Purification of C3b inactivator and demonstration of its two polypeptide chain structure

C3b inactivator (C3bINA) was isolated from plasma by sequential ammonium sulfate gradient solubilization, anion exchange chromatography, gel filtration, and repeat ammonium sulfate gradient solubilization. The final product was pure as assessed by alkaline disc gel electrophoresis, isoelectric focusing, and SDS polyacrylamide gel electrophoresis, and elicited a monospecific rabbit antiserum. The normal serum concentration of C3bINA was found to be 53 +/- 9 microgram/ml (mean +/- S.D.). Heterogeneity of purified C3bINA was apparent on alkaline disc gel electrophoresis and isoelectric focusing, but not with SDS polyacrylamide gel electrophoresis and thus is attributed to forms of C3bINA that differ in charge rather than in size. SDS polyacrylamide gel electrophoresis of unreduced, alkylated C3bINA yielded a single stained band with an apparent m.w. of 93,000, whereas the reduced protein demonstrated two bands of 55,000 and 42,000 m.w., thereby establishing a composition of two disulfide-linked polypeptide chains for C3bINA.     

Analysis of photoreceptor proteins of microorganisms by gradient gel electrophoresis and other biochemical separation methods

Photoreceptor proteins for photoorientation in microorganisms are usually membrane bound and can be isolated by standard biochemical methods. Three examples are shown: the flagellates Euglena gracilis, Peridinum gatunense and the slime mold Dictyostelium discoideum. The photoreceptor of Euglena is attached to the basis of the flagellum and is composed of at least four chromoproteins which can be separated by gradient sodium dodecyl sulfate - polyacrylamide gel electrophoresis (SDS-PAGE) fast protein liquid chromatography (FPLC) and isoelectric focusing (IEF); it contains pterins and a flavin as chromophoric groups. The photoreceptor of Peridinium absorbs in the red wavelength band. Though not yet identified in detail, multiple receptors are probably involved, as indicated by fluorescence spectroscopy. Dictyostelium shows positive and negative phototaxis in its amoebal form and exclusively positive phototaxis in its pseudoplasmodial form. It is still open to discussion whether the two stages use separate photoreceptors. From amoebae two photoreceptor pigments have been isolated, showing an absorption which resembles the action spectrum, one membrane bound with a molecular mass of 45 kDa and one cytoplasmic fraction with a molecular mass of 27 kDa.     

Preparative application of commercial automated gel electrophoresis apparatus to subcellular-sized particles: sequential isolations, fractions re-run, sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, yield and purity

The analytical and preparative potential of automated gel electrophoresis apparatus with intermittent fluorescence scanning of the migration path, the HPGE-1000 apparatus (LabIntelligence, Belmont, CA) was further developed in application to subcellular-sized particles. Resolution between two rat liver microsome components in agarose (MetaPhor) gel electrophoresis was found to increase with decreasing agarose concentration to 0.04%. It was less, even in an agarose solution at that low concentration, than that in laterally aggregated 4% polyacrylamide gel. The three components of the microsomal preparation were sequentially isolated from 0.6 and 0.8% agarose gel electropherograms. One fraction when re-electrophoresed was found to exhibit the original mobility and did not give rise to the other components. Yields of each component were near-quantitative after one or two electroelution steps. Based on protein content, no impurities could be detected in two of the microsome fractions; the third fraction contained 2% of nonmicrosome impurity. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) patterns of all three microsome fractions were indistinguishable from one another and from that of the unfractionated microsome preparation.     

Classification of Setaria worms from calves and adult cattle into Setaria digitata and Setaria marshalli by polyacrylamide gel electrophoresis

The protein profiles of solubilized whole worms of the species, Setaria digitata and Setaria marshalli were compared using sodium dodecyl sulfate polyacrylamide gel electrophoresis. The results showed that one band with a molecular size of 69 kDa was confirmed only in S. marshalli, while this band was not detected in S. digitata. There were no differences of the major bands between males and females of the respective worm species. As further investigation, two-dimensional gel electrophoresis was performed and at least one spot ranging from 64 to 73 kDa was confirmed in S. marshalli but not in S. digitata. Therefore, those worms could be classified into two species biochemically as well as by the morphological characteristics.     

pICln predominantly localizes at luminal surface membranes of distal tubules and Henle''s ascending limbs

We produced a highly specific antibody to the C-terminal peptide sequence of pICln. It recognized pICln with a 38-kDa molecular mass on SDS-polyacrylamide gel electrophoresis, coinciding with that previously reported. During native polyacrylamide gel electrophoresis, three immunoreactive bands (38, 70, and 130 kDa) were detected. The isoelectric point of pICln was calculated to be 4.0. Subcellular localization study showed the presence of pICln in the soluble and microsomal fraction. pICln can be easily solubilized from the membrane fraction with Triton X-100. From immunohistochemical observations, we found pICln to be obviously located on the luminal surface membranes of the distal tubules and Henle's loop ascending limbs, and it can also be found inside proximal tubular cells. The present results suggested that pICln functions as a "cytosolic anchor = membrane insertion" model, and it plays important roles in the "urine dilution segment" cells of nephrons.     

Polyacrylamide gel electrophoresis coupled with matrix-assisted laser desorption/ionization mass spectrometry for tRNA mutant analysis

In analogy to two-dimensional analysis, the mobility shift in native polyacrylamide gel electrophoresis (PAGE) due to a nucleotide substitution of a single-stranded transfer ribonucleic acid (tRNA) fragment serves as the first dimension for tRNA mutation analysis. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), as the second dimension, allows precise determination of the mass of the tRNA fragments resolved by native PAGE. Off-line combination of native PAGE with MALDI-MS is demonstrated for high-resolution analysis of tRNAval and its mutants, including a three-nucleotide deletion and 12 single-base substitutions. Three approaches, including direct extraction of tRNAs from gel into buffer solution, dissolution of membrane in the matrix solution, and direct desorption of tRNAs from the membrane, are studied for coupling native PAGE with MALDI-MS. The membrane dissolution method is simple, and the resulting mixture is amenable to MALDI-MS analysis. In the membrane dissolution method, as little as 1 microg or 40 pmol of tRNA sample is loaded on a native gel, separated, capillary eluted onto a nitrocellulose membrane, and recovered using the matrix solution of 2,4,6-trihydroxyacetophenone in acetone.     

Biochemical characterization of the Golgi-complex proteins of Tritrichomonas foetus

Using cell-fractionation techniques (differential and discontinuous gradient centrifugation), we obtained a highly enriched fraction containing the Golgi complex of Tritrichomonas foetus. This fraction was further subfractionated by sodium carbonate (150 mM) treatment at pH 11.5, leading to the isolation of the Golgi content and membrane subfractions. Both fractions were characterized by electron microscopy. The protein content of membrane and luminal subfractions was about 40% and 60% of the total Golgi protein, respectively. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis showed an enrichment of 15 protein bands in the Golgi fraction, with molecular masses varying between 15 and 116 kDa. Alkaline treatment released some proteins into the medium, but most of them were associated with the Golgi membrane.     

SDS agarose gels for analysis of proteins

A new agarose-based protein electrophoresis gel system is described. The system consists of a highly resolving agarose, MetaPhor XR (FMC BioProducts, Rockland, ME, USA) dissolved in urea and TBE buffer and a stacking gel composed of a high gel-strength agarose, SeaKem Gold (FMC BioProducts). TBE containing sodium dodecyl sulfate (SDS) is used as electrophoresis buffer. The disadvantages of traditional agarose gels have been overcome, and several advantages over polyacrylamide gels have been demonstrated. The system is capable of high-resolution separation of small proteins and has a dynamic separation range equivalent to a 4%-20% gradient polyacrylamide gel. Furthermore, the staining of protein bands by Coomassie Brilliant Blue is very uniform in this gel, and depending on the protein, higher detection sensitivity can be obtained compared to SDS polyacrylamide gels. In Western blotting, proteins are more efficiently transferred to the membrane from the agarose gel than from polyacrylamide gels. Finally, the exceptional stability of agarose allows for gels to be precast and stored for a year.     

Studies of peroxisomes. VIII. Evidence for framework protein of the cores of rat liver peroxisomes

The cores of peroxisomes were purified 670 fold from a rat liver homogenate and the protein in the preparation was examined by sodium dodecyl sulfate(SDS)-polyacrylamide gel electrophoresis. Two bands of protein were detected on 10% polyacrylamide gel, and their molecular weights were calculated to be about 32,000 and 27,000. On treatment of the core fraction with alkali, urate oxidase was solubilized and on 10% polyacrylamide gel this fraction gave a single band of protein with an estimated molecular weight of 32,000. These results suggests that the protein component having a molecular weight of 27,000 is the framework protein of the core of rat liver peroxisomes.     

Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis

We describe the extraction and enrichment of membrane proteins for separation by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) after differential solubilization of an Escherichia coli cell lysate. In a simple three-step sequential solubilization protocol applicable for whole cell lysates, membrane proteins are partitioned from other cellular proteins by their insolubility in solutions conventionally used for isoelectric focusing (IEF). As the first step, Tris-base was used to solubilize many cytosolic proteins. The resultant pellet was then subjected to conventional solubilizing solutions (urea, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate, dithiothreitol, Tris, carrier ampholytes). Following the completion of this step, 89% of the initial E. coli sample mass was solubilized. Finally, the membrane protein rich pellet was partially solubilized using a combination of urea, thiourea, tributyl phosphine and multiple zwitterionic surfactants. Using N-terminal sequence tagging and peptide mass fingerprinting we have identified 11 membrane proteins from this pellet. Two of these outer membrane proteins (Omp), OmpW and OmpX, have previously been known only as an open reading frame in E. coli, while OmpC, OmpT and OmpTOLC have not previously been identified on a 2-D gel. The prefractionation of an entire cell lysate into multiple fractions, based on solubility, results in simplified protein patterns following 2-D PAGE using broad-range pH 3.5-10 immobilized pH gradients (IPGs). Additional advantages of sample prefractionation are that protein identification and gel matching, for database construction, is a more manageable task, the procedure requires no specialized apparatus, and the sequential extraction is conducted in a single centrifuge tube, minimizing protein loss.     

Isolation of a relatively pure outer membrane fraction of Moraxella nonliquefaciens and a comparison of its characteristics with the cytoplasmic membrane-containing material

Cell envelope fractions of Moraxella nonliquefaciens were isolated by a slight modification of Osborn's method. Two main membrane fractions were characterized chemically and morphologically. The density of the fraction containing cytoplasmic membrane material was 1.17 to 1.18 g cm-3 compared with 1.24 to 1.27 g cm-3 for the outer membrane fraction. Lipopolysaccharide was detected almost exclusively in the outer membrane fraction and sodium dodecyl sulphate polyacrylamide gel electrophoresis of this fraction revealed one dominant protein band with an apparent molecular weight of 45 000. Cross-contamination of the fractions was estimated to be about 10%, as calculated on the basis of the lipopolysaccharide fatty acid 3-hydroxydodecanoic acid and on the relative activities of D-lactate dehydrogenase and succinate dehydrogenase.     

Fractionation on the microscale of brain polyribosomes by electrophoresis on acrylamide gels

A method is described for brain polyribosome fractionation by acrylamide gel electrophoresis. Brain polyribosomes were run in 2.0% gels in quartz capillaries of 800 mum inner diameter where the gels were supported by capillary force. The gels could then be ultraviolet-scanned in situ. Amounts of brain polyribosomes as small as 10-10(-3) A260nm unit could be analysed by this method. The method was checked by running a macroscale-prepared brain polyribosome sample. The various electrophoretic bands obtained showed a favourable A260nm: A280 ratio. A short RNase treatment caused the disappearance of the slowly migrating bands and the emergence of a predominant band migrating faster than the dimer. The various polyribosomal bands were then identified by comparison with the mobility of polyribosome fractions taken from a sucrose gradient fractionation. Finally, the electrophoretic pattern of brain polyribosomes compared favourably with the pattern obtained by the classic method of sucrose gradient sedimentation. The electrophoretic fractionation of polyribosomes prepared from one rat hippocampus (80 mg) is presented.     

Two-dimensional separation of erythrocyte membrane proteins

1). Erythrocyte membrane proteins eluted with Triton X-100 or dilute EDTA have been separated two-dimensionally by isoelectric focusing in polyacrylamide gels containing 1 percent Triton X-100 plus 8 M urea, followed by electrophoresis using sodium dodecyl sulfate. Characteristic patterns, consistent among 40 healthy donors, were obtained. 2. The resulting patterns contain at least 30 components. The "spectrin" components (sodium dodecyl sulfate Bands 1 and 2) focus in the same pH range. Other membrane components giving single bands in sodium dodecyl sulfate electrophoresis appear to be heterogeneous. 3. Triton X-100, but not EDTA, extracts the principal membrane glycoproteins and the major "intrinsic" protein. Otherwise, proteins preferentially eluted by EDTA extract poorly with Triton X-100 and vice versa. 4. Membrane glycoproteins migrate anodally during electrofocusing and can be purified in a simple, one-step procedure.     

Effect of protein application mode and acrylamide concentration on the resolution of protein spots separated by two-dimensional gel electrophoresis

Two-dimensional gel electrophoresis separates large numbers of proteins in two steps on the basis of differences in their pIs and molecular masses. The separation is usually performed on immobilized pH gradient strips, followed by gradient polyacrylamide gels separating proteins with molecular masses between 5-200 kDa. For the first-dimensional separation the protein samples are usually applied near one end of the strip. Using total soluble protein extracts of the bacterium Haemophilus influenzae, we found that simultaneous sample application at both the basic and the acidic ends of the strip resulted in detection of more and stronger protein spots in comparison with sample application at one end only. Because many proteins of an organism have similar pI and Mr values, an overlapping of protein spots is frequently observed in the second-dimensional separation. The soluble protein fraction of H. influenzae was further separated on gels of constant acrylamide concentration between 7.5% and 15.0%. We found that for proteins of molecular mass within certain ranges, the gels of homogeneous acrylamide concentration provided more efficient spot separation than the gradient gels. The observed improvements in spot resolution may be useful in the characterization of proteins from other organisms or cell lines.     

Isolation and some properties of factor VIII (antihemophilic factor)

A method for isolation of factor VIII from cryoprecipitate fraction of human plasma has been elaborated. The isolation procedure involves precipitation with dextran, removal of fibrinogen by means of defibrase, precipitation with ammonium sulfate, polyethylene glycol fractionation, and Sepharose 6B gel filtration step. Factor VIII has been purified 7000- to 13,000 -- fold.. The preparation is homogenous by ultracentrifugal examination and it has an S20,w value of 19.4. It also shows a single precipitin line when subjected to immunoelectrophoresis employing rabbit antibodies against factor VIII. The preparation did not enter a 7.5% polyacrylamide gel containing sodium dodecyl sulfate even in the presence of 8 M urea. After reduction of the protein with 2-mercaptoethanol, subunits were formed which migrated as one band in polyacrylamide gel electrophoresis.     

Analysis of developing enamel of the rat. II. Electrophoretic and amino acid studies

Amino-acid analyses showed that proline, glutamic acid and leucine were the most common amino acids in immature or developing enamel and in each of its fractions (i.e., in the 1st and 14th water-extractable fractions of a sequential series of extractions, EDTA-water soluble and water-insoluble fractions. The immature enamel and its 1st and 14th water-extractable fractions were similar in their proportions of the basic amino acids (lysine, histidine and arginine), the beta-hydroxylated aliphatic amino acids (valine, leucine, and isoleucine). On the other hand, the immature enamel differed from the water-extractable fractions chiefly in its relative content of aspartic acid, glutamic acid, alanine, proline, glycine, tyrosine and methionine. Also the 1st water-extractable fraction differed from the 14th in its amino-acid profile. tthe EDTA-water-soluble fraction most closely resembled the 14th water-extractable fraction except for its proportion of arginine and alanine residues. Although with polyacrylamide gel electrophoresis the EDTA-water-soluble and the water-extractable fractions exhibited companion bands (at least 7 peaks were evident at pH 9.3) they differed decidely as to which band was the most prominent. The water-insoluble fractions compared with any of the soluble fractions or with immature enamel showed a higher percent of serine, threonine, glycine, aspartic acid, alanine, valine, lysine, and arginine but relatively less glutamic acid, proline, methionine and histidine. Neither hydroxyproline nor hydroxylsine were detected in any of the samples.     

Rapid identification of comigrating gel-isolated proteins by ion trap-mass spectrometry

In the search for novel nuclear binding proteins, two bands from a sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel were analyzed and each was found to contain a number of proteins that subsequently were identified by tandem mass spectrometry (MS/MS) on a quadrupole ion trap instrument. The bands were digested with trypsin in situ on a polyvinylidene difluoride (PVDF) membrane following electroblot transfer. Analysis of a 2.5% aliquot of each peptide mixture by matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) followed by an initial database search with the peptide masses failed to identify the proteins. The peptides were separated by reversed-phase capillary high performance liquid chromatography (HPLC) in anticipation of subsequent Edman degradation, but mass analysis of the chromatographic fractions by MALDI-MS revealed multiple, coeluting peptides that precluded this approach. Selected fractions were analyzed by capillary HPLC-electrospray ionization-ion trap mass spectrometry. Tandem mass spectrometry provided significant fragmentation from which full or partial sequence was deduced for a number of peptides. Two stages of fragmentation (MS3) were used in one case to determine additional sequence. Database searches, each using a single peptide mass plus partial sequence, identified four proteins from a single electrophoretic band at 45 kDa, and four proteins from a second band at 60 kDa. Many of these proteins were derived from human keratin. The protein identifications were corroborated by the presence of multiple matching peptide masses in the MALDI-MS spectra. In addition, a novel sequence, not found in protein or DNA databases, was determined by interpretation of the MS/MS data. These results demonstrate the power of the quadrupole ion trap for the identification of multiple proteins in a mixture, and for de novo determination of peptide sequence. Reanalysis of the fragmentation data with a modified database searching algorithm showed that the same sets of proteins were identified from a limited number of fragment ion masses, in the absence of mass spectral interpretation or amino acid sequence. The implications for protein identification solely from fragment ion masses are discussed, including advantages for low signal levels, for a reduction of the necessary interpretation expertise, and for increased speed.     

Human auditory evoked potentials during speech-voice activity]

Pectinesterase (PE), from commercial orange peels or ammonium sulfate fractionation (50-80% saturation) of pea pods, was detected on polyacrylamide gels after native acidic polyacrylamide gel electrophoresis (PAGE) or sodium dodecyl sulfate (SDS)-PAGE by using the synthetic substrate beta-naphthyl acetate (beta-NA). The release of beta-naphthol (at 322 nm) from beta-NA was proportional to PE activity. The PE activity bands on polyacrylamide gels after native acidic PAGE or SDS-PAGE were stained with a combination of tetrazotized o-dianisidine and beta-NA. This fast and sensitive method can be used for enzyme purification and characterization.     

The resolution between two native proteins and between their sodium dodecyl sulfate-complexes in agarose and polyacrylamide gel electrophoresis

Commercial gel electrophoresis apparatus with intermittent fluorescence scanning of the migration path (HPGE-1000 apparatus, LabIntelligence) makes it possible to measure band width and migration distance as a function of the duration of electrophoresis. As a result, resolution can be evaluated quantitatively and therefore different gel media can be compared objectively. The resolution of fluorescein carboxylate labeled conalbumin (molecular mass 86 kDa) and soybean trypsin inhibitor (22.7 kDa) in gel electrophoresis was found to increase as a function of the gel type in the order SeaKem GTG-, SeaKem Gold-agarose, 2% N,N'-methylenebisacrylamide cross-linked polyacrylamide, MetaPhor-XR-, and SeaPrep-agarose. The advantage in resolving capacity of SeaPrep agarose over the polyacrylamide gel was by a factor of up to five. The resolving capacity of the agaroses was in indirect relation to the degree of electroendosmosis. In all media, resolution increased with migration distance (time). The same proteins when reacted with sodium dodecyl sulfate (SDS) resolve (i) better at up to 6% SeaPrep agarose concentration than in polyacrylamide, as in the gel electrophoresis of the native proteins; (ii) less effectively, by contrast, at SeaPrep agarose concentrations > 6%, than in polyacrylamide gel; and (iii) significantly better in 4-6% SeaPrep agarose than in 4-6% SeaKem GTG agarose. Since Ferguson plot analysis in both agarose and polyacrylamide gels shows that the two SDS-proteins are larger than the native proteins with which they are complexed, the superiority of polyacrylamide gels above 7% appears to be correlated with the fact that its mean pore radius, estimated for both media using identical assumptions and identical rigid spherical standards - proteins, is approximately seven times larger than that of SeaPrep agarose in the concentration range of 3-8%, and that therefore the molecular "fit" in polyacrylamide is closer than that in SeaPrep agarose of the concentration range used. The dependence of resolution on the ratio of particle radius to mean pore radius ("fit") is also suggested by the fact that the two SDS-proteins resolve in a biphasic dependence on gel concentration in both agarose and polyacrylamide, with a maximum at 6% agarose and 10% polyacrylamide.