Stepwise disassembly and apparent nonstepwise reassembly for the oligomeric RbsD protein

Many cellular proteins exist as homo-oligomers. The mechanism of the assembly process of such proteins is still poorly understood. We have previously observed that Hsp16.3, a protein exhibiting chaperone-like activity, undergoes stepwise disassembly and nonstepwise reassembly. Here, the disassembly and reassembly of a nonchaperone protein RbsD, from Escherichia coli, was studied in vitro. The protein was found to mainly exist as decamers with a small portion of apparently larger oligomeric forms, both of which are able to refold/reassemble effectively in a spontaneous way after being completely unfolded. Disassembly RbsD intermediates including pentamers, tetramers, trimers, dimers, and monomers were detected by using urea-containing pore gradient polyacrylamide gel electrophoresis, while only pentamers were detected for its reassembly. The observation of stepwise disassembly and apparent nonstepwise reassembly for both a chaperone protein (Hsp16.3) and a nonchaperone protein (RbsD) strongly suggests that such a feature is most likely general for homo-oligomeric proteins.     

Leu122对Hsp16.3组装过程中亚基相互作用的影响

小分子热休克蛋白是种类最多的热休克蛋白家族 ,它们均以寡聚体的形式存在 .研究表明 ,来自结核杆菌的小分子热休克蛋白Hsp16 3是以 3个三聚体的形式存在的九聚体 .为了探讨Hsp16 3体外组装过程中的亚基相互作用和识别 ,利用野生型Hsp16 3及其L12 2A突变体蛋白为模型 ,采用高效液相分子筛层析、非变性聚丙烯酰胺凝胶电泳和脲梯度凝胶电泳等方法进行研究 .结果表明 ,Hsp16 3在体外能自发地再组装成九聚体 .12 2位的亮氨酸残基对Hsp16 3体外再组装过程中的亚基相互作用有重要的影响 ,并且在Hsp16 3的组装过程中 ,亚基之间的相互识别是高度灵敏和特异的 ,野生型蛋白的亚基和L12 2A突变体蛋白的亚基并不能形成杂合体 ,只有完全相同的亚基才能组装成九聚体     

Electrophoretic analysis of the unfolding of proteins by urea.

The unfolding of several proteins by urea has been followed by electrophoresis of a band of protein through a slab gel of polyacrylamide in which there was a gradient of urea concentration perpendicular to the direction of electrophoresis. Unfolding was invariably manifested by a marked reduction of mobility, presumably due to molecular sieving of the expanded polypeptide chain by the polyacrylamide gel. The procedure provides a continuous two-dimensional pattern of the effect of urea on the shape of the protein and is especially sensitive to microheterogeneity of the protein.Experiments with pancreatic trypsin inhibitor, ribonuclease, lysozyme, chymotrypsin, chymotrypsinogen, staphylococcal nuclease, and cytochrome c were consistent with the results of others using orthodox methods and confirm the validity of the method. Where unfolding occurred, it was generally rapidly reversible and the curves were entirely consistent with the presence of only the native and the fully unfolded states. Serum albumin gave more complex curves and a remarkable illustration of micro-heterogeneity. β-Lactoglobulins A and B and ovalbumin refold very slowly and the unfolded molecules appeared to equilibrate preferentially with compact, but non-native, forms at low urea concentrations.     

The subunit interface of the Escherichia coli ribosome: Identification of proteins at the interface between the 30 S and 50 S subunits by crosslinking with 2-iminothiolane

The 70 S ribosomes of Escherichia coli were treated with 2-iminothiolane with the resultant addition of 110 sulfhydryl groups per ribosome. The modified ribosomes were oxidized to promote disulfide bond formation, some of which formed intermolecular crosslinks. About 50% of the crosslinked 70 S ribosomes did not dissociate when exposed to low concentrations of magnesium in the absence of reducting agent. Dissociation took place in the presence of reducing agents, which indicated that the subunits had become covalently linked by disulfide linkages. Proteins extracted from purified crosslinked 70 S ribosomes were first fractionated by polyacrylamide/urea gel electrophoresis. The proteins from sequential slices of these gels were analyzed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Monomeric proteins derived from crosslinked dimers appeared below the diagonal containing non-crosslinked proteins, since the second electrophoresis, but not the first, is run under reducing conditions to cleave the crosslinked species. Final identification of the proteins in each dimer was made by radioiodination of the crosslinked proteins, followed by two-dimensional polyacrylamide/urea gel electrophoresis in the presence of non-radioactive total 70 S proteins as markers. This paper describes the identification of 23 protein dimers that contained one protein from each of the two different ribosomal subunits. The proteins implicated must have some part of their structure in proximity to the other ribosomal subunit and are therefore defined as “interface proteins”. The group of interface proteins thus defined includes 50 S proteins that are part of the 5 S RNA: protein complex and 30 S proteins at the initiation site. Correlations between the crosslinked interface proteins and other functional data are discussed.     

The subunit interface of the Escherichia coli ribosome. Crosslinking of 30 S protein S9 to proteins of the 50 S subunit.

Purified 50 S ribosomal subunits were found to contain significant amounts of protein coincident with the 30 S proteins S9 and/or S11 on two-dimensional polyacrylamide/urea electropherographs. Peptide mapping established that the protein was largely S9 with smaller amounts of S11. Proteins S5 and L6 were nearly coincident on the two-dimensional polyacrylamide/urea electropherographs. Peptide maps of material from the L6 spot obtained from purified 50 S subunits showed the presence of significant amounts of the peptides corresponding to S5. Experiments in which ³⁵S-labelled 30 S subunits and non-radioactive 50 S subunits were reassociated to form 70 S ribosomes showed that some radioactive 30 S protein was transferred to the 50 S subunit. Most of the transferred radioactivity was associated with two proteins, S9 and S5. Sulfhydryl groups were added to the 50 S subunit by amidination with 2-iminothiolane (methyl 4-mercaptobutyrimidate). These were oxidized to form disulfide linkages, some of which crosslinked different proteins of the intact 50 S ribosomal subunit. Protein dimers were partially fractionated by sequential salt extraction and then by electrophoresis of each fraction in polyacrylamide gels containing urea. Slices of the gel were analysed by two-dimensional polyacrylamide/sodium dodecyl sulfate diagonal gel electrophoresis. Final identification of the constituent proteins in each dimer by two-dimensional polyacrylamide/urea gel electrophoresis showed that 50 S proteins L5 and L27 were crosslinked to S9. The evidence suggests that proteins S5, S9, S11, L5 and L27 are located at the interface region of the 70 S ribosome.     

Identification of neighboring protein pairs in the Escherichia coli 30 S ribosomal subunit by crosslinking with methyl-4-mercaptobutyrimidate

The 30 S ribosomal subunits of Escherichia coli were treated with methyl-4-mercaptobutyrimidate and oxidized to promote the formation of intermolecular disulfate bonds between neighboring proteins. Attention was focused on protein dimers, which were partially purified either by stepwise extraction of the 30 S particle with LiCl or by polyacrylamide/urea gel electrophoresis of the total crosslinked protein. Protein fractions were then analyzed by polyacrylamide/ sodium dodecyl sulfate diagonal gel electrophoresis. Final identification of the components of crosslinked protein pairs, indicated by molecular weight analysis, was accomplished by two-dimensional polyacrylamide/urea gel electrophoresis. The identification of 21 protein pairs is presented, 14 of which have not been reported previously.     

Isolation of outer membrane proteins of Escherichia coli and their characterization on polyacrylamide gel

Proteins from the outer membrane of Escherichia coli were studied on a ureadodecyl sulfate polyacrylamide gel by electrophoresis. A polyacrylamide gel containing sodium dodecyl sulfate and urea gave an excellent resolution of outer membrane proteins. Seventeen protein bands were reproducibly observed on a gel. By use of Sephadex G-200, DEAE-cellulose and polyacrylamide gel, eight proteins were purified to near homogeneity. Five of them were found to be heat-modifiable proteins. The behavior of these purified proteins was studied on a polyacrylamide gel under three different electrophoretic conditions, which had been used for the analysis of cell envelope proteins. Thus correspondence was made between these purified proteins and envelope proteins reported by other investigators.     

Effect of "stacking" on the resolving power of ultrathin-layer two-dimensional gel electrophoresis

The resolving power of two-dimensional ultrathin-layer polyacrylamide gel electrophoresis with and without "stacking" was investigated. Side-by-side analysis shows that the use of a properly adjusted upper gel improves the resolution and reproducibility of this sensitive analytical method. The effects of various detergents (Nonidet-P40, Zwittergent, urea) on the ultrathin-layer polyacrylamide gel electrophoresis were also investigated. For this case, whole cell proteins of Pseudomonas aeruginosa and Staphylococcus aureus treated with different detergents were electrofocused in the presence of the same detergents.     

Isolation of a stable tetramer of the low molecular weight component of neurofilaments (NF-L)

When crude neurofilaments were dissolved in a solution containing 8 M urea and 1% beta-mercaptoethanol (beta-ME), the component proteins of the neurofilaments and other contaminating filaments were solubilized into monomeric forms. However, when reassembled filaments were solubilized again by the addition of urea to 8 M without beta-ME, several bands which seemed to be oligomeric forms of filament proteins were observed on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Among them, a band which appeared between microtubule-associated protein-1 (MAP-1) and fodrin was most remarkable. This band was also observed when a triplet mixture of the neurofilaments (NF-H, NF-M, NF-L) was reassembled. The molecular weight of this band was estimated to be 280 kDa. In addition, much of this component was easily isolated on DE-52 column chromatography of the reassembled crude neurofilament proteins with buffers containing 6 M urea, while the low molecular weight component of the neurofilaments (NF-L, 70 kDa) was hardly detected. Furthermore, the isolated 280 kDa component was reduced to NF-L on the addition of beta-ME to 1%. In contrast, the 280 kDa component was produced on dialysis of isolated NF-L against the assembly buffer. From these results, it is deduced that this component is the stable tetramer of NF-L which is produced through spontaneous interchain disulfide formation among protofilament tetramers.     

Analysis of rat serum apolipoproteins by isoelectric focusing. I. Studies on the middle molecular weight subunits.

Analytical isoelectric focusing (IEF) has been applied to the study of the apolipoprotein components of rat serum high density and very low density lipoproteins. The apolipoproteins were separated on 7.5% polyacrylamide gels containing 6.8% urea, with a pH gradient of 4-6. The middle molecular weight range apolipoproteins were identified on IEF gels by the use of apolipoproteins purified by electrophoresis on gels containing sodium dodecyl sulfate (SDS). The A-1 protein focused as 4 to 5 bands from pH 5.46 to 5.82; the A-IV protein and the arginine-rich protein each focused as 4 to 6 bands from pH 5.31 to 5.46. The low molecular weight proteins focused from pH. 4.43 to 4.83 and are the subject of a separate communication. Comparisons of the IEF method with SDS gel electrophoresis, polyacrylamide gel electrophoresis in urea, and Sephadex chromatography are also reported. Additional studies were also carried out that tend to rule out carbamylation or incomplete unfolding of the proteins in the presence of urea as the causes of the observed heterogeneity.     

Constitutive HSP70: oligomerization and its dependence on ATP binding.

The constitutive HSP70 purified from CHO cells, which indicated a single band in SDS-polyacrylamide gel electrophoresis, showed multiple bands in native-polyacrylamide gel electrophoresis. These results indicate that the protein may exist in oligomeric forms. After crosslinking the oligomers with glutaraldehyde, SDS-polyacrylamide gel electrophoresis showed three protein bands of molecular weight 70 kDa, 153 kDa, and 200 kDa corresponded to monomer, dimer, and trimer, respectively. The relative amount of oligomeric forms was dependent upon ATP concentrations: it increased upon hydrolysis of ATP or decreased upon incubation with high concentrations of ATP (1-10 mM). Autoradiographic analysis of the native polyacrylamide gel electrophoresis of HSP70 following incubation with [gamma-32P]ATP revealed that ATP bound to only monomer. These results suggest that the equilibrium between oligomeric forms is dependent on ATP concentrations. Nonetheless, during heat shock, both monomer and oligomer might be indistinguishably associated with some proteins, probably denatured proteins.     

Unique Protein Moieties for 30S and 50S Ribosomes of Escherichia coli

Each major component of the proteins of 30S ribosomes from Escherichia coli was compared with the proteins of 50S ribosomes. The comparisons were done by using polyacrylamide gel electrophoresis in urea with differentially labeled proteins. The data show that no major protein is common to both ribosomes.     

Slab gel electrophoresis of oligomeric proteins under high hydrostatic pressure. I. Description of the system and demonstration of the pressure dissociation of a dimer

A high-pressure bomb was constructed to study the gel electrophoretic behavior of oligomeric proteins under pressure. The apparatus designed by us allows the use of a polyacrylamide slab gel with a capacity of up to 12 wells, therefore permitting the study of several samples in one experiment. The electrophoresis mobility of different single-chain proteins under pressure decreased in the same proportion and the elution pattern was similar to that of the control run at atmospheric pressure. Densitometric analysis of the gel did not show peak spread or asymmetric boundaries, indicating that their conformations were not drastically affected. On the other hand, high-pressure electrophoresis of a dimer, the tryptophan synthase beta 2 subunit, revealed the appearance of a second peak not present at atmospheric pressure. The mobility of the second peak was higher and its fraction increased by decreasing the protein concentration, indicating that the extra peak was the dissociated monomer. The separation under pressure occurs without drastic effects on the tertiary structure of the protein, which seems to furnish a method to study dissociation processes and to separate the constituent polypeptides of oligomeric complexes.     

Two-dimensional gel electrophoresis to separate large RNA molecules such as messenger RNAs

This paper describes a two-dimensional gel electrophoresis method for separating large RNA molecules such as messenger RNAs. RNAs were at first separated on a polyacrylamide plus agarose composite gel and subjected to a second dimension electrophoresis on a polyacrylamide gel containing urea. This method is illustrated by analyses of poly(A)+ yeast RNAs. About 80 discrete spots were detected on the gel, when RNAs from 1000 to 3500 nucleotides in size were examined.     

Dimerization and oligomerization of the chaperone calreticulin.

The chaperone calreticulin is a highly conserved eukaryotic protein mainly located in the endoplasmic reticulum. It contains a free cysteine SH group but does not form disulfide-bridged dimers under physiological conditions, indicating that the SH group may not be fully accessible in the native protein. Using PAGE, urea gradient gel electrophoresis, capillary electrophoresis and MS, we show that dimerization through the SH group can be induced by lowering the pH to 5-6, heating, or under conditions that favour partial unfolding such as urea concentrations above 2.6 m or SDS concentrations above 0.025%. Moreover, we show that calreticulin also has the ability to self-oligomerize through noncovalent interactions at urea concentrations above 2.6 m at pH below 4.6 or above pH 10, at temperatures above 40 degrees C, or in the presence of high concentrations of organic solvents (25%), conditions that favour partial unfolding or an intramolecular local conformational change that allows oligomerization, resulting in a heterogeneous mixture of oligomers consisting of up to 10 calreticulin monomers. The oligomeric calreticulin was very stable, but oligomerization was partially reversed by addition of 8 m urea or 1% SDS, and heat-induced oligomerization could be inhibited by 8 m urea or 1% SDS when present during heating. Comparison of the binding properties of monomeric and oligomeric calreticulin in solid-phase assays showed increased binding to peptides and denatured proteins when calreticulin was oligomerized. Thus, calreticulin shares the ability to self-oligomerize with other important chaperones such as GRP94 and HSP90, a property possibly associated with their chaperone activity.     

Identification of a distinct 9S form of soluble clathrin in cultured cells and tissues

We have used a monoclonal antibody (CHC5.9) to identify clathrin (Mr 180,000; 'heavy chain') in coated vesicles, triskelion structures prepared in vitro and in high-speed supernatants (HSS) of cell homogenates from a variety of tissues and species (e.g., brain and liver from rat, cow and man; Xenopus ovaries). HSS proteins were subjected to sucrose density gradient centrifugation and gel filtration, and the fractions obtained were assayed for clathrin by enzyme-linked immunosorbent assay (ELISA) and polyacrylamide gel electrophoresis (PAGE), followed by immunoblotting. The native soluble clathrin identified in such fractions was indistinguishable from triskelions produced in vitro from purified bovine brain clathrin by several criteria, e.g. by its sedimentation coefficient (9S) and elution profile on gel filtration using Sephacryl S 300. No other major forms of soluble clathrin were detected. The results indicate that cells contain a soluble pool of clathrin and that the predominant molecular form of this soluble clathrin has properties similar to those of the triskelion obtained by dissociation studies in vitro. We hypothesize that this distinct 9S form represents a major oligomeric subunit involved in assembly and disassembly of clathrin polyhedron coats in the living cell.     

Bulk Preparation of CNS Cytoskeleton and the Separation of Individual Neurofilament Proteins by Gel Filtration: Dye-Binding Characteristics and Amino Acid Compositions

Abstract: The three major proteins of mammalian neurofilaments, of molecular weight 70,000, 160,000, and 210,000, have been resolved by sodium dodecyl sulfate (SDS)-polyacrylamide gel eJectrophoresis, and more recently, by ion-exchange chromatography in urea solution. We describe here a method to separate the neurofilament proteins by gel filtration without the use of SDS. A bulk preparation of cytoskeleton from rat spinal cord was first characterized. This preparation was then solubilized in a buffer containing 8 M urea and subjected to gel filtration. Individual neurofilament proteins, in milligram quantities, were harvested following the pooling of appropriate fractions. Gel electrophoresis showed a high degree of homogeneity in each of the three pooled fractions. Dye binding studies demonstrated that the protein of molecular weight 210,000 was relatively underrepresented when stained with Coomassie Blue, while all three neurofilament proteins showed similar dye binding properties with Fast Green. Amino acid analysis indicated that (1) all three neurofilament proteins contained a high content of acidic residues; (2) the molecular weight 210.000 protein contained >8 mol% proline; and (3) no simple oligomeric relationship existed among the neurofilament triplets.     

Chemical alterations in cell envelopes of polymyxin-resistant Pseudomonas aeruginosa isolates.

Cell envelopes from Pseudomonas aeruginosa strains resistant to polymyxin were compared with cell envelopes from polymyxin-sensitive strains as to their content of total protein, carbohydrate, and 2-keto-3-deoxyoctonate and as to their protein composition as determined by slab polyacrylamide gel electrophoresis. The cell envelopes of the polymyxin-resistant strains had reduced amounts of lipopolysaccharide, as indicated a reduction in both carbohydrate and 2-keto-3-deoxyoctonate concentrations, and a greatly altered protein composition as shown by polyacrylamide gel electrophoresis. There was a quantitative increase in total cell envelop protein in these strains. However, those protein bands identified as being major outer membrane proteins upon polyacrylamide gel electrophoresis of separated outer and cytoplasmic membranes were reduced greatly in concentration in the polymyxin-resistant cell envelopes. Thus, it appears that polymyxin resistance in these strains is associated with the alteration of the outer membrane through a loss of lipopolysaccharide and outer membrane proteins.     

Sequential two-dimensional and acetic acid/urea/Triton X-100 gel electrophoresis of proteins

A method is described which combines the resolving power of two-dimensional gel electrophoresis with that of acetic acid/urea/Triton X-100 gel electrophoresis, avoiding the necessity of eluting protein from the gels at any step of the procedure. The combination of electrophoretic separation on the basis of charge, mass, and hydrophobic properties of the proteins has the potential of resolving modified forms and isoforms present in very complex protein populations. The technique can be used for analytical purposes, or it may be scaled up to yield microgram amounts of highly purified proteins. The resolution obtained by tandem application of nonequilibrium pH gradient electrophoresis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and polyacrylamide gel electrophoresis in the presence of nonionic detergent was evaluated using crude nuclear proteins of the nematode Caenorhabditis elegans.     

Inter-subunit Cross-linking Suppressed the Dynamic Oligomeric Dissociation of Mycobacterium tuberculosis Hsp16.3 and Reduced Its Chaperone Activity

Small heat shock proteins (sHsps) usually exist as dynamic oligomers and oligomeric dissociation was believed to be a prerequisite for their chaperone activities. The truth of this hypothesis was verified in our present study on Hsp16.3, one member of sHsps from Mycobacterium tuberculosis, mainly by utilizing chemical cross-linking. Analysis using size exclusion chromatography demonstrated that the heat-induced oligomeric dissociation of Hsp16.3 was severely blocked due to highly efficient inter-subunit cross-linkages generated by chemical cross-linking, as well as its chaperone activity being reduced. Further analysis by non-denaturing pore gradient polyacrylamide gel electrophoresis and fluorescence spectrometry revealed that the dynamic oligomeric dissociation/reassociation process of Hsp16.3 at room temperature was suppressed by inter-subunit cross-linkages, accompanied by significantly decreased exposure of hydrophobic surfaces that are usually hidden in oligomers. These findings supported the hypothesis that substrate-binding sites of sHsps are exposed presumably by dissociation of larger oligomers into smaller active oligomers, and therefore such a dissociation process could be adjusted to modulate chaperone activities.