Molecular symmetry and arrangement of subunits in extracellular hemoglobin from the nematode Ascaris suum

The arrangement of subunits and molecular symmetry of extracellular hemoglobin from the nematode Ascaris suum, an 11.7S molecular of molecular mass 332 kDa and composed of eight identical subunits, was studied. Dissociation of the molecule at alkaline and acid pH yielded 4.6S and 2.7S components, identified as polypeptide-chain dimers and monomers, respectively. Cross-linking with glutardialdehyde followed by SDS/PAGE resulted in a maximum number of eight bands identified in order of decreasing mobility as monomeric and 2-8 cross-linked-polypeptide-chain species. Comparison with values predicted from theory shows that the distribution of protein among the various cross-linked species, obtained after different extents of exposure to cross-linker, is consistent with a two-layered arrangement of subunits involving one type of interaction between subunits from different layers and another between subunits within the same layer. Electron micrographs of the molecule showed two profiles, a square and a rectangle. We propose a model for the molecule which is eight subunits arranged in two layers, stacked in an eclipsed orientation. The proposed model is consistent with the results from sedimentation, cross-linking and electron microscopy. Taken together, our findings indicate D4 symmetry for Ascaris hemoglobin.     

Structure of extracellular hemoglobin from the brine shrimp Artemia salina.

1. Hemoglobin from the brine shrimp Artemia salina, purified by ultracentrifugation and preparative gel electrophoresis in non-denaturing medium, gave in sodium dodecyl sulfate-polyacrylamide gel electrophoresis a single band corresponding to a polypeptide chain with Mr 150,000. 2. Crosslinking by glutardialdehyde resulted in the appearance of a band corresponding to a molecular mass twice that of a polypeptide chain. 3. Limited trypsinolysis gave eight proteolytic bands corresponding to submultiples 8/9-1/9 of a polypeptide chain. 4. We conclude that a molecule of Artemia hemoglobin is composed of two single polypeptide chain subunits and that each subunit consists of nine structural units roughly equal in size.     

Erythrocruorin from the water-flea Daphnia magna. Quaternary structure and arrangement of subunits.

The subunit structure of erythrocruorin from the cladoceran Daphnia magna was studied. The native protein was found to have a sedimentation coefficient (S2(20), w) of 17.9 +/- 0.2 S and a molecular weight, as determined by sedimentation equilibrium, of 494 000 +/- 33 000. Iron and haem determinations gave 0.312 +/- 0.011% and 3.84 +/- 0.04%, corresponding to minimal molecular weights of 17900 +/- 600 and 16 100 +/- 200 respectively. Sodium dodecyl sulphate/polyacrylamide-gel electrophoresis gave one band with mobility corresponding to a molecular weight of 31 000 +/- 1 500. The molecular weight of the polypeptide chain determined by sedimentation equilibrium in 6 M-guanidinium chloride and 0.1 M-2-mercaptoethanol is 31 100 +/- 1300. On a molecular-weight basis, Daphnia erythrocruorin is composed of 16 identical polypeptide chains carrying two haem groups each. The native structure is stable between pH5 and 8.5. At alkaline and acidic pH, a gradual decrease in the sedimentation coefficient down to 9.8S occurs. Above pH 10 and below pH4, a slow component with S20, w between 2.7S and 4.0S is observed. The 2.7S, 4.0S and 9.8S species are identified as single-chain subunits, subunit dimers and half-molecules respectively. We propose a model for the molecule composed of 16 2.7S subunits grouped in two layers stacked in an eclipsed orientation, the eight subunits of each layer occupying the vertices of a regular eight-sided polygon. Support for this arrangement is provided from electron microscopy and from analysis of the pH-dissociation pattern.     

The arrangement and role of some of the amino acid residues in the beta-ketoacyl synthetase site of chicken liver fatty acid synthetase

The beta-ketoacyl synthetase site of eukaryotic fatty acid synthetases is comprised in part of a pantetheinyl residue on one subunit juxtapositioned with a cysteinyl residue on the adjacent subunit. The present study has confirmed this arrangement and has identified 2 additional residues in the site. The active site residues were identified as summarized below. Sodium borohydride reduction of the keto derivatives of the dibromopropanone cross-linked residues yielded the alcohol derivatives which were amenable to isolation in good yields. The active enzyme yielded primarily a cysteinecysteamine derivative of 2-propanol, demonstrating that a cystyl and the pantetheinyl residues were cross-linked by dibromopropanone. However, in the cold-inactivated enzyme, the primary product of the cross-linking reaction was the dicystyl derivative. In addition, cross-linking between the cystyl and pantetheinyl residues, but not the two cystyl residues, resulted in the cross-linking of the two subunits. Therefore, it is proposed that there are two cystyl residues on one subunit juxtapositioned with the pantetheinyl residue on the adjacent subunit. The cystyl residues are highly reactive toward alkylating agents at pH 6.5, suggesting the presence of a cationic residue interacting with the thiolate anion. This proposal was supported using the bifunctional reagent o-phthalaldehyde which was found to cross-link the epsilon-amino group of lysine with the pantetheinyl-SH or the cystyl-SH in the beta-ketoacyl synthetase site to form a thioisoindole ring. The dialdehyde inhibited the enzyme by inactivating the beta-ketoacyl synthetase activity, and the inhibition could be prevented by malonyl-CoA and to a lesser extent by acetyl-CoA. Blocking the reactive thiol groups with dibromopropanone or 5,5'-dithiobis(2-nitrobenzoic acid) reduced the formation of the fluorescent thioisoindole ring. The close arrangement of a cystyl-SH, the pantetheinyl-SH, and the epsilon-amino group of lysine led us to propose that the positive epsilon-amino group may serve as an electron sink in a general acid-catalyzed decarboxylation reaction.     

Insights into the rotary catalytic mechanism of F0F1 ATP synthase from the cross-linking of subunits b and c in the Escherichia coli enzyme

The transmembrane sector of the F(0)F(1) rotary ATP synthase is proposed to organize with an oligomeric ring of c subunits, which function as a rotor, interacting with two b subunits at the periphery of the ring, the b subunits functioning as a stator. In this study, cysteines were introduced into the C-terminal region of subunit c and the N-terminal region of subunit b. Cys of N2C subunit b was cross-linked with Cys at positions 74, 75, and 78 of subunit c. In each case, a maximum of 50% of the b subunit could be cross-linked to subunit c, which suggests that either only one of the two b subunits lie adjacent to the c-ring or that both b subunits interact with a single subunit c. The results support a topological arrangement of these subunits, in which the respective N- and C-terminal ends of subunits b and c extend to the periplasmic surface of the membrane and cAsp-61 lies at the center of the membrane. The cross-linking of Cys between bN2C and cV78C was shown to inhibit ATP-driven proton pumping, as would be predicted from a rotary model for ATP synthase function, but unexpectedly, cross-linking did not lead to inhibition of ATPase activity. ATP hydrolysis and proton pumping are therefore uncoupled in the cross-linked enzyme. The c subunit lying adjacent to subunit b was shown to be mobile and to exchange with c subunits that initially occupied non-neighboring positions. The movement or exchange of subunits at the position adjacent to subunit b was blocked by dicyclohexylcarbodiimide. These experiments provide a biochemical verification that the oligomeric c-ring can move with respect to the b-stator and provide further support for a rotary catalytic mechanism in the ATP synthase.     

Evidence for heterodimeric nature of calpain molecules as studied by cross-linking modification

Purified calpain I and calpain II from porcine erythrocytes and kidney were cross-linked with a bifunctional reagent, disuccinimidyl suberate, and the cross-linked products were analyzed by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The major product had a molecular mass of 105 kDa, while the starting materials were resolved into 80-kDa and 30-kDa subunits. The cross-linking in the presence of 2 mM Ca2+ yielded several higher-molecular-weight species. The cross-linked products were shown to contain both the 80-kDa and 30-kDa proteins by means of immunoblotting with antibodies monospecific for the respective subunits, suggesting that the original calpain molecule existed in solution as an 80-kDa plus 30-kDa heterodimer and that Ca2+ induced closer association of these heterodimeric molecules.     

Cross-linking and labeling of the Escherichia coli F1F0-ATP synthase reveal a compact hydrophilic portion of F0 close to an F1 catalytic subunit

The subunit arrangement of the F0 sector of the Escherichia coli ATP synthase is examined using hydrophilic and hydrophobic (cleavable) cross-linking reagents and the water-soluble labeling reagent [35S] diazoniumbenzenesulfonate ( [35S]DABS). Cross-linking is performed on purified ATP synthase and inverted minicell membranes. ATP synthase incorporated into liposomes is labeled with [35S]DABS. Three cross-linked products involving the F0 subunits (a, b, and c) are observed with the purified ATP synthase in solution: a-b, b2, and c2 dimers. A cross-link between the F0 and F1 is detected and occurs between the a and beta subunits. A cross-linker independent association between the b and beta subunits is also evident, suggesting that the two subunits are close enough to form a disulfide bridge. A cross-linking reagent stable to reducing agents produces a b-beta dimer, as detected by immunoblotting with anti-beta serum. The c subunit does not cross-link with any F1 polypeptide. Minicell membranes containing ATP synthase polypeptides radioactively labeled in vivo similarly show b2 and c2 dimers after cross-linking. [35S]DABS labels the a and b, but not c, subunits, showing that the a and b, but not c, subunits possess hydrophilic domains. Thus, certain domains of subunits a and b extend from the membrane and are in close proximity to one another and the F1 catalytic subunit beta.     

The molecular morphology of bovine heart mitochondrial NADH-ubiquinone reductase. Cross-linking with dithiobis(succinimidyl propionate)

The molecular morphology of NADH-ubiquinone reductase (complex I) was investigated by cross-linking with the cleavable bifunctional reagent, dithiobis(succinimidyl propionate). Cross-linking inhibits the following activities of the complex--NADH----3-acetylpyridine adenine dinucleotide (oxidized), NADH----2,6-dichloroindophenol, NADH----ferricyanide, and NADH----menadione--to different degrees with the greatest inhibition occurring with either ferricyanide or 3-acetylpyridine adenine dinucleotide as electron acceptor. Addition of 150 microM NADH affords partial protection from inhibition. Cross-linking quenches the FMN fluorescence of complex I (288 nm excitation/515 nm emission), and addition of 150 microM NADH greatly reduces the quenching. Treatment of complex I (1 mg/ml) for 2 min with dithiobis(succinimidyl propionate) (0.2 mg/ml) at 4 degrees C revealed a cross-linked product consisting of the following seven subunits: 75-80, 53-57, 42, 33-35, 24-27, 17-18, and 12.5-15.5 kDa. Five minutes of treatment cross-linked the unidentified polypeptides of 69 and 51 kDa to six of the seven complex I subunits, but the 12.5-15.5-kDa subunit may be missing from this cross-linked product, while 15 min of treatment cross-linked additional unidentified polypeptides of 177, 107, 72, and 63 kDa. Since longer times of cross-linking result in a larger number of unidentifiable polypeptide spots, the shorter cross-linking time results are taken as a more accurate picture of the native enzyme conformation. This would indicate that within complex I the following subunits are within 12 A of each other at one or more points in space: 75-80, 53-57, 42-45, 33-35, 24-27, 17-18, and, perhaps, 12.5-15.5 kDa. These subunits represent portions of all three fractions of the enzyme, i.e. flavoprotein, iron-protein, and insoluble or hydrophobic fractions.     

Tetrameric structure of the nonactivated glucocorticoid receptor in cell extracts and intact cells

Mouse lymphoma cells contain a nonactivated glucocorticoid receptor of Mr approximately 330,000 which is heteromeric in nature and is unable to bind to DNA. Following affinity labeling of the steroid-binding subunit and subsequent cross-linking with dimethyl suberimidate at various times either in cell extracts or in intact cells, a series of labeled bands was detected in SDS gels. From the molecular masses of completely and partially cross-linked complexes we conclude that the large nonactivated receptor is a tetramer composed of two 90 kDa subunits, one 50 kDa polypeptide and one steroid-binding subunit.     

A study of the quaternary structure of Escherichia coli RNA polymerase using bis(imido esters).

The quaternary structure of Escherichia coli RNA polymerase has been studied by cross-linking with a periodate-cleavable bis(imido ester), N,N'-bis(2-carboximidoethyl)tartaramide dimethyl ester dihydrochloride (CETD). The cross-linked holoenzyme gives a characteristic five-band pattern after electrophoresis on sodium dodecyl sulfate-polyacrylamide gels. The components of each band have been unambiguously identified by (a) molecular-weight measurements, (b) comparisons of cross-linking patterns of holoenzyme and core enzyme, and (c) periodate cleavage of cross-links followed by a second dimension sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The bands are (1) alphabeta and alphabeta', (2) sigmabeta and sigmabeta', (3) alphasigmabeta', (4) betabeta', and (5) sigmabetabeta'. Bands 2 and 4 are the most prominent at low reagent concentrations (up to 2.5 mM) but band 5 becomes the most prominent at higher concentrations. There are no bands corresponding to alphaalpha and alphasigma; a faint band has been tentatively identified as alphabetabeta'. Shorter bis(imido esters) are much less effective cross-linking reagents than CETD and they do not give rise to any other cross-linked species. On the basis of these observations, a model for the subunit arrangement of RNA polymerase is proposed.     

Topography of a flexible ribonucleoprotein helix: protein-protein contacts in Sendai virus nucleocapsids.

Contacts among the three polypeptide species in the flexible helical nucleocapsids of a paramyxovirus were examined with bifunctional protein cross-linking reagents. Polypeptides L and P, minor components of Sendai virus nucleocapsids implicated in viral RNA polymerase activity, were efficiently cross-linked into large complexes, indicating that they enjoy abundant contacts with neighboring protein molecules in the helix. Less reactivity was found in the case of the major structural polypeptide, NP; about half of all molecules of NP formed large cross-linked complexes, most of the rest remaining as monomers along with a small proportion of homodimers and low-order oligomers. Marked heterogeneity in the cross-linking reactivity of NP molecules, which may reflect the conformational quasi-equivalence inherent in a flexible helix, was indicated by the production of several conformers of homodimers and other low-order oligomers of NP, and by failure of the kinetics of NP cross-linking to conform to a simple statistical model of random polmerization. The validity of the statistical model was shown by cross-linking experiments with the rigid helical virus, tobacco mosaic virus.     

Influence of ligation state and concentration of hemoglobin A on its cross-linking by glycolaldehyde: functional properties of cross-linked, carboxymethylated hemoglobin

The ligation state of hemoglobin during its cross-linking by glycolaldehyde influences the ultimate oxygen affinity of the cross-linked protein. Thus, if the cross-linking is performed with carbonmonoxy-hemoglobin, the oxygen affinity increases slightly to a P50 of 7 mmHg from a P50 of 9 mmHg for unmodified hemoglobin. In contrast, when deoxyhemoglobin is cross-linked with glycolaldehyde, the oxygen affinity of the product decreases (P50 = 15 mmHg). When deoxyhemoglobin is first carboxymethylated and then cross-linked with glycolaldehyde, an even lower oxygen affinity is achieved (P50 = 23 mmHg). Carboxymethylated hemoglobin is very responsive to the presence of 5% CO2 with a P50 of 33 mmHg, which is lowered further to 42 mmHg when chloride (0.1 M) is also present. Hemoglobin carboxymethylated and cross-linked under anaerobic conditions is also responsive to the modulators CO2 and chloride with a resultant oxygen affinity of 27 mmHg. The type of cross-linking of liganded hemoglobin by the mild reagent glycolaldehyde is dependent upon the initial hemoglobin concentration. Thus, with dilute hemoglobin (45 microM in tetramer), cross-linking by glycolaldehyde (50 mM) results in about 75% of 64,000 molecular weight species (some of which are cross-linked within tetramer) and 25% of intertetrameric cross-linked species with a range of molecular weights averaging 128,000-512,000. With hemoglobin solutions of higher concentration (360 microM), the amount of the higher molecular weight species increases to about 65% with a corresponding reduction to 35% in the 64,000 molecular weight component.     

The formation of a disulfide cross-link between the two subunits demonstrates the dimeric structure of the mitochondrial oxoglutarate carrier

Isolated oxoglutarate carrier (OGC) can be cross-linked to dimers by disulfide-forming reagents such as Cu²⁺-phenanthroline and diamide. Acetone and other solvents increase the extent of Cu²⁺-phenanthroline-induced cross-linking of OGC. Cross-linked OGC re-incorporated in photeoliposomes fully retains the oxoglutarate transport activity. The amount of cross-linked OGC calculated by densitometry of scanned gels depends on the method of staining, since cross-linked OGC exhibits a higher sensitivity to Coomassie brilliant blue as compared to silver nitrate. Under optimal conditions the formation of cross-linked OGC dimer (stained with Coomassie brilliant blue) amounts to 75% of the total protein. Approximately the same cross-linking efficiency was evaluated from Western blots. Cross-linking of OGC is prevented by SH reagents and reversed by SH-reducing reagents, which shows that it is mediated by disulfide bridge(s). The formation of SS bridge(s) requires the native state of the protein, since it is suppressed by SDS and by heating. Furthermore, the extent of cross-linking is independent of OGC concentration indicating that disulfide bridge(s) must be formed between the two subunits of native dimers. The number and localization of disulfide bridge(s) in the cross-linked OGC were examined by peptide fragmentation and subsequent cleavage of disulfide bond(s) by β-mercaptoethanol. Our experimental results show that cross-linking of OGC is accomplished by a single disulfide bond between the cysteines 184 of the two subunits and suggest that these residues in the putative transmembrane helix four are fairly close to the twofold axis of the native dimer structure.     

Cross-linking of protein by ω-maleimido alkanoylN-hydroxysuccinimido esters

A series of chemical bifunctional cross-linking reagents, the succinimidyl maleimides, has been synthesized. Using hemoglobin as a model protein, it has been shown that these molecules react rapidly with sulfhydryl groups and more slowly with amino groups. The result is a high degree of specific cross-linking between the intramolecular subunits.     

Histidinoalanine, a naturally occurring cross-link derived from phosphoserine and histidine residues in mineral-binding phosphoproteins

Native mineral-containing phosphoprotein particles were isolated from the Heterodont bivalve Macrocallista nimbosa. The native particles are discrete structures about 40 nm in diameter which migrate as a single band during electrophoresis in agarose gels. Removal of the mineral component with ethylenediaminetetraacetic acid dissociates the native protein into nonidentical subunits. The lower molecular weight subunits, representing 8% of the total protein, were obtained by differential centrifugation. The native protein is characterized by a high content of aspartic acid, phosphoserine, phosphothreonine, histidine, and the bifunctional cross-linking residue histidinoalanine. The low molecular weight subunits have the same amino acid composition except for a reduction in histidinoalanine and a corresponding increase in phosphoserine and histidine residues, demonstrating that the alanine portion of the cross-link is derived from phosphoserine residues. Ion-exchange chromatography and molecular sieve chromatography show that the low molecular weight subunits have a similar charge density but differ in molecular weight, and the relative mobilities of the subunits on agarose gels indicate that they are polymers of a single phosphoprotein molecule. The minimum molecular weight of the monomer is about 140 000 on the basis of the amino acid composition. The high molecular weight subunits are rich in histidinoalanine and too large to be resolved by either molecular sieve chromatography or gel electrophoresis. On the basis of the ultrastructural, electrophoretic, chromatographic, and compositional evidence, native phosphoprotein particles are composed of subunits ionically cross-linked via divalent cations. These subunits are variable molecular weight aggregates of a single phosphoprotein molecule covalently cross-linked via histidinoalanine residues. Evidence for a nonenzymatic cross-linking mechanism is discussed.     

Covalent cross-linking of vasoactive intestinal polypeptide to its receptors on intact human lymphoblasts

125I-labeled vasoactive intestinal polypeptide (125I-VIP) was covalently cross-linked with its binding sites on intact cultured human lymphoblasts by each of three bifunctional reagents: disuccinimidyl suberate (DSS), ethylene glycol bis(succinimidyl succinate) (EGS), and N-succinimidyl 6-(4'-azido-2'-nitrophenylamino) hexanoate (SANAH). A fourth cross-linking agent with a shorter chain length, N-hydroxysuccinimidyl 4-azidobenzoate (HSAB), was much less effective in cross-linking 125I-VIP to the site. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography demonstrated a band of Mr approximately equal to 50,000 +/- 3,000, regardless of which cross-linker was used. The labeling of this band was specific in that it was prevented by 10(-6) M unlabeled VIP and was partially blocked by the homologous hormones secretin and glucagon. The relative potencies of these peptides in blocking the cross-linking of 125I-VIP to the Mr approximately equal to 50,000 band of the lymphoblasts (VIP greater than secretin greater than or equal to glucagon) were similar to those previously found for competitive inhibition of 125I-VIP binding to its putative high-affinity receptor on these cells. The covalent cross-linking required a bifunctional reagent; it was dependent on both the number of Molt cells and the concentration of 125I-VIP. The apparent molecular weight of the cross-linked species was unchanged by treatment with dithiothreitol. These observations suggest that the Mr = 50,000 species represents 125I-VIP cross-linked to a specific plasma membrane receptor and that the receptor does not contain interchain disulfide bonds.     

Chemical cross-linking of bovine retinal transducin and cGMP phosphodiesterase

The bifunctional reagents para-phenyldimaleimide and maleimidobenzoyl-N-hydroxysuccinimide ester were used to chemically cross-link the subunits of the transducin and cGMP phosphodiesterase (PDE) complexes of bovine rod photoreceptor cells. The cross-linked products were identified by Western immunoblotting using antisera against purified subunits of transducin (T alpha and T beta gamma) and PDE. Oligomeric cross-linked products of transducin subunits as large as (T alpha beta gamma)3 were observed in the latent form of transducin with bound GDP. In addition to the expected T alpha beta and T beta gamma cross-linked products, a (T alpha gamma)2 structure was detected. The close proximity of T alpha and T gamma suggests that T gamma may play a role in conferring the specificity of the interaction between T alpha and rhodopsin. Most of the oligomeric cross-linked structures between T alpha and T beta gamma were diminished in the activated form of transducin, with guanosine 5'-(beta, gamma-imidotriphosphate) (Gpp(NH)p) bound. However, cross-linking between T beta and T gamma was not altered. These results suggest that transducin exists as an oligomer in solution which dissociates upon the binding of Gpp(NH)p. To identify the possible interacting domains between the T alpha, T beta, and T gamma subunits, the cross-linked products were subjected to limited tryptic proteolysis. Several cross-linked tryptic peptides of transducin subunits were found and include the cross-linked products of the N terminus 15-kDa fragment of T beta and the C terminus 5-kDa fragment of T alpha, T gamma and the 12-kDa fragment of T alpha, T gamma and the 15-kDa as well as the 23-kDa fragments of T beta, and an intra-T alpha cross-linked product of the 2- and 21-kDa fragments. These results have allowed the construction of a topographical model for the transducin subunits. The organization of the subunits of PDE (P alpha, P beta, and P gamma) was also studied. The formation of the high molecular size cross-linked products of PDE resulted in the concurrent loss of the P beta and P gamma subunits, suggesting that they are in close proximity. Finally, the interaction between transducin and PDE was examined by chemical cross-linking of transducin-Gpp(NH)p and PDE. Two additional cross-linked products of 180 and 210 kDa were obtained which could be due to the cross-linking of T alpha or T beta with P alpha beta subunits.(ABSTRACT TRUNCATED AT 250 WORDS)     

Composition of cross-linked 125I-follitropin-receptor complexes

Both of the alpha and beta subunits of intact human follitropin (FSH) were radioiodinated with 125I-sodium iodide and chloramine-T and could be resolved on sodium dodecyl sulfate-polyacrylamide gels. Radioiodinated FSH was affinity-cross-linked with a cleavable (nondisulfide) homobifunctional reagent to its membrane receptor on the porcine granulosa cell surface as well as to a Triton X-100-solubilized form of the receptor. Cross-linked samples revealed three additional bands of slower electrophoretic mobility, corresponding to 65, 83, and 117 kDa, in addition to the hormone bands. The hormone alpha beta dimer band corresponded to 43 kDa. Formation of the three bands requires the 125I-hormone to bind specifically to the receptor with subsequent cross-linking. Binding was prevented by an excess of the native hormone but not by other hormones. A monofunctional analog of the cross-linking reagent failed to produce the three bands. Reagent concentration-dependent cross-linking revealed that their formation was sequential; smaller complexes formed first and then larger ones. When gels of cross-linked complexes were treated to cleave covalent cross-links and then electrophoresed in a second dimension, 18-, 22-, and 34-kDa components were released, in addition to the alpha and beta subunits of the hormone.     

Protein topography of the 40 S ribosomal subunit from Saccharomyces cerevisiae as shown by chemical cross-linking

Protein-protein cross-linking was used to examine the spatial arrangement of proteins within the 40 S ribosomal subunits of Saccharomyces cerevisiae. Purified ribosomal subunits were treated with either 2-iminothiolane or dimethyl 3,3'-dithiobispropionimidate under conditions such that the ribosomal particle was intact and that formation of 40 S subunit dimers was minimized. Proteins were extracted from the treated subunits and fractionated on Sephadex G-150 or by acid-urea-polyacrylamide gel electrophoresis. Cross-linked proteins in these fractions were analyzed by two-dimensional diagonal sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Constituent members of cross-linked pairs were radiolabeled with 125I and identified by two-dimensional gel electrophoresis and comparison with nonradioactive ribosomal protein markers. Forty-two pairs involving 25 of the 32 40 S subunit proteins were identified. Many proteins were detected in several cross-linked dimers. These proteins with multiple cross-links form foci for the construction of a schematic model of the spatial arrangement of proteins within the 40 S subunit.