Interference study should be performed for every protein measurement method used

It is particularly important, when analyzing biological material, for the measurement procedure to be specific to the analyte and not to suffer interference by the matrix effect. Tissue fraction studies also require rapid and accurate methods to estimate the concentration of protein in solutions as well as many measurement methods used in medical laboratories. The design of this study is based on a comparison of the Lowry and the bicinchoninic acid (BCA) methods for the measurement of the total protein concentrations of rat liver subcellular fractions. In our experiment, subcellular fractions enriched in peroxisomes (POs) obtained by differential centrifugation were then further separated by means of density gradient centrifugation. We performed the protein measurement assays on all fractions obtained during the purification steps. The protein contents of the fractions obtained were determined by the two methods. The method comparison statistics were performed by linear Deming regression analysis and Altman and Bland bias plot. The regression equation was unacceptable, indicating that the last three fractions separated by means of Nycodenz discontinuous density gradient centrifugation gave remarkably divergent results. For the Lowry method, the Nycodenz effect could not be eliminated with the use of interference blank. In addition to Nycodenz, the potentially interfering compound used in the isolation procedure as isolation medium was 3-(morpholino)propane sulfonic acid (MOPS). In decreased concentrations of MOPS (10 mM), interference blank should be used for correct measurement with Lowry, but in practical use 10 mM does not provide buffering potency. In the BCA method, interference blank correction seemed to eliminate the measurement error in all concentrations of Nycodenz. There was no MOPS effect on the BCA measurement assay. Referring to deviations as sample-inherent matrix effects, we concluded that not only one, but more measurement methods should be used in order to make a correct protein measurement.     

New application of a subcellular fractionation method to kidney and testis for the determination of conjugated linoleic acid in selected cell organelles of healthy and cancerous human tissues

To clarify the mechanism of the anticarcinogenic effect of conjugated linoleic acid (CLA), its intracellular distribution needs to be determined. Subcellular fractionation using centrifugation techniques is a method that is frequently used for isolation of cell organelles from different tissues. But as the size and density of the organelles differ, the method needs to be optimised for every type of tissue. The novelty of this study is the application of a subcellular fractionation method to human healthy and cancerous renal and testicular tissue. Separation of total tissue homogenate into nuclei, cytosol, and a mixture of mitochondria and plasma membranes was achieved by differential centrifugation. As mitochondria and plasma membranes seemed to be too similar in size and weight to be separated by differential centrifugation, discontinuous density-gradient centrifugation was carried out successfully. The purity of the subcellular fractions was checked by measuring the activity of marker enzymes. All fractions were highly enriched in their corresponding marker enzyme. However, the nuclear fractions of kidney and renal cell carcinoma were slightly contaminated with mitochondria and plasma membrane fractions of all tissues with lysosomes. The fraction designated the cytosolic fraction contained not only cytosol, but also microsomes and lysosomes. The CLA contents of the subcellular fractions were in the range 0.13–0.37% of total fatty acids and were lowest in the plasma membrane fractions of all types of tissue studied. C16:0, C18:0, C18:1 c9, C18:2 n-6, and C20:4 n-6 were found to be the major fatty acids in all the subcellular fractions studied. However, marked variations in fatty acid content between subcellular fractions and between types of tissue were detectable. Because of these differences between tissues, no general statement on characteristic fatty acid profiles of single subcellular fractions is possible.     

One-step separation of endocytic organelles, Golgi/trans-Golgi network and plasma membrane by density gradient electrophoresis

Many different methods for the fractionation of subcellular organelles have been reported. However, no protocol for rapid separation of plasma membrane, Golgi/trans-Golgi network (TGN) and endosomes is available to date. Such a method is a prerequisite for a quantitative biochemical analysis of vesicular transport from the Golgi/TGN compartment to plasma membrane and endosomes. Here a density gradient electrophoresis protocol is described that allows the fractionation of these organelles in one step. This protocol requires only low-cost instrumentation available in most biochemical laboratories.     

Separation of mitochondria by flow field-flow fractionation for proteomic analysis

Flow field-flow fractionation (FlFFF) has been utilized for size-based separation of rat liver mitochondria. Collected fractions of mitochondria of various sizes were examined by confocal microscopy, and mitochondria of each fraction were lysed and analyzed by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for the comparison of protein patterns in differently sized mitochondria by densitometric measurements, and for protein characterization of some gel spots with nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS). FlFFF fractions of the mitochondria were also tryptically digested for shotgun proteomic characterization of mitochondrial proteins/peptides by nLC-ESI-MS-MS. Peak area (integrated ion counts) of some peptides extracted from LC-MS chromatograms were examined at different fractions for the quantitative comparison. Among 130 proteins, 105 unique proteins were found to be mitochodrial from the off-line combination of FlFFF and nLC-ESI-MS-MS analysis. It also showed that 23 proteins were found in all fractions but some proteins were found exclusively in certain fractions. Among 25 proteins listed from other subcellular species, seven proteins were known to exist in mitochondria as well as in other subcellular locations, which may support the possible translocation or multiple localizations of proteins among organelles. This study demonstrated effective use of FlFFF for the isolation and/or enrichment of intact mitochondria isolated from cells, as well as its potential use for the fractionation of other subcellular components in the framework of subcellular functional proteomics.     

Analytical fractionation of microsomal cytochrome P-450 isoenzymes from rat liver by high-performance ion-exchange chromatography

Ion-exchange Fast Protein Liquid Chromatography (FPLC) on Mono Q and Mono S was optimized for the analytical separation of microsomal cytochrome P-450 species from rat liver. The effects of detergent, pH, gradient profile and column load on resolution are demonstrated. Successive application of anion- and cation-exchange chromatography leads to eleven separated P-450 fractions. The altered microsomal P450 pattern after treatment of rats with various inducers is reflected by distinct elution profiles. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis and enzymatic analysis imply that several FPLC fractions contain more than one P-450 species. Preliminary results are presented showing the suitability of immobilized metal affinity chromatography (MAC) for general P-450 fractionation and thus for the further resolution of Mono Q and Mono S fractions. Scale-up for preparative P-450 fractionation is easily done by adapting the optimized analytical FPLC procedures to Q- and S-Sepharose Fast Flow.     

Isolation of peroxisomal subpopulations from mouse liver by immune free-flow electrophoresis

Peroxisomes (PO) are a heterogeneous population of cell organelles which in mammals are most abundant in liver and kidney. Commonly, differential and density gradient centrifugation are used for their isolation which, however, give only rise to the so-called "heavy" PO with a buoyant density of 1.22-1.24 g/cm(3). Subpopulations other than the heavy PO which are also present in both of these tissues have escaped adequate purification because of their sedimentation characteristics which are close to those of other major organelles, in particular microsomes. Since the purification of these subpopulations has become an essential task in view of the putative importance of peroxisomal subpopulations in the biogenesis of this organelle, alternatives to density gradient centrifugation are required. Recently, we have introduced such a novel approach, named immune free flow electrophoresis (IFFE). IFFE combines the advantages of eletrophoretic separation with the high selectivity of an immune reaction. It makes use of the fact that the electrophoretic mobility of a subcellular particle, complexed with an antibody directed against the cytoplasmic domain of one of its integral membrane proteins is greatly diminished, provided the pH of the electrophoresis buffer is adjusted to pH approximately 8.0, the pI of immunoglobulin G (IgG) molecules. pH-values other than 8.0 proved to be less efficient, probably because IgG molecules only focus at pH 8.0 but are scattered at any other. Applying IFFE to heavy and light mitochondrial as well as microsomal fractions of rat liver not only regular PO (rho = 1.22-1.24 g/cm(3)) but also other subpopulations could be isolated. To substantiate the validity of this approach, we now have subfractionated mouse liver homogenates accordingly. Of the PO subpopulations collected, mainly that obtained from the heavy mitochondrial fraction differed in its composition of matrix and membrane proteins as revealed by immunoblotting. This is in line with the data reported on rat liver thus confirming the potential of IFFE in the isolation of distinct subpopulations of hepatic PO.     

Reversed-phase high-performance liquid chromatography of some ultra-heterogeneous and covalently-modified proteins from human hair

A new procedure for the fractionation of the heterogeneous cystine-rich proteins from human hair, utilizing reversed-phase high-performance liquid chromatography, is described. Of these proteins 27 fractions have been collected and analyzed for amino acid composition. There seems to be little correlation between the elution order and the hydrophobicity of the fraction constituents except for the late-eluting fractions. Based on the elution profiles and amino acid contents, these fractions appear to fall into four families. The effects of alkyl chain length, flow-rate and gradient slope, as well as various additives to the organic modifier on the separation have also been investigated. A low flow-rate (0.4 ml/min) and a shallow gradient were essential for the separation of these proteins as was the use of short alkyl chain (C4) or medium alkyl chain (C8) columns. However, with the C4 column reproducibility and recovery were excellent.     

Use of magnetic beads with immobilized monoclonal antibodies for isolation of highly pure plasma membranes

In plasma membrane proteome research, contamination of the isolated plasma membrane fraction with proteins from other organelles is still a problem. Even if highly specific isolation methods are used, such as density gradient centrifugation combined with selective extraction, contaminating proteins cannot be completely removed. To solve this problem, a protocol for the isolation of highly pure plasma membrane fractions from rat liver and two different hepatocellular carcinoma cell lines was developed. Magnetic beads with immobilized mAb's against highly expressed membrane proteins were used for specific binding of membrane vesicles and their separation from other organelles. Isolated plasma membranes were further selectively solubilized with different reagents and analyzed by use of different methods, such as Western blotting, 1- and 2-DE, and MS. Purification and further selective solubilization was validated by use of mAb's against the marker integral plasma membrane protein carcinoembryonic antigen cell adhesion molecule 1, and identification of isolated proteins by MS. The method presented here minimizes contamination with other organelles and enables further identification of membrane proteins.     

Fast electrophoretic analysis of individual mitochondria using microchip capillary electrophoresis with laser induced fluorescence detection

The analysis of mitochondria by capillary electrophoresis usually takes longer than 20 min per replicate which may compromise the quality of the mitochondria due to degradation. In addition, low sample consumption may be beneficial in the analysis of rare or difficult samples. In this report, we demonstrate the ability to analyze individual mitochondrial events in picoliter-volume samples (approximately 80 pL) taken from a bovine liver preparation using microchip capillary electrophoresis with laser-induced fluorescence detection (micro-chip CE-LIF). Using a commercial "double-T" glass microchip, the sample was electrokinetically loaded in the "double-T" intersection and then subjected to electrophoretic separation along the main separation channel. In order to decrease interactions of mitochondria with channel walls during the analysis, poly(vinyl alcohol) was used as a dynamic coating. This procedure eliminates the need for complicated covalent surface modifications within the channels that were previously used in capillary electrophoresis methods. For analysis, mitochondria, isolated from bovine liver tissue, were selectively labelled using 10-nonyl acridine orange (NAO). The results consist of electropherograms where each mitochondrial event is a narrow spike (240 +/- 44 ms). While the spike intensity is representative of its NAO content, its migration time is used to calculate and describe its electrophoretic mobility, which is a property still largely unexplored for intracellular organelles. The five-fold decrease in separation time (4 min for microchip versus 20 min for capillary electrophoresis) makes microchip electrophoretic separations of organelles a faster, sensitive, low-sample volume alternative for the characterization of individual organelle properties and for investigations of subcellular heterogeneity.     

Cardiac sarcoplasmic reticulum and sarcolemmal proteins separated by two-dimensional electrophoresis: surfactant effects on membrane solubilization

We evaluated the use of the alkyaryl amidosulfobetaine zwitterionic detergent, designated as C8psi, to facilitate the solubilization of cardiac subcellular, membrane-associated proteins. Hearts from 7-week-old male Sprague-Dawley rats were isolated, and the left ventricles dissected and subsequently homogenized. The sarcolemma (SL) and the sarcoplasmic reticulum (SR) were isolated from different homogenate preparations originating from rat hearts by ultracentrifugation methods. The isolated membrane preparations were solubilized and the proteins precipitated. After resuspension, protein separation was achieved in first-dimensional IEF using an immobilized (pH 4-7) gradient and in the second dimension using 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Gels were then stained, images analyzed, and protein spots excised for subsequent identification. Protein identification from both SR and SL samples did not identify any of the known major membrane-associated proteins. Solubilization of whole tissue lysates with C8psi resulted in no increase in the total number of proteins detected relative to samples solubilized in the presence of 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulforate (CHAPS). The data suggest the utility of newer surfactants such as C8psi to improve both the resolution of (2-D) protein profiles and increase the number of proteins extracted from subcellular organelle fractions.     

Preparation of subcellular fractions from granulation tissue by density gradient centrifugation

The 7000 g pellet of homogenized mature sponge-induced granulation tissue was fractionated by centrifugation in a stepwise sucrose gradient in order to study the synthesis and secretion of collagen and other components of this tissue on the subcellular level. As indicated by chemical and enzymatic assays, by electron microscopy and by incorporation experiments, the collagen-synthethesizing rough endoplasmic reticulum fraction was isolated free from the secretory vesicles (smooth endoplasmic membranes and Golgi elements) and fibrous extracellular matrix. Collagen differed from other proteins in the distribution among the subcellular fractions. In pulse-chase experiment the translocation of 14C-labelled collagen was demonstrated from the rough endoplasmic reticulum through the secretory vesicles to extracellular fibrillar collagen. This fractionation method will be used to study the modulation of collagen synthesis and secretion in the reparative tissue.     

Activation analysis study on subcellular distribution of trace elements in human brain tumor

The concentrations of up to 11 elements in subcellular fractions of human brain (normal and malignant tumor) have been determined by a combination of gradient centrifugation and INAA methods. Samples of human brain were homogenized in a glass homogenizer tube, the homogenate was separated into nuclei, mitochondrial, myelin, synaptosome fractions, and these fractions were then analyzed using the INAA method. The discussions of elemental subcellular distributions in human brain malignant tumor are presented in this paper.     

Subcellular distribution of rat pituitary homogenates by poly(ethylene glycol)-dextran countercurrent partitioning

Rat pituitary homogenates were subjected to two phase countercurrent partition in a poly(ethylene glycol)-dextran mixture using a simple apparatus with enhanced gravity to facilitate the phase separations. Assay of the fractions for organelle marker enzymes and prolactin after 17 transfers showed similar distributions for endoplasmic reticulum, lysosomes, prolactin granules and plasma membrane at the lowest dextran concentrations. Increasing the dextran concentrations had a differential effect on the various organelles. Excellent resolution of endoplasmic reticulum from the other organelles was obtained and marked organelle heterogeneity was demonstrated. Two-phase countercurrent partition thus offers an alternative approach to the subcellular fractionation of pituitary homogenates and should prove useful in separating endoplasmic reticulum from plasma membrane and other cell components.     

Toroidal Coil Countercurrent Chromatography: A Fast Simple Alternative to Countercurrent Distribution Using Aqueous Two Phase Partition: Principles,Theory, and Apparatus

Abstract

The principles, theoretical basis and equipment for continuous two phase toroidal coil chromatography are described. Rat liver homogenates were subjected to analytical subcellular fractionation by toroidal coil chromatography in a phase mixture of 3.3% (w/w) dextran T500, 5.4% (w/w) poly(ethylene glycol) 6000, 10 mM sodium phosphate-phosphoric acid buffer, pH 7.4, in 0.26 M sucrose containing 0.05 mM Na₂EDTA and 1 mM ethanol. The distribution of organelles, as reflected by their marker enzymes, was compared to that obtained by discrete counter-current partition in a 17 transfer apparatus. Toroidal coil chromatography showed enhanced resolution of certain organelles. In particular, almost complete separation of plasma membrane from endoplasmic reticulum was achieved and some resolution of plasma membrane from lysosomes was obtained. It is concluded that toroidal coil chromatography offers a potentially useful alternative approach to organelle separation techniques.     

Multistage electrophoresis system for the separation of cells, particles and solutes

It is common to operate equilibrium-based separation methods, such as distillation and extraction, as multistage unit operations, in which equilibrium is presumably achieved within each stage. Two rate-based separation processes, free electrophoresis and magnetic particle separation, have now been operated in multistage mode. Preparative free electrophoresis of particles and solutes has resisted scale-up and is confined to a narrow range of ionic compositions. Natural convection induced in electrophoresis buffers by Ohmic heating has been a strong deterrent and has led to such measures as radial electrophoresis in Couette flow, free-flow electrophoresis, low-gravity electrophoresis, density gradient electrophoresis, and reorienting density gradient electrophoresis, to name a few. The short vertical electrophoresis path exploited in the last-mentioned forms the basis for multistage electrophoresis. A thin-layer countercurrent distribution apparatus was designed and constructed so that up to 20 fractions could be collected on the basis of electrophoretic mobility by applying an electric field. The mixture to be separated starts in a bottom cavity, and successive top cavities collect fractions as separand particles or molecules are electrophoresed upward out of the bottom cavity. Mathematical models of this process were developed, and experiments were performed to verify the predictions of the models by collecting and counting particles in each cavity after fractionation.     

Automated separation and quantitation of lipid fractions by high-performance liquid chromatography and mass detection

This report describes an improved separation and quantitation of lipid fractions in a total lipid extract by high-performance liquid chromatography using a modified solvent and gradient system delivered by dual pumps and incorporating a mass detector and autosampler. The detector responses for various lipid fractions (cholesteryl esters, triacylglycerols, free cholesterol, and seven major phospholipid classes) were fitted to a quadratic equation, y = ax2 + bx + c, and quantified after detector calibration by a computer. This new system has the advantage of automation and reproducible separation. The present method was applied to rat liver analysis.     

Isolation of tomato pectin methylesterase and polygalacturonase on monolithic columns

An improved cation-exchange chromatographic procedure on Convective Interaction Media (CIM, BIA Separations, Ljubljana, Slovenia) short monolithic methacrylate disk columns was used for the isolation of salt-independent pectin methylesterase (PME; EC 3.1.1.11) isoform and endo-polygalacturonase PG1 (PG, EC 3.2.1.15) from ripe tomato fruit extract after studying the chromatographic conditions including type of disk, binding buffer, pH, eluent composition and different gradients. Between 10 and 20 microg of proteins gave reliable chromatograms. Both carboxymethyl (CM) and sulfonyl (SO3) disks were equally suitable for the fractionation of tomato extract using the new gradient, but only CM disk was appropriate for further purification of the PME and PG fractions, and provided fast and sharp separation of proteins. The isolation of pure PG1 could be achieved only by addition of 20% of acetonitrile to the mobile phase. About 200 microg of proteins were loaded at one chromatographic run at the fractionation and purification. Determination of the molecular weights of the separated proteins showed that dimer of salt-independent PME isoform was formed in concentrated solutions of the enzyme but dissociated upon dilution of the solution. From 6 kg of fresh tomato flesh, 28 mg of purified salt-independent PME, 12.5mg of purified and active PG1 and 4 mg of PG2 fraction contaminated with salt-dependent PME isoform were obtained by means of semi-preparative chromatography on CIM disks.     

Targeting hepatocytes from liver tissue by laser capture microdissection and proteomics expression profiling

A tissue proteomics process is presented where hepatocyte cell isolation in combination with two-dimensional (2-D) gel electrophoresis and mass spectrometric identification were used to annotate the liver proteome. Laser microdissection of 8 microm liver tissue sections was performed and protein expression profiling was compared using a variety of quantities of input cells, and gel separation conditions. The 30 microm diameter laser generated the highest protein yields from the polymer coated caps following microsolubilization. We found that 6000 laser pulses (approximately 7200 hepatocytes) were required in order to generate high-resolution gel maps. Within homogeneous tissue samples, this could be accomplished in a total cycle time of 20 min using an automated dissection procedure. Close to 1000 high-quality gel annotations were generated from the corresponding 2-D gel expression profiles which matched closely the corresponding patterns of analytical-scale liver preparations detected by silver staining.     

Effects of soluble fractions from untreated and SiO2-treated subcellular particles of macrophages on nucleic acid metabolism in isolated nuclei of experimental granulation tissue.

Nuclei isolated from proliferating granulation tissue were incubated with 20 000 g supernatants from untreated and SiO2-treated subcellular particles of rat peritoneal macrophages in the presence of radioactive nucleic acid precursors. The supernatant from SiO2-treated subcellular particles increased the incorporation of [3H]CTP into nuclear RNA maximally by 26% at 5 min, and that of [methyl-3H]dTTP into DNA by 16% at 20 min. The release of radioactivity from labeled DNA was suppressed simultaneously. An RNase preparation from rat peritoneal macrophages enhanced the release of radioactivity from labeled DNA similarly as the soluble fraction from untreated subcellular particles of macrophages. The results suggest that the effects of the soluble fractions upon DNA metabolism of granuloma cells are at least partly independent of the effects on RNA metabolism and that the soluble fraction from SiO2-treated subcellular particles of macrophages stabilizes DNA through inhibition of nuclease activity.     

Single-step purification of rat C-reactive protein and generation of monospecific C-reactive protein antibody

Although Sepharose-phosphorylcholine affinity chromatography has been used extensively to purify some acute phase proteins, the operation has usually been a laborious multi-step procedure. By modifying previously described multi-step protein purification assays, centigram quantities of pure rat C-reactive protein (CRP) could be obtained in a single chromatographic step using affinity chromatography. Rat serum was passed over a column of p-aminophenylphosphorylcholine and extraneous proteins eluted with Tris-saline-Ca2+ buffer. Similar to other purification procedures, CRP was eluted with phosphorylcholine in a Tris-saline-Ca2+ buffer. The technical detail which distinguished this procedure from others, was the use of a phosphorylcholine gradient shallow enough (0.95 mM-2.5 mM) to resolve the eluent into two peaks; the first peak was composed largely of the contaminant, serum amyloid protein (SAP), and the second was composed of CRP. Although there was some overlap between the first and second peak, pure CRP could be obtained by pooling fractions from the trailing shoulder of the second peak. Using this single step procedure, a greater than 25% yield of SAP-free, purified CRP could be obtained. The purified CRP was free of SAP contamination as measured by sodium dodecyl sulfate gradient polyacrylamide gel electrophoresis. Purified CRP was determined to be free of rat albumin, IgG and the C3 component of complement using immunoelectrophoresis. This one-step affinity column chromatography procedure provides a simple, efficient method for collecting large quantities of rat CRP pure enough to be used to obtain a monospecific goat, anti-rat CRP antibody.