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PubMed2002

High-efficiency solid-phase capture using glass beads bonded to microcentrifuge tubes: immunoprecipitation of proteins from cell extracts and assessment of ras activation.

We have bonded glass microbeads (425-600 microm diameter) to the inner walls of polypropylene microcentrifuge tubes. In addition to increasing the surface area of the tubes manyfold, the beads provide surface Si groups which can be reacted with a silane compound such as aminopropyltriethoxysilane, yielding a free amino group. The amino group is reacted with another cross-linking reagent, for example, the homobifunctional compound dimethyl suberimidate, which can form a covalent bond with amine groups of proteins. After binding protein A or G to the dimethyl suberimidate, the beads were used to immunoprecipitate proteins from cell extracts; we show that the protein A/G-coated glass beads yield similar amounts of immunoprecipitated proteins as a standard method using protein A- or G-agarose beads, but with fewer contaminating proteins. In addition, we show that when immunoprecipitating Ras from cell extracts and measuring the amounts of Ras-bound GTP and GDP, the new method yielded higher guanine nucleotide levels than protein G-agarose beads, suggesting that it caused less denaturation of Ras. Because the glass beads are bonded to the walls of the tubes, the immunoprecipitates can be washed rapidly and efficiently, and we show that 20-30 tubes can be washed in 1/10 the time required to wash immunoprecipitates on protein A- or G-agarose beads.

3T3 Cells↗

PubMed1981

The subunit structure of bovine heart mitochondrial transhydrogenase.

Reaction of purified bovine heart transhydrogenase with bifunctional cross-linking reagents dimethyl adipimidate, dimethyl pimelimidate, dimethyl suberimidate, and dithiobis(succinimidyl propionate) results in the appearance of a dimer band on sodium dodecyl sulfate polyacrylamide gels with no higher oligomers formed. Treatment of the enzyme with 6 M urea led to inactivation and prevented cross-linking by dimethyl suberimidate. Transhydrogenase reconstituted into phosphatidylcholine proteoliposomes also yielded a dimer band on cross-linking. These data indicate that soluble and functionally reconstituted transhydrogenase possesses a dimeric structure.

Animals↗

PubMed1984

Chemical modifications of metallothionein. Preparation and characterization of polymers.

Reaction of rat liver metallothionein-II with two bifunctional cross-linking reagents, glutaraldehyde and dimethyl suberimidate, produces high yields of polymeric species. It is argued that cross-linking is trapping preformed aggregates of the protein, which therefore represent a stabilized quaternary structure of metallothionein. The two polymeric species differ in a number of respects. With dimethyl suberimidate, the polymer retains all metal-binding sites of the monomer, and has an unaltered isoelectric point. Reaction with glutaraldehyde causes loss of one or two Cd2+/Zn2+-binding sites and elevates the pI. Both species are nearly spherical aggregates, in contrast with the highly asymmetrical metallothionein. Both polymers are linked through lysine residues, and the thiol groups remain reduced. The biological significance of these aggregates is discussed.

Amino Acids↗

PubMed1982

Mitochondrial membrane-bound hexokinase of ascites tumor cells. Functional implications of lysine residues studied by modification with imidoesters.

Conformational changes of hexokinase from ascites tumor cells have been studied by chemical modification of lysine residues with imidoesters with the following results: 1) The membrane-bound enzyme, in contrast to the soluble enzyme, is not inactivated by treatment with dimethyl suberimidate, which suggests (a) lysine residue(s) essential for the activity that is protected in the membrane-bound enzyme. 2) Three different conformations have been detected in the membrane-bound enzyme. Two of these are induced by glucose and glucose 6-phosphate, respectively. 3) Treatment of the membrane-bound enzyme with dimethyl suberimidate affects its sensitivity to the inhibition by glucose 6-phosphate, but not its activity or degree of maximal inhibition. This suggests that lysine(s) is related to the binding of glucose 6-phosphate to its allosteric regulatory site. 4) In intact tumor cells, most, if not all, of the hexokinase activity seems to be in a membrane-bound form.

Allosteric Regulation↗

PubMed1979

Topographical studies on poliovirus capsid proteins by chemical modification and cross-linking with bifunctional reagents.

Poliovirus capsid proteins comprise 15.1 lysines in VP1, 5.6 lysines in VP2, 11.7 lysines in VP3 and 5.5 lysines in VP4. Treatment with monofunctional reagent N-succinimidyl 2,3-3H-proprionate leads to the modification of 3.4 lysines in VP1, 0.6 lysines in VP2, 2.0 lysines in VP3 and 0.03 lysines in VP4. Chemical modification with the monofunctional reagent N-succinimidyl 3-(4-hydroxy,5-125I-iodophenyl)propionate results in a predominant labelling of VP1 and VP3, whereas VP2 is less accessible and VP4 is not modified. Cross-linking of poliovirus with bifunctional imidoesters, dimethyl suberimidate (DMS, 1.1 nm) and dimethyl adipimidate (DMA, 0.8 nm) leads to a new protein complex of mol. wt. which corresponds to the sum of VP1 and VP3. By cleavage with ammonia and electrophoresis on polyacrylamide gels in SDS, the proteins are identified as VP1 and VP3. This result gives evidence for a direct neighbourhood of VP1 and VP3 in the virus capsid. Treatment of the virus with the mono- and bifunctional reagents has no influence on the stability of the particle. The infectivity is reduced only by the bifunctional reagent.

Chemical Phenomena↗

PubMed1981

Purification and properties of alanine tRNA synthetase from Escherichia coli A tetramer of identical subunits.

Escherichia coli alanine tRNA synthetase has been purified from a strain which carries the gene on a recombinant pBR322 plasmid. Several per cent of the soluble protein can be obtained as alanine tRNA synthetase in the plasmid containing host cell. The enzyme was proven to be an alpha 4 tetramer with a Mr = 380,000 by the following criteria: i) a single band of Mr = 95,000 was found in sodium dodecyl sulfate gel electrophoresis; ii) gel filtration chromatography gives a single peak at a Mr = 360,000 for the native enzyme; iii) dimethyl suberimidate cross-linking indicates a tetrameric structure; iv) a single undecapeptide N-terminal sequence was found which is Ser-Lys-Ser-Thr-Ala-Glu-Ile-Arg-Gln-Ala-Phe. Limited proteolysis generates a fragment of the native enzyme. The fragment has a Mr = 48,000 (one half that of the native subunit) and, in contrast to the native enzyme, oligomerization of the fragment could be not detected either by gel filtration chromatography or by dimethyl suberimidate cross-linking. The fragment is derived from the NH2-terminal half of the native subunit as shown by their common decapeptide NH2-terminal amino acid sequences. The ATP-PPi exchange activity of 1 mol of fragment is identical with that of 1 mol of native subunit, but aminoacylation activity is absent from the fragment. Therefore, in the fragment, the aminoacyl adenylate formation activity is cleanly separated from tRNA aminoacylation and subunit association properties. These results also mean that, with respect to aminoacyl adenylate formation activity, each subunit in the native tetramer acts independently.

Alanine-tRNA Ligase↗

PubMed1982

Quaternary structure of assimilatory NADH:nitrate reductase from Chlorella.

Gel chromatography experiments over a wide range of protein concentrations showed that Chlorella nitrate reductase is a nonassociating protein with a Stokes radius of 81 A. Sedimentation equilibrium of nitrate reductase in H2O-D2O solvents yielded a partial specific volume of 0.800 +/- 0.014 (n = 12) and a Mr = 360,000 +/- 25,000. No lipid was found associated with nitrate reductase. Cross-linking with the bifunctional reagent, dimethyl suberimidate, and subsequent separation of products by sodium dodecyl sulfate-polyacrylamide gel electrophoresis yielded four protein-staining bands in which the molecular weights of the cross-linked products were integral multiples of the monomeric molecular weight (90,000). Extensive cross-linking of the enzyme resulted in one principal protein-staining band of 360,000, corresponding to a tetramer. The cross-linked tetramer of nitrate reductase appeared to have identical physical properties as the native enzyme. The cross-linking pattern produced by reaction with dimethyl suberimidate suggested that nitrate reductase is an isologous tetramer which has at least two different types of bonding domains. Gel filtration, sedimentation equilibrium, and density gradient experiments at very low enzyme concentrations indicated that nitrate reductase dissociates to a species with a Stokes radius of 54 A, s20.w of 7.1, and Mr = approximately 200,000 at these low enzyme concentrations. No change in specific activity of the enzyme was observed over this concentration range. Treatment of nitrate reductase with trypsin or with cyanogen bromide yielded the number of peptides expected for identical subunits. From these results, it is concluded that Chlorella nitrate reductase is a homotetramer with dihedral symmetry ("dimer of dimers").

Chlorella↗

PubMed1986

Polyamine binding sites on Escherichia coli ribosomes.

To determine the binding sites of polyamines on Escherichia coli ribosomes, ribosomal proteins crosslinked with polyamines through bifunctional reagents were analyzed. When 1,5-difluoro-2,4-dinitrobenzene was used as a crosslinking reagent, spermine was bound to S3, S8, S9, L1, L2, L3, L5, L6, L13, L18, L24, and L27 proteins. When dimethyl suberimidate was used, spermine was bound to S1, S3, S4, S5, S7, S8, S9, S15, L1, L2, L3, L6, L18, and L24 proteins. In addition to crosslinking with the above proteins, spermidine, when crosslinked with dimethyl suberimidate, bound to S2, S14, S20, L4, L5, L9, L13, and L16 proteins. The relationship between the binding site(s) of polyamines on ribosomes and the function of polyamines is discussed.

Bacterial Proteins↗

PubMed1976

The functional repressor parts of a tetrameric lac repressor-beta-galactosidase chimaera are organized as dimers.

The chimaeric protein repressor-galactosidase, in which fully active lac repressor is covalently linked to the active enzyme beta-galactosidase, was used as a system for probing the quaternary structure of lac repressor. Electron micrographs revealed repressor-galactosidase to be a tetrameric aggregate. When lac repressor, alone, was crosslinked with dimethyl suberimidate, dimers, trimers, tetramers, and oligomers of the protein subunit were produced, whereas crosslinking of the tetrameric repressor-galactosidase resulted in the production of only dimers of the chimaera. Treatment of lac repressor with iodine resulted in the formation of protein dimers; the same result was obtained with repressor-galactosidase. After limited proteolysis of lac repressor, no crosslinking was obtained after treatment with dimethyl suberimidate, whereas iodine still produced a covalent linkage. These results are interpreted as evidence that the lac repressor parts of the tetrameric repressor-galactosidase-chimaera are organized as dimers on the tetrameric-beta-galactosidase core. Because this chimaera has been previously shown to have normal repressor activity [B. Müller-Hill and J. Kania (1974) Nature, 249,561-563], we conclude that lac repressor still is biologically active as a dimeric aggregate.

Bacterial Proteins↗

PubMed1980

Methylamine dehydrogenases of Methylomonas J and Pseudomonas AM1. Hybridization of light and heavy subunits and some properties of an isolated hybrid enzyme.

Hybridization reactions were carried out in vitro between the light and heavy subunits of two methylamine dehydrogenases obtained from Methylomonas J (formerly Pseudomonas sp. J) and Pseudomonas AM1. Enzymatic activity was restored with a combination of L3(MW: 13,000) and HA(MW: 40,000) but not with LA(MW: 13,000) and HJ(NW: 40,000). This active hybrid enzyme was isolated with a Sephadex G-150 column after incubation of LJ and HA. Its molecular weight was nearly identical to that of the two native enzymes (MW: 105,000). The electrophoretic pattern of proteins cross-linked by dimethyl suberimidate showed the formation of a tetrameric structure. Its absorption spectrum was similar to that of the native enzymes. The specific activity was 4.3 and the substrate specificity resembled that of the Methylomonas J enzyme rather than that of the Pseudomonas AM1 enzyme. Michaelis constants were 290 microM for methylamine and 14 microM for phenazine methosulfate. The circular dichroism spectrum and thermal stability resembled those of the Pseudomonas AM1 enzyme. No appreciable amount of an inactive hybrid enzyme was formed in the reaction between LA and HJ, there being neither restoration of the enzymatic activity nor formation of cross-linked tetrameric proteins with dimethyl suberimidate. Hybridization of LJ and HA was further confirmed by the appearance of three enzymatic active bands on a gel after electrophoresis of an incubation mixture of LJ, HJ, and HA. The results are consistent with a previous observation; the two methylamine dehydrogenases from either obligate of facultative metaylotrophs are the alpha 2 beta 2-type and homologous enzymes. It is also suggested that substrate specificity and catalytic activity are directed by the light subunit, and binding affinity of the substrate to the active site, electrophoretic mobility, and thermal stability of the enzyme are endowed by the heavy subunit.

Kinetics↗

PubMed1983

Cross-linking study on skeletal muscle actin: interaction of suberimidate-treated actin with deoxyribonuclease I.

We have recently reported that actin modified with dimethyl suberimidate takes a filamentous form even under depolymerizing conditions, and this phenomenon is accounted for by the conformational fixation caused by the introduction of an intramolecular cross-link (Ohara, O., Takahashi, S., Ooi, T., & Fujiyoshi, Y. (1982) J. Biochem. 91, 1999-2012). The suberimidate-treated actin (SA) is not immediately depolymerized by deoxyribonuclease I (DNase I) but is depolymerized after incubation for one day, i.e., depolymerization is much slower than that for intact F-actin. The results on circular dichroic spectra of a mixture of SA and DNase I suggest that DNase I flips the conformation of SA into a G-actin-like state from the F-actin-like one when a tight SA-DNase I complex is formed. The suberimidate cross-link introduced in an SA molecule does not completely prevent the conformational change from the F-state to the G-state but stabilizes the actin conformation very greatly in the F-state.

Actins↗

PubMed1988

Modification of sodium and gating currents by amino group specific cross-linking and monofunctional reagents.

To test the possible role of lysine residues in Na channel function the effects of several imidoesters on Na and gating currents were studied in voltage-clamped single frog nerve fibers. Mono- and bisimidoesters were used. These reagents modify amino groups exclusively and do not change the net charge. The three bisimidoesters used easily introduce cross-links between neighboring amino groups. Their structure is almost identical; only the length of the spacers between the two amino-reactive groups is different. An irreversible reduction of Na currents and gating currents was observed with the longest (dimethyl suberimidate [DMS]) and the shortest (dimethyl adipimidate [DMA]) of the cross-linkers used. Of the three cross-linking reagents only the shortest made Na current inactivation slow and incomplete. The steady-state inactivation curve, h infinity (E), was shifted by greater than 25 mV in the hyperpolarizing direction by each of the reagents. The voltage dependence of activation, however, remained unchanged. Furthermore, the effects of two different monoimidoesters (ethyl acetimidate [EAI] and isethionyl acetimidate [IAI]) on gating currents were tested. EAI can penetrate a membrane, whereas IAI is membrane impermeant. IAI was almost without effect, whereas EAI caused a considerable reduction of the gating currents. EAI and DMS reduced the Qoff/Qon ratio without affecting the decay of the Na currents. The results show that lysine residues are critically involved in Na channel gating.

Animals↗

PubMed1979

Identification of suberimidate cross-linking sites of four histone sequences in H1-depleted chromatin. Histone arrangement in nucleosome core.

The arrangement of 8 histones in the nucleosome core has been investigated by identifying the sites of 4 histone sequences cross-linked with a bifunctional amino-group reagent, dimethyl suberimidate, selected from among 4 diimidoesters of various linker lengths examined. H1-depleted calf thymus chromatin was allowed to react with 14C-labeled suberimidate at pH 8.5 and 0 degrees C. The cross-linked chromatin was then digested exhaustively with trypsin. Almost all the histone fragments were released from the chromatin with 0.25 M HCl and chromatographed on several columns and on paper. Cross-linked peptides were detected by analyzing the content of radioactive suberimidoylbislysine after acid hydrolysis. The chromatographic procedure developed here showed that the whole histone fragments contained 29 mol% of the total linked reagent as suberimidoylbisylsine. The 5 finally purified cross-linked peptides were identified from the total and N-terminal amino acids of each pair of peptides separated by two-dimensional cellulose thin layer chromatography after cutting the linker by ammonolysis. Thus, intramolecular cross-linking was found between Lys-5 and Lys-9 of H2A, and Lys-34 and Lys-85 of H2B, while intermolecular cross-linking was found between Lys-24 (or 27) of H2B and Lys-74 of H2A, Lys-85 of H2B and Lys-91 of H4, and Lys-120 of H2B and Lys-115 of H3 and/or Lys-77 of H4. Most of these lysine residues are located in the DNA-binding segments of the 4 histone sequences identified previously [Kato, Y. & Iwai, K, (1977) J. Biochem. 81, 621--630]. All the 5 or 6 cross-links can be located in a heterotypic tetramer consisting of one molecule each of H2A, H2B, H3, and H4, and a model of the histone arrangement in the tetramer is proposed. Two such tetramers may compose to the histone octamer in the nucleosome core.

Amino Acids↗

PubMed1997

The quaternary geometry of transcription termination factor rho: assignment by chemical cross-linking.

Transcription termination factor rho from Escherichia coli is a ring-shaped homohexamer of 419 amino acid subunits and catalyzes an ATP-dependent release of nascent RNA transcripts. Previous chemical cross-linking studies suggested that the rho hexamer might have D3 symmetry with three isologous dimers as protomers. However, our recent mutational analysis of rho alongside its putative structural homology to F1-ATPase rather argued for C6 symmetry. To resolve this discrepancy, we have re-investigated the pattern of cross-linking of rho using various cross-linkers with different functional groups and spacer lengths. Upon reaction with dimethyl suberimidate followed by SDS-polyacrylamide gel electrophoresis, rho protein generated a series of cross-linked oligomers up to hexamers, of which dimers migrated as distinct doublet bands of approximately equal intensities. However, the lower band became much stronger than the upper one with dimethyl adipimidate and difluorodinitrobenzene, and vice versa with disuccinimidyl glutarate, disuccinimidyl suberate and disulfosuccinimidyl tartarate. Furthermore, the trimeric products also produced doublet bands, whose relative intensities were again variable with cross-linkers, but in an inverse correlation with those of the dimer bands. These results combined with theoretical considerations support a C6 symmetry model in which cross-linking is assumed to occur stochastically at one of two alternative sites within each subunit interface with variable relative frequencies depending on cross-linkers. The D3 symmetry is excluded, for the putative trimeric subspecies should always retain mutually equal intensities in that case. Detailed inspections of the cross-linking kinetics further revealed a moderate characteristic of C3 symmetry for the rho hexamer such that the collective as well as relative rates of cross-linking at the two available sites could fluctuate between alternating interfaces. The final model designated as C3/6 is also compatible with other functional and structural properties known for rho.

Cross-Linking Reagents↗

PubMed1983

Chemical cross-linking of cyclic AMP-dependent protein kinase and its dissimilar subunits.

Previous kinetic studies have demonstrated that the activation of cyclic AMP-dependent protein kinase by cyclic AMP involves the formation of a ternary complex of cyclic AMP, the regulatory subunit (R) and the catalytic subunit (C). It is suggested that only this ternary complex breaks down to liberate the enzymically active catalytic subunit. We have performed cross-linking experiments with the holoenzyme and its dissimilar subunits in the presence of MgATP and various concentrations of cyclic AMP. Results from these cross-linking studies indicate that regulatory subunits exist as dimers in the native form. Moreover, dissociation of the holoenzyme or the reconstituted enzyme is promoted by cyclic AMP, and the effect of MgATP is to stabilize the enzyme in the tetrameric form. The success in cross-linking the regulatory and the catalytic subunits of protein kinase with the lysine-specific bifunctional cross-linking reagent dimethyl suberimidate may be attributed to the presence of a large number of lysine residues in the enzyme.

Adenosine Triphosphate↗

PubMed1996

The membrane-bound rat serotonin transporter, SERT1, is an oligomeric protein.

The synaptic actions of the neurotransmitter serotonin are terminated by a selective re-uptake system located in the axonal membrane. To gain information about the quaternary structure of this membrane protein, we transiently expressed the recombinant rat serotonin transporter, SERT1, in human embryonic kidney 293 cells. Treatment with sulfhydryl oxidizing agents and the homobifunctional cross-linker dimethyl suberimidate (DMS) generated adducts of 130-180 kDa and 220-270 kDa, respectively. These data indicate an oligomeric structure of SERT1.

Animals↗

PubMed1978

Purification and properties of glutamate synthase and glutamate dehydrogenase from Bacillus megaterium.

Bacillus megaterium N.C.T.C. no. 10342 exhibits glutamate synthetase (EC 2.6.1.53) and glutamate dehydrogenase (EC 1.4.1.4) activities. Concentrations of glutamate synthase were high when the bacteria were grown on 3mM-NH4Cl and low when they were grown on 100mM-NH4Cl, whereas glutamate dehydrogenase concentrations were higher when the bacteria were grown on 100mM-NH4Cl than on 3mM-NH4Cl. Glutamate synthase and glutamate dehydrogenase were purified to homogeneity from B. megaterium grown in 10mM-glucose/10mM-NH4Cl. The purified enzymes had mol.wts. 840000 and 270000 for glutamate synthase and glutamate dehydrogenase respectively. The Km values for substrates with NADPH and coenzyme were (glutamate synthase activity shown first) 9 micron and 360 micron for 2-oxoglutarate, 7.1 micron and 8.7 micron for NADPH, and 0.2 mM for glutamine and 22 mM for NH4Cl, similar values to those of enzymes from Escherichia coli. Glutamate synthase contained NH3-dependent activity (different from authentic glutamate dehydrogenase), which was enhanced 4-fold during treatment at pH 4.6 NH3-dependent activity was generally about 2% of the glutamine-dependent activity. Amidination of glutamate synthase by the bi-functional cross-linking reagent dimethyl suberimidate inactivated glutamine-dependent glutamate synthase activity, but increased NH3-dependent activity. A cross-linked structure of mol.wt. approx 200000 was the main product formed.

Amino Acids↗

PubMed1978

Molecular characteristics of the transferrin-receptor complex of the rabbit reticulocyte.

A macromolecular complex of transferrin and a membrane component was isolated by gel filtration chromatography from Triton X-100-solubilized ghosts of reticulocytes previously incubated with 125I-labeled transferrin. This complex is believed to be transferrin specifically associated with its primary receptors. Following the procedures of Clark [14], the complex in Triton X-100 was found to behave as an asymmetric molecule with a molecular weight of approximately 250,000 and an axial ratio of 9:1. On SDS-poly-acrylamide gel electrophoresis the complex displays, in addition to transferrin, components of molecular weights 176,000 and 95,000, respectively. The larger component may be a dimer of the smaller. Each appears to crosslink, with dimethyl suberimidate, to transferrin. These results are compatible with the hypothesis that the transferrin receptor itself has a molecular weight near 175,000 and may be a dimer of two smaller components each of molecular weight near 95,000.

Animals↗