Investigation of the quaternary structure of beef liver glutamate dehydrogenase with bifunctional reagents

The six identical polypeptide chains of the smallest enzymatically active unit of beef liver glutamate dehydrogenase are shown to be arranged in two trimers. Cross-linking with bifunctional reagents of varying chain length and subsequent SDS polyacrylamide gel electrophoresis of the protein shows main bands corresponding to molecular weights of 168,000 and 336,000 daltons which is three times and six times, respectively, the molecular weight of the polypeptide chain (56,000 daltons). This finding supports a model for the quaternary structure of the glutamate dehydrogenase proposed by Reisler and Eisenberg (Biopolymers $\text{9}$, 877 (1970)).     

Lateral organization of proteins in the chromatophore membrane ofRhodospirillum rubrum studied by chemical cross-linking

The organization of proteins in the chromatophore membrane, particularly of the reaction center and the light-harvesting polypeptide, was examined by the use of a hydrophobic and a hydrophilic cross-linking reagent, namely DSP (dithiobis-succinimidyl propionate) and glutaraldehyde. The linkage of proteins was studied by SDS polyacrylamide pore gradient electrophoresis. DSP was shown to link proteins within the core of the membrane. The subunit H of the reaction center is linked with DSP at a low concentration, either with itself or with other membrane proteins but not to the subunits M and L. In isolated reaction centers the subunits H are exclusively linked with each other. With increasing concentrations of DSP the bands of the subunits M, L, and the light-harvesting polypeptide disappear simultaneously from the gel, suggesting that these proteins are linked together. This hypothesis is supported by the finding that reaction centers isolated from chromatophores treated with DSP retain an appreciable amount of light-harvesting polypeptide. With increasing concentrations of the hydrophilic cross-linking reagent glutaraldehyde, the bands of all the three subunits of the reaction center, H, M, and L, progressively disappear from the gel, suggesting that they are linked together. The light-harvesting polypeptide remains free when this reagent is used.     

Studies of glutamate dehydrogenase: analysis of functional areas and functional groups.

1. It is shown by limited tryptic digestion of beef liver glutamate dehydrogenase under native conditions that the amino terminus of the polypeptide chain is located at the surface of the molecule. End-group analysis after trypsin treatment yields aspartic acid as the new N-terminal amino acid while the C-terminal threonine remains unchanged. 2. NADH, especially in the presence of 2-oxoglutarate, protects the enzyme against tryptic degradation. In the absence of the coenzyme, glutamate dehydrogenase is rapidly inactivated. 3. The regulatory effects of ADP and GTP are only slightly altered by trypsin. A small shift of the pH dependence of the activation by ADP is observed. 4. The quaternary structure of the unimer of the enzyme is not affected by limited tryptic digestion indicating that the N-terminal part of the polypeptide chain is not located in the contact domains between the polypeptide chains. The association of the hexamer to large associated particles is reduced but not abolished. 5. It is shown by treatment of the enzyme with iodo[2(-14)C]acetic acid as well as with Ellman's reagent that the six - SH groups of the polypeptide chain are buried and not accessible to these reagents in phosphate buffer. In Tris buffer they become exposed and react in the order 89, 55, 197, 115, 270, 319. This together with the result that in Tris buffer the rat of inactivation caused by trypsin is higher than in phosphate buffer indicates that Tris buffer changes drastically the properties of the enzyme. 6. Cross-linking of the enzyme molecule with bifunctional reagents and subsequent dodecylsulfate-polyacrylamide electrophoresis shows that the six identical polypeptide chains are arranged in two groups of three. 7. The implications of these results for the tertiary and quaternary structure of beef liver glutamate dehydrogenase are discussed.     

Stoichiometry and molecular weight of the minimum asymmetric unit of canine renal sodium and potassium ion-activated adenosine triphosphatase

Sodium and potassium ion-activated adenosine triphosphatase is known to be composed of at least two different polypeptides, alpha and beta. When a detergent-treated supernatant preparation of the enzyme is reacted with the cross-linking reagent, cupric phenanthroline, a single, covalent heterodimer is formed. This product is formed from one of each of the two polypeptides. The remaining, unreacted alpha and beta chains maintain a constant ratio to each other throughout the reaction. The same heterodimer is formed in membrane-bound enzyme when reacted with several other cross-linking reagents. The protein mass ratio between the chains in the native enzyme, determined by two methods, is 2.15 +/- 0.16. Using this value and a value of 121,000 +/- 6,000 for the molecular weight of the larger polypeptide, a molecular weight of 56,000 +/- 7,000 can be calculated for the protein portion of the smaller polypeptide. Upon removal of a substantial portion of the carbohydrate from the smaller polypeptide, a change in its electrophoretic mobility is observed, while that of the larger polypeptide remains unaffected. The apparent length of this unglycosylated small chain is 450 residues, corresponding to a molecular weight of 51,000. Taken together, these results demonstrated that the two polypeptides of the (Na+ + K+)-ATPase exist in an equimolar, noncovalent association in the native enzyme, and that the protein molecular weight of the minimum asymmetric unit is 177,000 +/- 13,000, Previous results which address the question of the quaternary structure of the ATPase are re-examined in light of these determinations.     

Reaction of dimethyl-3,3'-dithiobispropionimidate with intact human erythrocytes. Cross-linking of membrane proteins and hemoglobin.

Dimethyl-3,3'-dithiobispropionimidate penetrates intact human erythrocytes and cross-links many of the membrane proteins to hemoglobin as well as to each other. The cross-linked complexes so produced have been analyzed by both one- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis, making use of the easy cleavability of the disulfide-containing reagent. The basic pattern of cross-linked complexes appears identical with that seen with unsealed ghosts. Although subtle relative motions cannot be ruled out, no rearrangement of nearest neighbor peptide chains, on a scale that would alter the cross-linking pattern, occurs during osmotic lysis of erythrocytes. Superimposed on the basic pattern was a series of complexes involving globin chains. Bands 1, 2, 2.2, 2.4, 3, 4.1, 4.2, 6, and 7 (nomenclature of Steck, T.L. (1972) J. Mol. Biol. 66, 295-305) are all cross-linked to hemoglobin. Bands 2.2 and 2.4, recently shown to be accessible to the external surface of the membrane (Staros, J. V., and Richards, F. M. (1974) Biochemistry 13, 2720-2726), may be transmembrane proteins on the basis of the present findings. Band 5 is the only major band to show no detectable complexes with hemoglobin; oligomers of Band 5 itself, however, are seen. The absence of hemoglobin/Band 5 cross-linking in this case could reflect a special, as yet unexplained, environment for the Band 5 peptide. The amount of Band 6 in isolated membranes diminishes with increasing reagent concentration.     

Cross-linking of dark-adapted frog photoreceptor disk membranes. Evidence for monomeric rhodopsin.

A model for random cross-linking of identical monomers diffusing in a membrane was formulated to test whether rhodopsin's cross-linking behavior was quantitatively consistent with a monomeric structure. Cross-linking was performed on rhodopsin both in intact retinas and in isolated rod outer segment (ROS) membranes using the reagent glutaraldehyde. The distribution of covalent oligomers formed was analyzed by SDS-polyacrylamide gel electrophoresis and compared to predictions for the random model. A similar analysis was made for ROS membranes cross-linked by diisocyanatohexane and retinas cross-linked by cupric ion complexed with o-phenanthroline. Patterns of cross-linking produced by these three reagents are reasonably consistent with the monomer model. Glutaraldehyde was also used to cross-link the tetrameric protein aldolase in order to verify that cross-linking of a stable oligomer, under conditions comparable to those used for ROS, yielded the pattern predicted for a tetrameric protein having D2 symmetry. This pattern is markedly different from the one for a random-collision model. Moreover, a comparison of rates showed that aldolase cross-linking with glutaraldehyde is significantly faster than cross-linking of membrane-bound rhodopsin. It is concluded that rhodopsin is monomeric in dark-adapted photoreceptor membranes and that the observed cross-linking results from collisions between diffusing rhodopsin molecules.     

Isolation of an Fcgamma-binding protein from the cell membrane of a macrophage-like cell line (P388D1) after detergent solubilization

Lactoperoxidase-catalyzed iodination, NP-40 lysis, and subsequent affinity chromatography on IgG-Sepharose were used in an attempt to define some of the molecular properties of the Fc receptor of P388D1, a macrophage-like mouse tumor line. Radioiodinated material retained on columns of Sepharose coupled either to monomeric mouse IgG2a or monomeric human IgG1 appeared on SDS polyacrylamide gel electrophoresis to contain principally three labeled components, a major band of about 57,000 m.w. and two minor bands of 28,000 and 24,000 m.w. The mobilities of these components changed little on reduction, which suggested that they represented single polypeptide chains, An identical pattern was obtained with Sepharose-linked Fc fragments of human IgG1, but neither Fab fragments of IgG1 nor IgM appeared to bind these components. Since the specificity of binding to the immobilized proteins is the same as that observed in vivo, it is postulated that these proteins represent either all or some portion of the P388D1 Fc receptor.     

Photodynamic action of bilirubin on human erythrocyte membranes. Modification of polypeptide constituents.

The photodynamic action of bilirubin on isolated human erythrocyte membranes (ghosts) has been studied. When incorporated into ghosts (pH 8.0,10 degrees) the bile pigment photosensitizes in blue light the peroxidation of unsaturated lipids, as evidenced by a positive color reaction with 2-thiobarbituric acid. Accompanying lipid peroxidation was the disappearance of most of the major membrane proteins (Coomassie Blue staining in sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and appearance of polypeptide photoproducts of greater size (mol wt greater than 250,000). The association of membrane proteins (presumably by cross-linking) was insignificant when bilirubin-ghost suspensions were kept in the dark, or when ghosts were irradiated in the absence of bilirubin. Electrophoretic bands 1 and 2 (Fairbanks, G., Steck, T.L., and Wallach, D. F.H (1971), Biochemistry 10, 2606) diminished rapidly during the photoreaction, whereas band 3 and the three sialoglycoproteins disappeared at a much slower rate. Dispersal of membrane consituents by treatment with sodium dodecyl sulfate prior to irradiation resulted in relatively little peroxidation and no noticeable formation of high molecular weight polypeptide complexes. The possibility that malonaldehyde, a product of lipid peroxidation, is involved in cross-linking during irradiation was studied by incubating ghosts with exogenous malonaldehyde. Although the reagent did cross-link membrane proteins (electrophoretic bands 1, 2, 2.1 2.2, and 4.1 diminished most rapidly and high molecular weight bands appeared), the reaction could only be demonstrated with malonaldehyde concentrations several orders of magnitude greater than those detected in irradiation experiments. If malonaldehyde cross-linking occurs, it does not appeare to be the predominant mechanism of polypeptide association during irradiation of bilirubin-containing ghosts.     

A 220 kDa polypeptide, immunolocalized to epithelial tight junctions, is associated with brain clathrin preparations

Antibodies were raised in rabbits to highly purified preparations of bovine brain clathrin. The serum stained by immunofluorescence rat liver sections at tight junctions in a pattern that was identical to that previously reported (B. R. Stevenson et al.: J. Cell Biol. 103, 755-766 (1986] in which a monoclonal antibody specific to a 220 kDa (ZO-1) liver tight junction component was used. The serum also stained regions of the cell surface corresponding to the positions of intercellular junctions in confluent MDCK and HepG-2 cell cultures. Analysis of brain clathrin preparations resolved by polyacrylamide gel electrophoresis by immunoblotting with the serum indicated reaction with clathrin heavy and light chains as well as towards a 220 kDa polypeptide that was a minor component. Affinity purification of the serum provided antibodies directed mainly to clathrin light chains and these antibodies, as well as an independent antiserum to clathrin heavy chains, immunofluorescently stained liver tissue and cells in a manner typical of coated membranes/vesicles. These results suggested, by difference, that antibodies to a 220 kDa polypeptide, a minor constituent in brain clathrin preparations, were responsible for staining intercellular tight junctions in epithelia. The 220 kDa polypeptide present in brain clathrin preparations was demonstrated to be immunologically distinct from liver myosin heavy chain as well as erythrocyte and brain ankyrin. Comparison by two-dimensional mapping of the 220 kDa in brain clathrin with the clathrin heavy chain (180 kDa) polypeptide showed they were different proteins, but the 220 kDa polypeptide present in rat liver tight junctions was highly similar to the 220 kDa present in bovine brain clathrin preparations.(ABSTRACT TRUNCATED AT 250 WORDS)     

Studies of glutamate dehydrogenase. Analysis of quaternary structure and contact areas between the polypeptide chains

Cross-linking of the unimer of glutamate dehydrogenase from beef liver (consisting of six polypeptide chains each having a molecular weight of 56000) with dimethyladipimidate and subsequent analysis by sodium dodecylsulfate electrophoresis shows predominantly the trimeric species (molecular weight 168000). Treatment with dimethylimidates of other chain length yields significantly less trimeric species indicating that the amino groups being cross-linked are within a distance of about 0.85 nm. Comparison of the molar amount of incorporated [14C]dimethyladipimidate with the number of modified amino groups (determined with trinitrobenzenesulfonic acid) shows that although 8-9 of the 34 amino groups have reacted, only 2-3 of them are involved in cross-links. Reaction with dimethylimidates inactivates the enzyme. The loss of the activity is partly concomitant to cross-linking to the trimeric species and not simply due to the modification of essential lysine residues. This is supported by the fact that, although more lysine residues react with mono-functional methylimidates, the loss of activity is reduced. Purified chymotryptic and tryptic peptides of the radioactive-labeled trimeric species were subjected to sequence analysis. Six peptides containing 75% of the total label were identified: one involves the amino-terminal residue alanine-1 and the others involve lysine-105, lysine-154, lysine-269, lysine-358 and lysine-399. Quantitative analysis of the specific radioactivity of each peptide/mol lysine leads to the conclusion that only lysine-105, lysine-154, lysine-269 and lysine-358 participate in cross-links, lysine-269 and lysine-358, respectively, being at isologous and lysine-105 cross-linked with lysine-154 at heterologous contact domains of the enzyme. A model for the planar arrangement of the trimeric species in the quaternary structure of glutamate dehydrogenase is discussed. It includes both isologous and heterologous contact areas between the polypeptide chains.     

Analysis of inter-alpha-trypsin inhibitor and a novel trypsin inhibitor, pre-alpha-trypsin inhibitor, from human plasma. Polypeptide chain stoichiometry and assembly by glycan

The polypeptide chain composition of protein material referred to in the literature as "inter-alpha-trypsin inhibitor" was investigated. The material was found to consist of distinct proteins of 125,000 and 225,000 Da, each of which contained more than one polypeptide chain. The links that assemble each protein were found to be stable to various strong denaturants, but susceptible to treatment with trifluoromethanesulfonic acid or hyaluronidase, indicating a glycan nature. The 225,000-Da protein migrated with inter-alpha mobility on agarose gel electrophoresis and is designated inter-alpha-trypsin inhibitor, whereas the 125,000-Da protein migrated with pre-alpha mobility, and we designate it pre-alpha-trypsin inhibitor. Analysis of the proteins, the separated chains, and proteolytic derivatives thereof revealed that each protein contained a single, identical, trypsin-inhibitory chain of 30,000 Da. Inter-alpha-trypsin inhibitor contains noninhibitory heavy chains of 65,000 and 70,000 Da, whereas pre-alpha-trypsin inhibitor contains a heavy chain of 90,000 Da. Our data allow identification of several recently reported cDNA clones and clarify the confusion surrounding the composition of plasma proteins referred to as inter-alpha-trypsin inhibitor.     

Potential molecular chaperones involved in laminin chain assembly

To explore potential molecular chaperones involved in the intracellular assembly of laminin chains, bovine aortic endothelial cells were treated with a thiol cleavable divalent cross-linking reagent, dithio-bis-(succinimidylpropionate), and cellular proteins cross-linked to laminin chains were co-immunoprecipitated with anti-laminin antiserum. Sodium dodecylsulfate (SDS) gel electrophoresis of the precipitate under reducing condition showed polypeptides with estimated sizes of 80, 60 and 50 kDa together with laminin chains. Two dimensional electrophoresis, in which non-reducing and reducing SDS electrophoresis were combined, suggested that many molecules of these polypeptides were cross-linked to each laminin chain. Sepharose CL-4B beads conjugated with E8 fragment of mouse laminin-1 was prepared. Affinity chromatography with the beads of microsomal proteins from rat liver showed that Bip and HSP70 associated to laminin chains and dissociated upon ATP hydrolysis. Protein-disulfide isomerase also showed affinity to the column. GRP94 and calnexin showed strong affinity and were washed out only with a detergent solution. Thus, many molecular chaperones are suggested to be involved in the intracellular assembly of laminin chains. This revised version was published online in June 2006 with corrections to the Cover Date.     

Chemical cross-linking of Ia alloantigen alpha and beta chains with dimethyl 3,3'-dithiobispropionimidate.

We have examined the polypeptide chain composition of membrane-bound and detergent-solubilized Ia antigens using the chemical cross-linking reagent dimethyl 3,3'-dithiobispropionimidate (DTBP). Products of the I-E/C subregion of the major histocompatibility complex, which were solubilized from spleen cells with the detergent NP-40 and partially purified by affinity chromatography on lentil lectin-agarose, could be almost completely cross-linked by DTBP. Thus, the characteristic 33,000 m.v. (alpha) and 28,000 (beta) polypeptide chains seen on sodium dodecylsulfate polyacrylamide gels disappeared and a major new species of 60,000 m.w. appeared after cross-linking. When isolated and reduced with 2-mercaptoethanol, the 60,000 m.w. peak was found to be comprised to alpha and beta chains. Similar results were obtained when I-E/C, as well as I-A, alpha and beta chains were crosslinked on the cell surface. These data demonstrate that the alpha and beta chains of the Ia antigens exist primarily in the form of a dimer both in detergent solution and in situ.     

Quaternary structure of erythrocruorin from the nematode Ascaris suum. Evidence for unsaturated haem-binding sites.

The quaternary structure of erythrocruorin from the nematode Ascaris suum was studied. The native protein had a sedimentation coefficient, at a protein concentration of 1 mg/ml, of 11.6 +/- 0.3 S and an Mr, as determined by sedimentation equilibrium, of 332,000 +/- 17,000. SDS/polyacrylamide-gel electrophoresis gave one band with a mobility corresponding to an Mr of 43,000 +/- 2000. The Mr of the polypeptide chain was determined to be 41,600 +/- 1,500 by sedimentation equilibrium in 6 M-guanidinium chloride and 0.1 M-2-mercaptoethanol. Cross-linking with glutaraldehyde followed by SDS/polyacrylamide-gel electrophoresis yielded a maximal number of eight bands. The haem content of Ascaris erythrocruorin was observed to vary from one preparation to another. This finding was shown to be due to non-realization of the full binding capacity for haem. By titration with haemin, the haem content was found to attain a maximal value of 2.86 +/- 0.14%, corresponding to a minimal Mr per haem group of 21,000 +/- 1,000. Our findings indicate that Ascaris suum erythrocruorin is composed of eight identical polypeptide chains, carrying two haem sites each.     

The acetylcholine receptor as part of a protein complex in receptor-enriched membrane fragments from Torpedo californica electric tissue

The acetylcholine receptor from Torpedo californica electric tissue consisting of polypeptide chains of molecular weight 42000 (+/- 2000) is part of a protein complex. Cross-linking experiments with bifunctional reagents have shown that this complex has possibly a pentameric structure with a molecular weight of 270000 (+/- 30000). Besides the receptor subunit (alpha-chain), at least three further classes of polypeptide chains are part of the complex: beta (Mr 48000), gamma (Mr 62000) and delta (Mr 68000). This can be shown by cross-linking the proteins extracted from receptor-enriched membrane fractions with a cleavable reagent: From the 270000 molecular weight particle the four predominant polypeptide chains of the membrane, alpha, beta, gamma, and delta, can be obtained. The gamma-polypeptide chains appear to form a dimer connected by an inter-chain disulphide bridge.     

The use of azidoarylimidoesters in RNA-protein cross-linking studies with Escherichia coli ribosomes

A series of related hetero-bifunctional RNA-protein cross-linking reagents has been prepared, carrying an imidoester or N-hydroxysuccinimide ester function at one end of the molecule, and a phenylazido function at the other. These compounds have been applied to RNA-protein cross-linking studies with ribosomal subunits, and one of them, p-azido-phenylacetic imidoester, has proved to be a particularly useful reagent for this purpose. The reagent first reacts specifically with protein amino groups, and subsequent photolysis of the azide group leads to cross-linking to the RNA in yields of up to 8% of the total protein. The whole reaction takes place under very mild conditions in aqueous solution.The individual proteins concerned in the cross-links have been identified by two-dimensional gel electrophoresis, and the existence of a covalent cross-link was confirmed by the isolation by two different methods of protein-oligonucleotide complexes carrying a ³²P label. Although most of the ribosomal proteins could be cross-linked to their corresponding ribosomal RNA within the individual subunits, RNA-protein cross-links at the ribosomal subunit interface were only detectable in vanishingly small amounts.The advantages of this type of genuine hetero-bifunctional reagent in RNA-protein cross-linking studies are discussed.     

The molecular organization of the protein HC-IgA complex (HC-IgA)

Complexes of protein HC and monoclonal IgA1 or IgA2 or polyclonal IgA were isolated from human blood plasma. Dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting showed that all complexes contain three types of chains: two light immunoglobulin chains, one regular IgA alpha-chain, and one chain with Mr = 90,000 carrying both alpha-chain and protein HC epitopes. The complexes were split into Fab alpha and Fc alpha fragments by bacterial IgA proteases. The protein HC epitopes were linked to the Fc fragments. Complexes of protein HC and an alpha-chain devoid of the variable region and the first heavy chain constant domain could also be demonstrated to be present in the blood plasma of a patient with alpha-heavy chain disease. Pepsin digestion of HC-IgA released a fragment containing all the protein HC epitopes and the C-terminal nonapeptide of the IgA alpha-chain. The light immunoglobulin chains, the regular alpha-chain, and the 90,000-Da chain from monoclonal HC-IgA1 were isolated by preparative dodecyl sulfate-polyacrylamide gel electrophoresis and by repeated gel filtration in dodecyl sulfate-containing buffer. The N-terminal amino acid sequence of the alpha-chain was identical with that of a regular human heavy immunoglobulin chain of subgroup III. Subtractive degradations of the 90,000-Da chain displayed 2 amino acid residues in each position in a pattern suggesting simultaneous degradations of a chain identical with the regular alpha-chain of HC-IgA and of uncomplexed, low molecular weight, protein HC. All the results are compatible with a model for HC-IgA in which a single low molecular weight protein HC polypeptide chain is covalently linked, side by side, to the C-terminal nonapeptide of one of the two alpha-chains of a regular monomeric IgA unit.     

Isolation of polypeptide chains with heme from the extracellular hemoglobin of Amphitrite ornata (Polychaeta, Annelida)

From the extracellular hemoglobin of Amphitrite ornata four constituent polypeptide chains containing heme and designated AI, AII, BI and BII according to the elution order were obtained by DE52-cellulose ion-exchange chromatography with dithiothreitol (DTT) as a reducing reagent. The NH2-terminal sequences for the chains are AI, Asp-Ser-Asn-Ala; AII, Glu-Tyr-Thr; BI, Asp-Phe-Asn-Thr; and BII, Asp-Ser-Glu. Each of the isolated chains showed spectra similar to those of vertebrate hemoglobins, and they bound oxygen reversibly. Acid urea polyacrylamide gel electrophoresis separated four bands, corresponding to the isolated chain, from the intact extracellular hemoglobin reduced with DTT. These results and our failure to detect an appreciable amount of non-heme protein suggest that the extracellular hemoglobin of A. ornata is composed of four polypeptide chains, each containing a heme.