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At least 19 recordsLinked to original sources
PubMed1981

Topography of the C. coli 5S RNA-protein complex as determined by crosslinking with dimethyl suberimidate and dimethyl-3,3'-dithiobispropionimidate.

5S RNA-protein complexes were prepared in vitro using partially purified E. coli 5S RNA and total E. coli 70S ribosomal proteins. The complexes were isolated from sucrose gradients and shown to contain proteins L5, L18, L25 and a fourth protein not heretofore characterized and designed L31. The complexes were treated with the crosslinking reagents dimethyl suberimidate and dimethyl-3,3'-dithiobispropionimidate. Both reagents gave identical patterns of crosslinked proteins when analyzed by one-dimensional polyacrylamide/dodecylsulfate gel electrophoresis. Dimers of L5-L31', L5-L18 and L18-L18 and a trimer containing L5, L18 and L31' were identified by diagonal polyacrylamide/dodecylsulfate gel electrophoresis of the proteins crosslinked with dimethyl-3,3'-dithiobispropionimidate. No crosslinking was detected between L25 and the other three proteins.

Carrier Proteins↗
PubMed1980

Identification of neighboring protein pairs in rat liver 60S ribosomal subunits cross-linked with dimethyl suberimidate or dimethyl 3,3'-dithiobispropionimidate.

Protein-protein neighbors in rat liver 60S ribosomal subunits were investigated by using two bifunctional imidoesters; dimethyl suberimidate (DMS) and dimethyl 3,3'-dithiobispropionimidate (DTP). 1. Complexes cross-linked with DMS were separated by two-dimensional acrylamide/urea gel electrophoresis. Each complex in the gel was labeled with 125I (1) and was cleaved into the original monomeric protein constituents of ammonolysis. The products were analyzed by two-dimensional acrylamide/urea gel electrophoresis, followed by radioautography of the stained gel. Eight protein pairs are proposed according to our numbering system (2): L1-L3(L3-L5), L2-L21 (L4-L26), L5-L13 (L7/L7a-L15), L5-L34 L7/L7a-L36), L6-L34 (L8-L36), L6-L32 (L8-L35), L12-L32 (L13/L13a-L35), and L18-L27 (L18-L27/L27a). The designations according to the proposed uniform nomenclature (3) are given in parentheses. 2. Complexes cross-linked with DTP were analyzed by acrylamide/SDS diagonal gel electrophoresis (4), and the molecular weights of the complexes and their components were determined. The monomer components of cross-linked pairs were labeled with 125I in the gel, and identified by two-dimensional acrylamide/urea gel electrophoresis followed by radioautography. Six pairs are proposed; L1-L5 (L3-L7/L7a), L1-L6 (L3-L8). L5-L19 (L7-/L7a-L21/L23/L23a), L13-L15 (L15-L14), L13-L16 (L15-L19), and L23-L27 (L30-L27/L27a). 3. Two pairs which were formed by protein-protein interaction without the use of cross-linking reagents were identified as L2-L4 (L4-L6) and L4-L30 (L6-L29).

Animals↗
PubMedDate not supplied

Dimethyl suberimidate cross-linking of oligo(dT) to DNA-binding proteins.

Dimethyl suberimidate is a bifunctional reagent that is used for cross-linking the protein components of oligomeric macromolecules. In this report, dimethyl suberimidate is shown to specifically cross-link oligo(dT) of varying lengths to the DNA-binding subunits of a multimeric helicase-primase encoded by herpes simplex virus type 1. This result indicates that dimethyl suberimidate and other imidoester cross-linking reagents may be useful for characterizing the interaction of oligo(dT) with proteins that bind single-stranded DNA.

Cross-Linking Reagents↗
PubMed1998

The accessible surface of the nicotinic acetylcholine receptor. Identification by chemical modification and cross-linking with 14C-dimethyl suberimidate.

To obtain structural information on the nicotinic acetylcholine receptor from Torpedo electric tissue we modified and cross-linked lysine residues with the agonistic bifunctional reagent [14C]dimethyl suberimidate. This reagent labels exposed lysine residues, especially those located near the ligand-binding site, and cross-links lysine residues located not more than 11 A, the length of the cross-linker, apart. Using this method, we identified a cross-link located between betaLys177 and betaLys191 showing that the 13 amino acids in between form a loop with these two residues located at the surface. Cross-linking also occurred between the vicinal lysine residues alphaLys76 and alphaLys77, indicating that these neighbouring lysine residues are not involved in a beta-sheet structure. A total of 21 out of 97 lysine residues present in the receptor were modified by [14C]dimethyl suberimidate. Thus these residues are located on the accessible extramembrane surface. The two lysine residues alphaLys76 and alphaLys179 were predominantly labelled. Because of the agonistic property of [14C]dimethyl suberimidate [Watty, A., Methfessel, C. & Hucho, F. (1997) Proc. Natl Acad. Sci. USA 94, 8202-8209] this might be due to their close proximity to the ligand binding site.

Amino Acid Sequence↗
PubMed1976

Use of dimethyl suberimidate and novel periodate-cleavable bis(imido esters) to study the quaternary structure of the pyruvate dehydrogenase multienzyme complex of Escherichia coli.

Two new symmetrical bis(imido esters), N,N'-bis(2-carboximidoethyl)tartarimide dimethyl ester dihydrochloride and N,N'-bis(2-carboximidomethyl)tartarimide dimethyl ester dihydrochloride, have been synthesized. Tests with the tetrameric enzyme, fructose diphosphate aldolase, show that these reagents closely resemble dimethyl suberimidate in their ability to cross-link protein subunits. However, identification of the cross-linked species, separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis, is greatly facilitated since the cross-links can be broken by a simple treatment with sodium periodate. The periodate cleavage step can be introduced between the two dimensions of a diagonal gel electrophoretic separation, the contributors to a cross-linked species then moving off the diagonal formed by uncross-linked proteins and reverting to the positions in the gel that correspond with their regenerated monomeric form. When the pyruvate dehydrogenase multienzyme complex of Escherichia coli was treated with dimethyl suberimidate or N,N'-bis(2-carboximidoethyl)tartarimide dimethyl ester dihydrochloride, cross-links rapidly formed between the subunits of the transacetylase and lipoamide dehydrogenase components. On the other hand, cross-links failed to form between the subunits of the decarboxylase component themselves, or between the decarboxylase and the other two types of subunit in the complex. Cross-linking experiments with the isolated lipoamide dehydrogenase were compatible with the accepted dimeric structure of this enzyme is free solution, whereas the isolated pyruvate decarboxylase component also failed to cross-link when treated with dimethyl suberimidate in free solution. The cross-linking experiments with the intact multienzyme complex provide evidence for the existence of the lipoamide dehydrogenase dimer in the assembled enzyme and show the need to interpret such experiments with care since, from other evidence, the pyruvate decarboxylase component is known to be bound to the transacetylase "core" of the complex.

Binding Sites↗
PubMed1990

Investigation of the properties of bovine heart creatine kinase cross-linked with dimethyl suberimidate.

Dimeric bovine heart creatine kinase (EC 2.7.3.2, ATP: creatine N-phosphotransferase) has been cross-linked with the bifunctional reagent dimethyl suberimidate at several concentrations to yield modified enzyme with enhanced stability towards heat denaturation. The degree of thermal stability is dependent on the degree of cross-linking with optimal stabilization occurring when approx. half of all the available amino groups are covalently attached to dimethyl suberimidate. Accelerated storage studies were performed and the results used to predict the storage time of the native and modified enzyme at lower temperatures. The cross-linked derivative was predicted to have a longer shelf-life at 4 degrees C than the native enzyme. Modification caused a reduction in the specific activity of the enzyme. The pH profile was altered following cross-linking, but the Michaelis constants were not changed. The modified enzyme exhibited a marked resistance to the action of some denaturing agents.

Animals↗
PubMed1991

Dimethyl suberimidate as an effective crosslinker for antibody-enzyme conjugation.

Dimethyl suberimidate (DMS), a bifunctional reagent was used for the first time to crosslink the alpha-feto protein monoclonal antibodies (AFPMAb) to horse radish peroxidase (HRP). Three batches of conjugates were prepared, purified by Sephadex gel chromatography and evaluated for their immunological reactivity. The Rz values obtained for AFPMAb-HRP conjugate were 0.39 to 1.36. Under optimised conditions the ELISA results showed the optical density of 1.9. The iso-electric focusing for the conjugate revealed different degrees of crosslinking between antibodies and HRP. It was evident that isoperoxidase-C was involved in the crosslinking process. From the dot ELISA, as low as 25 pg of AFP in the test samples could be detected with AFPMab-HRP conjugate. The conjugate prepared by DMS was stable at 0 degrees C for more than 10 months.

Antibodies, Monoclonal↗
PubMed1982

Modifications in the allosteric properties of phosphofructokinase in rat erythrocytes and reticulocytes cross-linked with dimethyl suberimidate and 3,3'-dithiobispropionimidate.

The kinetic behaviour of phosphofructokinase (ATP:D-fructose-6-phosphate 1-phosphotransferase, EC 2.7.1.11) has been studied in situ, by using rat erythrocytes and reticulocytes treated with dimethyl suberimidate and 3,3'-dithiobispropionimidate as cross-linking reagents and with digitonin as the delipidating agent. Comparison of the ATP and fructose-6-P saturation curves of phosphofructokinase in dimethyl suberimidate-permeabilized cells with those obtained in haemolysates showed the enzyme to have reduced allosteric properties under in situ conditions, although it still responded to cyclic AMP (300 microM) added as allosteric effector. Non-sigmoidal fructose-6-P saturation curves were also observed using 3,3'-dithiobispropionimidate-permeabilized erythrocytes, either in the absence or in the presence of cyclic AMP. A hyperbolic behaviour was shown after cross-linking reversal of 3,3'-dithiobispropionimidate-permeabilized erythrocytes by treatment with dithiothreitol. Specific activity values of phosphofructokinase were always lower in permeabilized cells than in haemolysates. A significant inhibition of phosphofructokinase specific activity, without any effect on its allosteric behaviour, is exerted by reaction of dimethyl suberimidate or 3,3'-dithiobispropionimidate with erythrocyte lysates in the presence of an inhibitory concentration of ATP. These results suggest that penetration of the cross-linking reagent and its subsequent reaction with intracellular phosphofructokinase will have a direct effect upon the results obtained using this in situ approach.U

Adenosine Triphosphate↗
PubMed1978

Methylamine dehydrogenases of Pseudomonas sp. J and Pseudomonas AM1. Study on subunit structure by dimethyl suberimidate.

Methylamine dehydrogenase (MW: 105,000) of Pseudomonas sp. J was treated with a bifunctional cross-linking reagent, dimethyl suberimidate. Cross-linked proteins having different molecular -eights of 53,000, 64,000, 80,000, 93,000, and 103,000 were found in addition to 13,000 (light subunit) and 40,000 (heavy subunit) by SDS polyacrylamide gel electrophoresis. Isolated light and heavy subunits were separately treated with the reagent. The product having a molecular weight of 80,000 was found to be a major cross-linked protein for the heavy subunit but no product was found for the light subunit. A similar electrophoretic pattern was also obtained for the reconstituted enzyme from the subunits of Pseudomonas sp. J and for methylamine dehydrogenase of Pseudomonas AM1. These results suggest that methylamine dehydrogenases obtained from these two bacteria are both the alpha2beta2-type subunit enzyme and have a geometrically analogous subunit structure.

Chemical Phenomena↗
PubMed1980

Identification of neighbouring protein pairs in the rat liver 40-S ribosomal subunits cross-linked with dimethyl suberimidate.

(1) The 40-S ribosomal subunits of rat liver were treated with a bifunctional cross-linking reagent, dimethyl suberimidate. Cross-linked protein-protein dimers were separated by two-dimensional acrylamide gel electrophoresis. The stained cross-linked complexes within the gel were radioiodinated without the elution of proteins from the gel and were cloven into the original monomeric protein constituents by ammonolysis. The proteins in each dimer were finally identified by two-dimensional acrylamide gel electrophoresis of the cloven monomeric proteins, followed by radioautography of the stained gel. (2) The molecular weights of cross-linked complexes were determined by SDS-polyacrylamide gel electrophoresis and were compared with those of their constituent proteins. (3) The following dimers were proposed from these results: S3-S12 (S3 or S3a-S11), S4-S12 (S3b-S11, S5-S7 (S4-S6), S5-S22 (S4-S23 or S24), S6-S8 (S5-S7), S8-S16 (S7-S18), S17-S21 (S16--S19) and S22A-S22B (S23-S24), designated according to our numbering system [1]. The designations according to the proposed uniform nomenclature [2] are described in parentheses.

Acetates↗
PubMed1980

Properties of soluble and membrane bound dopamine-beta-monooxygenase from bovine adrenal medulla cross-linked with dimethyl suberimidate.

Bovine dopamine-beta-monooxygenase from chromaffin granules in its soluble and membrane-bound forms was cross-linked with the bifunctional reagent dimethyl suberimidate, and its structural and kinetic properties were studied. 1. The cross-linking reaction does not affect the activity of soluble dopamine-beta-monooxygenase; it produces a ten percent inactivation in the membrane-bound enzyme, possibly because the linkage to other membrane proteins hinders its activity. 2. The soluble dopamine-beta-monooxygenase reaction mixture was analyzed by sodium dodecyl sulfate gel electrophoresis, showing appreciable amounts of dimer and tetramer, but only small amounts of trimer. In membrane-bound dopamine-beta-monooxygenase, subjected to the same treatment, appreciable amounts of dimer and higher aggregates were found. 3. The kinetic properties of soluble dopamine-beta-monooxygenase after the crosslinking reaction are the same as those of the native enzyme, with a ping-pong kinetic mechanism and the same real Michaelis constants for tyramine and ascorbate: KmT = 0.36 mM and KmA = 0.32 mM. Membrane-bound dopamine-beta-monooxygenase does not present a ping-pong mechanism before or after cross-linking; its real Michaelis constants are slightly modified by the cross-linking reaction: KmT = 0.4 mM and KMA = 0.4 mM.

Adrenal Medulla↗
PubMed2001

[Dimethyl suberimidate as a specific inductor of apoptosis in transformed cells].

A modification of protein-protein interactions can be considered to be a way to regulate cell death. Chemical cross-linking agents have been traditionally used for protein complexing. This study has been undertaken to test a possibility to induce and(or) to modify cell death by a homobifunctional cross-linker dimethyl suberimidate (DMS). It was shown that the protein cross-linking by DMS resulted in a death of transformed cells by apoptosis. DMS-induced apoptosis was accompanied by cell cycle perturbations and down-regulation of p21/Waf1 mRNA expression. The RT-PCR analysis of bcl-2 family genes revealed the engagement of mitochondria in DMS-induced cytotoxicity. Then, the influence of DMS treatment on TNF-dependent and Fas-mediated apoptosis was investigated. Cell pre-incubation with DMS resulted in their increasing sensitivity for the TNF cytotoxic effect, though activities of anti-Fas cytotoxic antibodies were inhibited. The effects observed are probably due to cross-linking of TNF-receptors. Thus, this study first demonstrated that a chemical cross-linker DMS in capable of inducing apoptosis in transformed cells and modifying TNF-dependent and Fas-mediated apoptosis.

Animals↗
PubMed1976

Single major polypeptide of a calicivirus: characterization by polyacrylamide gel electrophoresis and stabilization of virions by cross-linking with dimethyl suberimidate.

A calicivirus, San Miguel sea lion virus serotype 4, isolate 15FT, externally labelled with 125I, was shown by gel electrophoresis to possess a single major polypeptide. The polypeptide migrated anomalously upon electrophoresis in two sodium dodecyl sulfate (SDS) systems: more slowly than bovine serum albumin in a continuous phosphate-buffered system and more rapidly than bovine serum albumin in a discontinuous system. Estimated molecular weights in the two systems were approximately 71,000 and 64,000, respectively. There was no clear evidence for a minor virion polypeptide. Treatment of purified San Miguel sea lion virions with dimethyl suberimidate, a cross-linking reagent, preserved virion integrity during long-term storage at 4 degrees C. Oligomeric species of the polypeptide were observed upon electrophoresis of products from cross-linked virions. Based upon a preferred polypeptide molecular weight estimate of 71,000 and distribution of oligomeric species, a calicivirion model with 120 monomeric protein units is proposed as an alternative to a 180-unit model.

Animals↗
PubMed1970

Use of dimethyl suberimidate, a cross-linking reagent, in studying the subunit structure of oligomeric proteins.

Amidination of aldolase, glyceraldehyde-3-phosphate dehydrogenase, tryptophan synthetase B protein, L-arabinose isomerase, and the catalytic subunit of E. coli aspartate transcarbamylase with the bifunctional reagent dimethyl suberimidate produces cross-linked proteins, with reaction predominating within oligomers. Disc electrophoresis of a modified protein on polyacrylamide gel in the presence of sodium dodecyl sulfate resolves a set of species with molecular weights equal to integral multiples of the protomer molecular weight. For oligomers composed of identical protomers, the number of principal species observed is identical to the number of protomers in the oligomer. Application of the method to two proteins composed of dissimilar protomers, native aspartate transcarbamylase and tryptophan synthetase alpha(2)beta(2) complex of E. coli, revealed differences in the reactivities of the different kinds of protomer within each oligomer.

Amidines↗
PubMed1994

Arrangement of phosphatidylethanolamine molecular species in Escherichia coli membranes and reconstituted lipids as determined by dimethyl suberimidate cross-linking of nearest neighbor lipids.

Dimethylsuberimidate cross-linking has been used to determine the arrangement of phosphatidylethanolamine (PE) molecular species in Escherichia coli membranes. No large deviations from random mixing were found in wild-type strain AB1623, either in whole cells or in extracted lipids which were reconstituted into multilamellar vesicles. These results suggest, first, that there is little difference in the PE molecular species composition of the three lipid monolayers (the inner and outer monolayers of the inner membrane and the inner monolayer of the outer membrane) which contain significant amounts of PE. Secondly, the results suggest that the molecular species within each monolayer and in the extracted lipids are arranged close to randomly with no tendency for like molecular species to cluster. E. coli strain L8-2, which has a defect in beta-oxidation and a temperature-sensitive mutation in total fatty acid synthesis, was grown on cis-vaccenate (cis-11,12- octadecenate) to enrich the cells in divaccenoyl PE. Again, in whole cells or in lipids extracted from whole cells and reconstituted into multilamellar vesicles, the species were close to randomly arranged. However, a consistent, slight tendency of divaccenoyl species to pair with like species as compared to pairing with the second most common species, vaccenoyl, palmitoleoyl PE, was noted in both extracted lipids and in whole cells.

Cell Membrane↗