of epinephrine to adrenochrome unless the tetrazolium was present, and under those circumstances superoxide dismutase did inhibit adrenochrome formation. When the tetrazolium and ferricytochrome c were present simultaneously, addition of superoxide dismutase was seen to accelerate the reduction of the cytochrome. This is explainable by the reduction of O2- by the reduced phenazine, which thus competes with cytochrome c for the available O2-. When the O2- was eliminated by superoxide dismutase, more of the reduced phenazine was available for the direct reduction of cytochrome c.     

A modified method for amino acid analysis with ninhydrin of Coomassie-stained proteins from polyacrylamide gels

Triton X-100 (from three different suppliers) and Brij 35, substituted ethers of polyoxyethylene alcohols, were found to contain variable amounts of powerful oxidizing impurities representing a range of 0.04-0.22% H₂O₂ equivalents. These detergents contain also a considerable quantity of carbonyl compounds (0.5-2%) originating from carboxylic acids and ketones or aldehydes. Tween 20, also a polyoxyethylene detergent, and sodium dodecyl sulfate were free from oxidizing contamination. Aqueous solutions of Triton X-100 and Brij 35 (1–4%) reacted readily with SH groups of protein and nonprotein molecules as well as with Fe²⁺ ion. Both detergents were purified from the oxidizing impurities by treating aqueous solution of detergent with either NaHSO₃ or SnCl₂ followed by an extraction procedure. The present findings may clarify as well as complicate the interpretation of previous studies where these detergents were used for biological purposes, especially in enzyme and protein purifications, or when present in assay procedures that are based on the formation or consumption of reducing reagents.     

Detection of aldolase activity on polyacrylamide gels: application to 2-keto-4-hydroxyglutarate aldolase.

A method is described for the detection of 2-keto-4-hydroxyglutarate aldolase activity after electrophoresis of the enzyme on polyacrylamide gels. When gels are incubated with substrate (2-keto-4-hydroxyglutarate), activity is seen as a yellow-colored band due to interaction of the product )glyoxylate) with ortho-aminobenzaldehyde and glycine. Positive results have been obtained using either crude cell-free preparations or homogeneous enzyme from Escherichia coli as well as with highly purified samples of aldolase from bovine liver or kidney extracts. The method is potentially applicable to other aldolases that liberate an aliphatic aldehyde as a product; modifications and limitations of the procedure for detecting fructose 1,6-diphosphate aldolase, 2-keto-3-deoxy-6-phosphogluconate aldolase, and 2-deoxyribose-5-phosphate aldolase activities have been explored.