Ferguson Plot Analysis Research Articles

Different behavior of Ferguson plot between agarose and polyacrylamide gels

In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, our investigation extended to model proteins with acidic isoelectric points and larger molecular weights, namely Ferritin and caseinolytic peptidase B (ClpB). Notably, these proteins displayed distinct Ferguson plot slopes when subjected to agarose gel electrophoresis. Intriguingly, when polyacrylamide gel was employed, ClpB exhibited multiple bands, each with its unique Ferguson plot slope, deviating from the expected behavior based on molecular size. This divergence in Ferguson plot characteristics between agarose and polyacrylamide gels points to an interesting and complex interplay between protein properties and gel electrophoresis conditions.

Ferguson plot analysis of multiple intermediate species of thermally unfolded bovine serum albumin

Ferguson plot was used to characterize the multiple intermediate species of bovine serum albumin (BSA) upon thermal unfolding. Differential scanning calorimetry showed an irreversible melting of BSA in Tris-HCl and phosphate buffers with a mid-transition temperature, Tm, of ∼68 °C. Thermally unfolded BSA was analyzed by agarose native gel electrophoresis stained by Coomassie blue and SYPRO Orange staining as a function of pH or protein concentration. SYPRO Orange was used to stain unfolded proteins. BSA heated at 70 and 80 °C, i.e., above the Tm, formed multiple intermediate species, which depended on the pH between 7.0 and 8.0, protein concentration and which buffer was used. These intermediate species were analyzed by Ferguson plot, which showed that BSA heated at 60 °C had a similar size to the native BSA, indicating that they are either native or native-like state consistent with no SYPRO Orange staining. The intermediate species observed at higher temperatures with the mobility less than that of the native BSA showed a steeper Ferguson plot and were stained by SYPRO Orange, indicating that these species had a larger hydrodynamic size than the native BSA and were unfolded.

Interaction between gold nanoparticles and blood proteins to define disease states

Introduction: Gold Nanoparticles (AuNPs) have been used for several drug delivery applications with promising results, although a detailed model for interaction between AuNPs and biomolecules present in the bloodstream is still lacking [1,2]. Furthermore, some diseases alter the serum protein content profile, influencing the composition of adsorbed proteins at the AuNP surface, the so-called protein corona, indicating a possibility for future diagnostic tools [3]. In this work, we study the interaction between blood proteins, such as Albumin (a globular protein with 66 kDa) and Fibrinogen (Fib), a cylindrically-shaped protein with 340 kDa), with AuNPs, in order to improve our understanding of this interaction on a complex protein mixture such as Human Serum. Data from individual proteins can hopefully be used to model AuNP-plasma proteins interaction, as the basis for future studies and applications of AuNPs in the diagnosis of important diseases and in vivo treatment. Materials and methods: Spherical AuNPs with a diameter of ca. 15 nm were chemically synthesized, functionalized with an alkanethiol (11-MUA) to increase their colloidal stability, and further conjugated by simple incubation with Bovine Serum Albumin (BSA) or bovine Fib, used as homologs of their human counterparts. The protein corona was analyzed by Agarose Gel Electrophoresis (AGE), SDS-PAGE, Dynamic Light Scattering (DLS) and Nanoparticle Tracking Analysis (NTA). Zeta-potential values were estimated by Ferguson Plot Analysis of the AGE runs or were determined by Electrophoretic Light Scattering (ELS). Computational methods were applied to the analysis of electrophoretic mobility as observed in video sampling of the AGE runs. Results: Size and concentration of the synthesized AuNPs was determined by UV-vis spectroscopy. rom a Langmuir Isotherm fitting of the observed bioconjugation curves, binding constants were obtained for AuNP-MUA conjugation with BSA (1.5 × 10−2 ± 0.1), or Fib (34.3 × 10−2 ± 1.2); and for AuNP-CALNN conjugation with Fib (51.2 × 10−2 ± 4.7). AuNP-CALNN conjugation with BSA lead to band smearing on AGE, not allowing an evaluation of the binding process. Overnight competitive incubation of a protein mixture with AuNP-MUA, favoured Fib adsorption over BSA. Discussion and conclusions: Electrostatic protein conjugates show a robust structure in AGE runs, with generally low band dispersion, especially for AuNP-MUA conjugates. Video analysis revealed protein corona stabilization and a constant band migration velocity. Binding affinity constants and competitive behaviour confirmed a higher affinity for Fib conjugation over BSA to the functionalized AuNPs. This higher binding affinity for Fib can be explained by its higher surface contact area and a possible cooperativity mechanism, deserving further analysis.

The N-terminal fragment of Acanthamoeba polyphaga mimivirus tyrosyl-tRNA synthetase (TyrRSapm) is a monomer in solution

Acanthamoeba polyphaga mimivirus tyrosyl-tRNA synthetase (TyrRSapm) was the first reported aminoacyl-tRNA synthetase of viral origin. The previous crystal structure of TyrRSapm showed a non-canonical orientation of the dimer conformation and the CP1 domain, responsible for dimer formation, displays a major modification of a motif structurally conserved in other TyrRS structures. An earlier study reported that Bacillus stearothermophilus N-terminal TyrRS exists as a dimer under native conditions. N-terminal TyrRSapm (ΔTyrRSapm, 1–234 aa) was constructed to remove the C-terminal anticodon-binding domain. Here we show by Ferguson plot analysis and analytical ultracentrifugation that ΔTyrRSapm exists as a monomer and contains a disulfide-bridge. The ΔTyrRSapm loses the ability to bind tRNATyr, however it remains active in pyrophosphate exchange with similar ligand dissociation constants as the full-length enzyme. Structured summary of protein interactionsTyrRSapm and TyrRSapmbind by cosedimentation in solution (View interaction) TyrRSapmandTyrRSapmbindbyblue native page(View interaction)TyrRSapmandTyrRSapmbindbyfluorescence technology(View interaction)TyrRSapmandTyrRSapmbindbyfluorescence technology(View interaction)

A Biotin-Coupled Bifunctional Enzyme Exhibiting Both Glutamine Synthetase Activity and Glutamate Decarboxylase Activity

Purpose: To purify and study native form and enzymatic activity of the 42 kDa biotin-coupled protein (p42), which is related to glutamate action in chick retina.Methods: p42 was purified using molecular filtration in the presence of 0.7 M sodium chloride. Purity and identification of p42 were studied by SDS-PAGE, 2D-PAGE, LC-MS/MS, and MALDI-TOF MS. The native form of p42 was investigated using native-PAGE and Ferguson plot. Biotin-coupled property was examined by Western blot analysis. Enzymatic actions of p42 were studied using glutamate as substrate in the presence or absence of glutamine.Results: p42 was successfully purified from chick retinal protein solution using the molecular filtration. Western blot analysis with avidin showed that p42 was a biotin-coupled protein. Using SDS-PAGE, 2D-PAGE, LC-MS/MS, and MALDI-TOF MS, purified p42 was identified as a glutamine synthetase with four isoforms. Native-PAGE, followed by Ferguson plot analysis, showed two molecular forms of p42 corresponding to homotetramers and homooctamers. Enzymatic reaction followed by paper chromatography showed that p42 catalyzed the synthesis of glutamine from glutamate in the presence of ammonium ion, ATP, and magnesium ion. At prolonged reaction time, γ-aminobutyric acid (GABA) was also formed. With glutamate and glutamine present at equal concentrations in the reaction mixture, GABA could be rapidly detected, but GABA could not be detected when glutamate concentration was more than four-fold that of glutamine. The results indicated that p42 also had glutamate decarboxylase activity. Both enzymatic activities were inhibited by avidin. High concentrations of Mn2+ inhibited synthetase activity of p42 but not decarboxylase activity.Conclusion: p42 was purified from chick retinal protein solution using molecular filtration in the presence of sodium chloride. The protein was a biotin-coupled bifunctional enzyme that contained glutamine synthetase activity and glutamate decarboxylase activity. Biotin was possibly involved in these activities. Mn2+ showed different effects on the two activities.

Carbohydrate-recognition domains of galectin-9 are involved in intermolecular interaction with galectin-9 itself and other members of the galectin family

Galectin-9 (Gal-9) is a tandem-repeat-type member of the galectin family associated with diverse biological processes, such as apoptosis, cell aggregation, and eosinophil chemoattraction. Although the detailed sugar-binding specificity of Gal-9 has been elucidated, molecular mechanisms that underlie these functions remain to be investigated. During the course of our binding study by affinity chromatography and surface plasmon resonance (SPR) analysis, we found that human Gal-9 interacts with immobilized Gal-9 in the protein-protein interaction mode. Interestingly, this intermolecular interaction strongly depended on the activity of the carbohydrate recognition domain (CRD), because the addition of potent saccharide inhibitors abolished the binding. The presence of multimers was also confirmed by Ferguson plot analysis of result of polyacrylamide gel electrophoresis and matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). Moreover, this intermolecular interaction was observed between Gal-9 and other galectin members, such as Gal-3 and Gal-8, but not Gal-1. Because such properties have not been reported yet, they may explain an unidentified mechanism underlying the diverse functions of Gal-9.

Native and subunit molecular mass and quarternary structure of the hemoglobin from the primitive branchiopod crustacean Triops cancriformis

Many branchiopod crustaceans are endowed with extracellular, high-molecular-weight hemoglobins whose exact structural characteristics have remained a matter of conjecture. By using a broad spectrum of techniques, we provide precise and coherent information on the hemoglobin of one of the phylogenetically 'oldest' extant branchiopods, the tadpole shrimp Triops cancriformis. The hemoglobin dissociated under reducing conditions into two subunits, designated TcHbA and TcHbB, with masses of 35,775+/-4 and 36,055+/-4 Da, respectively, determined by ESI-MS. Nonreducing conditions showed only two disulfide-bridged dimers, a homodimer of TcHbA, designated D1 (71,548+/-5 Da), and the heterodimer D2 (71,828+/-5 Da). Carbamidomethylation of free SH groups revealed the presence of three cysteines per subunit and indicated one intrasubunit and one intersubunit disulfide bridge. Ultracentrifugation and light-scattering experiments under nondenaturating conditions yielded mass estimates that suggested an uneven number of 17 subunits forming the native hemoglobin. This unrealistic number resulted from the presence of two size classes (16-mer and 18-mer), which were recognized by native PAGE and Ferguson plot analysis. ESI-MS revealed three hemoglobin isoforms with masses of 588.1 kDa, 662.0 kDa, and 665.0 kDa. The 16-mer and the smaller 18-mer species are supposed to be composed of TcHbA only, given the dominance of this subunit type in SDS/PAGE. Transmission electron microscopy of negatively stained specimens showed a population of compact molecules with geometrical extensions of 14, 16 and 9 nm. The proposed stoichiometric model of quarternary structure provides the missing link to achieve a mechanistic understanding of the structure-function relationships among the multimeric arthropodan hemoglobins.

Alkaline phytase from Lilium longiflorum: Purification and structural characterization

Phytases catalyze the hydrolysis of phytic acid ( myo-inositol hexakisphosphate), the most abundant inositol phosphate in cells. Phytases are of great commercial importance because their use as food and animal feed supplement has been approved by many countries to alleviate environmental and nutritional problems. Although acid phytases have been extensively studied, information regarding alkaline phytases is limited. Alkaline phytases with unique catalytic properties have been identified in plants, however, there is no report on the purification or structural properties. In this paper, we describe the purification of alkaline phytase from plant tissue. The purification was challenging because of contamination from non-specific phosphatases and acid phytases and low endogenous concentration. The purification of alkaline phytase from pollen grains of Lilium longiflorum involved selective precipitation by heat and ammonium sulfate followed by anion exchange and chromatofocusing chromatography and, finally, gel electrophoresis. Alkaline phytase was purified ∼3000-fold with an overall recovery of 4.2%. The native molecular mass was estimated to be in the range of 118 ± 7 kDa by Ferguson plot analysis and M r of denatured protein in the range of 52–55 kDa by SDS–PAGE suggesting that the enzyme is a homodimer. Separation by 2-D gel and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometric analysis of separated proteins indicates the presence of multiple mass and charge isoforms with p I values between 7.3 and 8.3. To our knowledge, this is the first alkaline phytase to be purified from plant sources. The unique properties suggest that the enzyme has the potential to be useful as a feed and food supplement.

Vitellogenin exists as charge isomers in the Indian freshwater murrel, Channa punctatus (Bloch)

Three charge isomeric forms of vitellogenin are reported in the blood of estrogen-treated murrel, Channa punctatus on the basis of the results of native and SDS–PAGE, isoelectric focusing, and Ferguson plot analysis. Vitellogenin was induced in adult murrels by exogenous administration of estradiol-17β and labelled with 32P in vivo. Labelled vitellogenin isolated from other plasma proteins on Ultrogel AcA 34 columns resolve into three bands on native-PAGE. Ferguson plot analysis reveals free electrophoretic mobilities of the three bands as 6.0, 4.5, and 3.7, which are very similar to the isoelectric point values of 5.9, 4.6, and 3.8, respectively. The apparent molecular weight of native murrel vitellogenin is 530 kDa. It consists of a single peptide with a molecular weight of 175 kDa. All the three bands on native PAGE resolves into a single peptide on SDS–PAGE. N-terminal amino acid sequence for murrel vitellogenin peptide is MKAVVLALLL. The protein phosphorus:lipid phosphorus ratio for murrel vitellogenin is 0.9. The total lipid content is 32.8%, consisting of 45% neutral lipids and 30% phospholipids. Phosphatidyl choline is the major phospholipid whereas triglycerides are the major neutral lipids. Results of these analytical analyses indicate that murrel native vitellogenin circulates as three charge isomers; poor in phosphorus but rich in lipids content.

Native and sodium dodecyl sulfate-capillary gel electrophoresis of proteins on a single microchip.

Simultaneous electrophoresis of both native and Sodium dodecyl sulfate (SDS) proteins was observed on a single microchip within 20 min. The capillary array prevented lateral diffusion of SDS components and avoided cross contamination of native protein samples. The planar sputtered electrode format provided a more uniform distribution of separation voltage into each of the 36 parallel microchannel capillaries than platinum wire electrodes commonly used in conventional electrophoresis. The customized geometry of the stacking capillary machined into the cover plate of the microchip facilitated reproducible sample injection without the requirement for stacking gel. Polyimide served as a mask and facilitated insulation of the anode and cathode to prevent electrode lift off and deterioration during continuous electrophoresis, even at a constant current of 8 mA. Improved protein separation was observed during capillary electrophoresis at lower currents. Ferguson plot analysis confirmed the electrophoretic mobility of native globular proteins in accordance with their charge and size. Corresponding Ferguson plot analysis of SDS-associated proteins on the same chip confirmed separation of marker proteins according to their molecular weight.

Supramolecular DNA-Streptavidin Nanocircles with a Covalently Attached Oligonucleotide Moiety

Covalent hybrid conjugates consisting of streptavidin (STV) and a 24-mer single-stranded DNA oligonucleotide have been used as a starting material for the synthesis of supramolecular nanocircles. For this, the covalent hybrid conjugates were oligomerized by cross-linking with 5′,5′-bis-biotinylated double-stranded DNA (dsDNA) fragments of various length. Heat denaturation of the resulting oligomeric conjugates and subsequent rapid cooling led to the formation of the nanocircles, in which the oligonucleotide-containing STV molecule is coupled with both ends of the circular bis-biotinylated dsDNA fragment. The circular structure of the bioconjugates was established by electrophoretic studies including Ferguson plot analysis as well as by scanning force microscopy (SFM) inspection. The formation process and the stability against degradation by ligand exchange with free D-biotin was compared for the nanocircles obtained from covalent oligonucleotide-STV hybrids and native STV. The former nanocircles revealed a decreased stability with respect to ring opening than the circles obtained from native STV. This suggested that the affinity of the covalent oligonu- cleotide-STV hybrid for binding biotinylated DNA is significantly decreased. Nevertheless, the single-stranded oligonucleotide moiety of the hybrid nanocircles can be used as a molecular handle for further functionalization. For instance, it was used for the selective DNA-directed immobilization at a surface, previously functionalized with complementary capture oligonucleotides. Moreover, we demonstrate that a pair of nanocircles, containing complementary oligonucleotide moieties, can be hybridized to form specific dimers, thereby generating a novel type of supramolecular DNA-protein nanostructures.

Isolation and Characterization of a Novel 530-kDa Protein Complex (PC530) Capable of Associating with the 20S Proteasome from Starfish Oocytes

A novel protein complex called PC530 was purified concomitantly with proteasomes from oocytes of the starfish, Asterina pectinifera, by chromatography with DEAE–cellulose, phosphocellulose, Mono Q, and Superose 6 columns. The molecular mass of this complex was estimated to be 530 kDa by Ferguson plot analysis and about 500 kDa by Superose 6 gel filtration. Since the 1500-kDa proteasome fractions contain the PC530 subunits as well as the 20S proteasomal subunits, and also since the purified PC530 and the 20S proteasome were cross-linked with a bifunctional cross-linking reagent, it is thought that PC530 is able to associate with the 20S proteasome. The PC530 comprises six main subunits with molecular masses of 105, 70, 50, 34, 30, and 23 kDa. The 70-kDa subunit showed a sequence similarity to the S3/p58/Sun2/Rpn3p subunit of the 26S proteasome, whereas the other subunits showed little or no appreciable similarity to the mammalian and yeast regulatory subunits. These results indicate that starfish oocytes contain a novel 530-kDa protein complex capable of associating with the 20S proteasome, which is distinctly different from PA700 or the 19S regulatory complex in molecular size and subunit composition.

Identification and partial purification of DnaK homologue from extremely halophilic archaebacteria, Halobacterium cutirubrum.

The levels of synthesis of six proteins were increased at elevated growth temperature of the extremely halophilic archaebacterium Halobacterium cutirubrum. One of these proteins, with an apparent molecular mass of 97 kDa on sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE), bound to an ATP-agarose column in the presence of 4 M NaCl, but not in the absence of salt, indicating that this protein retained its ATP-binding activity only at high salt concentration. The NH2-terminal sequence of this protein and the internal sequences of the tryptic peptides covering 1/3 of the total number of residues coincided with that deduced from the nucleotide sequence of the dnaK gene isolated from H. cutirubrum. The results strongly suggest that this apparent 97-kDa protein is the gene product of dnaK, although the molecular mass calculated from the nucleotide sequence is only 68,495, much smaller than the value of this protein determined by SDS-PAGE. Ferguson plot analysis indicated that this protein showed anomalous mobility on SDS-PAGE. We have purified DnaK homologue to greater than 90% homogeneity with stepwise elution from an ATP-agarose column.

PhastSystem electrophoresis in beta-octylglucoside containing gels with immunodetection of a nondenatured vesicle-associated membrane protein.

Recombinant vesicle-associated membrane protein (rVAMP), implicated as a participant in membrane exocytosis and fusion (a "SNARE protein"), was subjected to gel electrophoresis in the miniaturized gels of the PhastSystem (Pharmacia) containing the nondenaturing, nonionic detergent beta-octylglucoside (OG), followed by immunodetection of the protein. Three major components of nondenatured rVAMP are detected by Western blotting both in 0.5% OG and in the absence of detergent. Their separation increases with increasing gel concentration above 7%T. Ferguson plot analysis indicates that the three species of VAMP are size isomers (i.e., they differ in size but share a common surface net charge density), the common point of intersection of the plots (mu-point) being a measure of their common free mobility. By the criteria of size and free mobility (related to surface net charge), VAMP components I, II and III in 0.5% OG-containing buffer are indistinguishable from components II, III and IV, respectively, observed in the absence of the detergent. The feasibility of immunodetection of nondenatured rVAMP on gels containing nondenaturing detergents opens up the possibility of gaining biochemical information regarding nondenatured SNARE protein complexes and SNARE proteins linked to membrane fragments.

Identification of a silencing element in the chicken lipoprotein lipase gene promoter: characterization of the silencer-binding protein and delineation of its target nucleotide sequence

Lipoprotein lipase (LPL) hydrolyzes triglycerides in chylomicrons and very low density lipoproteins (VLDL) and plays a central role in lipid metabolism. It is regulated tissue-specifically. By deletion analysis, a negative regulatory element was identified in the chicken LPL gene promoter at base pairs (bp) −263 to −241. This sequence contained two palindromic halves with a three nucleotide spacer. Either half was sufficient for full inhibitory function. A protein complex bound specifically to this element and a high correlation was found between binding of the complex and inhibition of transcription. Its molecular mass, evaluated by native gel electrophoresis and Ferguson plot analysis, was 120 kDa. UV cross-linking followed by SDS–PAGE revealed two protein subunits of 48 kDa and 44 kDa, respectively. This inhibitory protein complex may contribute to the tissue-specific regulation of LPL gene transcription. It was much more abundant in liver than in adipose tissue and heart. Our data showed that this negative element inhibited transcription even when placed at an upstream location (−666), but failed to function in the herpes simplex virus thymidine kinase promoter, indicating that it acted in conjunction with other element(s) in the chicken LPL gene to inhibit transcription.

Capillary electrophoretic separation of 1 to 10 kbp sized dsDNA using poly(ethylene oxide) solutions in the presence of electroosmotic counterflow.

DNA fragments of 1 to 10 kbp in length were separated by capillary electrophoresis (CE), using poly(ethylene oxide) (PEO) solutions in the presence of electroosmotic flow. The technique requires filling the capillary with the polymer solution by means of electroosmotic flow (EOF). Separation times of 6-7 min in PEO solutions ranging from 0.3 to 8 x 10(6) Mr at 375 V/cm were sufficient to separate the 11 components of the dsDNA ladder (0.5 to 10 kbp) by size. The migration behavior of the double-stranded (ds)DNA fragments, interpreted by "Ferguson plot analysis", in the system is indistinguishable from that previously reported for capillary zone electrophoresis (CZE) in a polyacrylamide solution without EOF. Potential advantages of conducting CZE using polymer solutions in the presence of EOF are: (i) Possibility of long migration times on short columns; (ii) possibility of introducing relatively viscous, high Mr polymer solutions into narrow capillaries; (iii) possibility of establishing polymer concentration gradients in capillaries; (iv) possibility of concentrating the starting zone by balancing electrophoretic migration and electroosmotic transport.

Separation and microgram-scale isolation of sea urchin egg granules by electrophoresis in polyvinylpyrrolidone solution, using horizontal gel electrophoresis apparatus with fluorescence detector.

A homogenate of sea urchin (Lytechinus pictus) eggs rich in exocytotic membrane vesicles (granules) was subjected to analytical and preparative electrophoresis in the commercial automated horizontal gel electrophoresis apparatus (HPGE-1000, LabIntelligence, Belmont, CA) capable of intermittent scanning of the migration path, using buffered solutions of polyvinylpyrrolidone (PVP). The nonfluorescent granules were detected by "fluorescence reduction", i.e., a decrease of fluorescence intensity due to the absorbance and/or light scattering properties of the particle. Granules migrated at linear migration rates in buffers ranging from 0 to 2.5% PVP. Two bands were observed and optimally separated in 1.5% PVP solution. As shown by sodium dodecyl sulfate (SDS)-polypeptide patterns, the material recovered from the bands was qualitatively indistinguishable from the two major fractions A and C of granules previously separated by free-flow electrophoresis in the absence of polymer. Ferguson plot analysis failed to provide the sizes of the granules in view of the narrow PVP concentration range available for mobility measurement and the unavailability of chemically homogeneous size standards.

Denaturation and self-association of apolipoprotein A-I investigated by electrophoretic techniques.

Purified human apolipoprotein A-I (apoA-I), when run across a transverse urea gradient at alkaline pH, gives a complex pattern characterized by a number of parallel sigmoidal curves, in which the transition between high- and low-mobility forms, i.e. from folded to unfolded structure, occurs between 1.1 and 3.2 M urea. Size differences appear to be the major cause of this isomerism. When migrated across a wide pH range in the presence of varying amounts of urea to display its titration curve, apoA-I is resolved into two pairs of bands, running parallel in the neutral to basic pH region while merging at acidic pH; such a finding does not correlate with a differential exposure of His residues, as shown by diethyl pyrocarbonate titration. Ferguson plot analysis, confirmed by cross-linking experiments, demonstrates a gradual shift from higher to lower mass aggregates as the urea concentration is raised; the monomeric form undergoes denaturation by swelling to an approximately 50% larger hydrodynamic volume than in its native state. At alkaline pH, where apoA-I exists as aggregated species, disaggregation and unfolding appear to happen at once, the larger aggregates being less stable than the smaller ones. At acidic pH, apoA-I does not form aggregates and has little secondary structure; unfolding is then a progressive rather than a cooperative process.

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.

Regulatory subunit complex dissociated from 26S proteasome: isolation and characterization

A ubiquitin (Ub)/ATP-dependent proteolytic complex (26S proteasome) purified from rabbit skeletal muscle was dissociated into two subcomplexes, a 20S proteasome and a regulatory subunit complex, by preparative non-denaturing polyacrylamide gel electrophoresis (PAGE). The isolated regulatory subunit complex preparation gave a single broad band on analytical non-denaturing PAGE, and several bands ranging between 33 and 110 kDa on SDS-PAGE. This complex was found to consist of about 20 subunits on the basis of two-dimensional PAGE, the pattern of which appeared identical or very similar to that of the 33–110 kDa 26S proteasome subunits. The apparent molecular mass of the complex was estimated to be 1100 kDa by Ferguson plot analysis and also by Superose 6 gel filtration. Unlike the 26S proteasome, neither ATPase activity nor protease activities toward Suc-Leu-Leu-Val-Tyr-MCA, Boc-Phe-Ser-Arg-MCA, Z-Leu-Leu-Glu-βNA, [ 14C]-casein, [ 125I]-lysozyme and Ub-[ 125I]-lysozyme were significantly detectable in the regulatory subunit complex. This complex was found to be capable of associating with itself in MgATP-dependent manner. These results suggest that a regulatory subunit complex dissociated from the 26S proteasome comprises all the higher molecular mass subunits of the 26S proteasome, and has no detectable ATPase and protease activities, although the homo-oligomerization occurs in an ATP-dependent fashion.