The quatenary structure of Pseudomonas cytochrome oxidase studied by electron microscopy.

Pseudomonas cytochrome oxidase (EC 1.9.3.2) was studied by negative staining in the electron microscope. The best resolution was obtained with uranyl oxalate (pH 6.0) as negative stain. Electron micrographs confirm the idea of the dimeric structure of the enzyme. A rough model of cytochrome oxidase was constructed based on different projections of the molecule seen in the electron micrographs. In this model the subunits are identical and sterically equivalent.     

Computer modeling 16 S ribosomal RNA

A three-dimensional structure for 16 S RNA has been produced with a computer protocol that is not dependent on human intervention. This protocol improves upon traditional modeling techniques by using distance geometry to fold the molecule in an objective and reproducible fashion. The method is based on the secondary structure of RNA and treats the molecule as a set of double-stranded helices that are linked by flexible single-strands of variable length. Data derived from chemical cross-linking studies of 16 S RNA and tertiary phylogenetic relationships provide the constraints used to fold the molecule into a compact three-dimensional form. Possibly subjective evaluation of the input data are transformed into verifiable quantitative parameters. Relationships based on general locations within the 30 S subunit or on protein-RNA interactions have been specifically excluded. The resolution of the model exceeds that of electron micrographs and approaches that obtained in preliminary X-ray crystal structures. The model size of 245 x 190 x 140 A is compatible with that of the 30 S subunit as determined by electron microscopy. The volume of the model is 1.87 x 10(6) A which is similar to that of the small subunit in a preliminary X-ray crystal structure. The radius of gyration of the model structure of 76 A is intermediate to that seen for partially denatured and fully folded 16 S RNA. Computer graphics are used to display the results in a manner that maximizes the opportunities for human visual interpretation of the models. A format for displaying the structures has been developed that will make it possible for researchers who have not devoted themselves to ribosomal modeling to comprehend and make use of the information that the models embody. On this basis the computer-generated models are compared with models developed by other researchers and with structural data not included in the folding parameter data set.     

Three-dimensional structure of pig muscle phosphoglucose isomerase at 6 A resolution

A 6 Å resolution electron density map of pig muscle phosphoglucose isomerase has been obtained. From this map it has been possible to isolate a single molecule and to assign tentative subunit boundaries. The binding of the competitive inhibitor 6-phosphogluconate has been studied. The binding site appears to be close to the subunit interface.     

An electron microscopic approach to the quaternary structure of mitochondrial F1-ATPase

The three-dimensional structure of F1-ATPase from beef heart mitochondria was investigated by electron microscopic techniques. The presence of high concentrations of nucleotides is essential for preservation of the quaternary structure. When investigated under such conditions, monodisperse F1-ATPase could not be distinguished from the membrane-bound enzyme. At low resolution, the particle shape resembles an oblate ellipsoid of revolution with an axial ratio of about 2:1. From several lines of evidence (including field micrographs at higher magnifications, Markham rotational analysis, and tilting experiments), two conclusions may be drawn concerning the three-dimensional fine structure of F1-ATPase. 1. At the periphery of the molecule, six globular protein masses are orientated in a way similar to the chair conformation of cyclohexane. This array is interpreted to be made up of an alternating sequence of alpha and beta subunits. 2. Part of the central space is occupied by a seventh protein mass, protrusions of which are likely to be in contact with some of the outer subunits. A gamma subunit is supposed to be constituent part of this central protein mass. As a consequence, this model favours a stoichiometry of alpha 3 beta 3 gamma for the large subunits of beef heart F1-ATPase.     

Three-dimensional structure of cat muscle pyruvate kinase at 6 Angstrom resolution.

A 6 Å resolution electron density map of cat muscle pyruvate kinase has been calculated. From this map it has been possible to isolate a single molecule and to assign subunit boundaries. The binding of substrates, products and the divalent metal cation has been studied.     

Further Characterization of Glycerol Dehydrogenase from Cellulomonas sp. NT3060

Glycerol dehydrogenase prepared from Cellulomonas sp. NT3060 by an improved purification procedure was characterized. The molecular weight was calculated to be about 390,000 by gel filtration and about 336,000 by the sedimentation equilibrium method. The enzyme was composed of eight identical subunits whose molecular weight was 42,000 ~ 43,000. The NH₂-terminal and COOH-terminal amino acids of the subunit were identified as serine and histidine, respectively. The octameric subunit model of the enzyme was confirmed by electron micrographs, which showed as octad aggregate, composed of two tetragons face to face. Studies on the initial velocity and product inhibition were consistent with an ordered Bi-Bi mechanism in which NAD⁺ is bound first to the enzyme and NADH released last.     

The purification and properties of the glutamine synthetase from the cytosol of Soya-bean root nodules.

The major portion of glutamine synthetase activity in root nodules of soya-bean plants is associated with the cytosol rather than with Rhizobium japonicum bacteroids. Glutamine synthetase accounts for about 2% of the total soluble protein in nodule cytosol. Glutamine synthetase from nodule cytosol has been purified by a procedure involving fractionation with protamine sulphate, ammonium sulphate and polypropylene glycol, chromatography on DEAE-Bio-Gel A and Bio-Gel A-5m and affinity chromatography on glutamate-agarose columns. The purified preparation appeared to be homogeneous in the analytical ultracentrifuge. From sedimentation-equilibrium experiments a mol. wt. of about 376000 was determined for the native enzyme and 47300 for the enzyme in guanidinium chloride. From these data and measurements of electron micrographs, we have concluded that glutamine synthetase from nodule cytosol consists of eight subunits arranged in two sets of planar tetramers which form a cubical configuration with dimensions of about 10 nm (100 A) across each side. Glutamine synthetase from nodule cytosol has a higher glycine and proline content and a lower content of phenylalanine than the glutamine synthetase that has been prepared from pea seed. The cytosol enzyme contains four half-cystine molecules per subunit, which is in contrast with two reported for the enzyme from pea seed. Enzyme activity is striking influenced by the relative proportion of Mg2+ and Mn2+ in the assay medium. Activity is inhibited by feedback inhibitors and is influenced by energy charge.     

Ultrastructure and composition of bovine conglutinin.

Conglutinin binds in a Ca2+-dependent manner to the carbohydrate portion of zymosan and cell-bound iC3b (complement subcomponent C3b cleaved by Factor I in the presence of factor H) similarly to lectin-like proteins that participate in the clearance of plasma glycoproteins. This carbohydrate-binding protein has been found to include both collagenous and non-collagenous domains. Electron micrographs of bovine conglutinin are presented in which conglutinin appears as a tetramer of four 'lollipop' structures emanating from a central hub. The stem region, linking each head to the central hub, is quite stiff, whereas the hub-stem junction is a flexible hinge. From electron micrographs of a pepsin digest of conglutinin, the linkage region is identified as the collagenous portion of the macromolecule. Conglutinin is a multimer of a single polypeptide chain. From sedimentation equilibria of unreduced as compared with reduced and alkylated conglutinin, there are determined to be three disulphide-linked chains. These data, combined with information on the subunit polypeptide of conglutinin, suggest a model for conglutinin in which four disulphide-linked trimers are associated via the N-termini to form the intact macromolecule as viewed in the electron microscope. The ultrastructure of conglutinin appears ideally suited to its lectin-like function.     

Size and shape of the Escherichia coli lactose permease measured in filamentous arrays

The Escherichia coli lactose permease has been purified on cation exchanger to contain a minimal amount of phospholipids, i.e., 4-5 mol/mol of permease, in the presence of the detergent dodecyl beta-maltoside at its critical micelle concentration. This preparation is active in galactoside binding. When the detergent level is further reduced by dialysis, the lactose permease forms filaments one molecule wide and up to several micrometers long. The filaments tend to associate laterally to form sheets. Analysis of electron micrographs of negatively stained filamentous arrays indicates an average filament spacing of 51 A and a subunit period of 26-30 A along individual filaments. These values most probably correspond to the dimensions of the lactose permease molecule measured parallel to the membrane plane. In many filaments, the subunits show a stain-penetrated cleft. It suggests that the lactose permease molecule comprises two domains, which may be correlated with internal repeats between the N- and C-terminal halves of the polypeptide sequence.     

Purification and properties of xanthine dehydrogenase from Pseudomonas acidovorans.

Xanthine dehydrogenase (EC 1.2.1.37) from Pseudomonas acidovorans has been purified to near homogeneity (approx. 65-fold). The enzyme has a molecular weight of about 275 000. Electrophoresis in gels containing sodium dodecyl sulphate showed the presence of two types of subunit with molecular weights of about 81 000 and 63 000. Thus the intact molecule probably contains two of each type of subunit. Xanthine and hypoxanthine are good substrates, and NAD+ is an effective electron acceptor. With xanthine and NAD+ as substrates the purified enzyme has a specific activity of about 20 mumol NADH formed/min per mg protein. Michaelis constants for xanthine and NAD+ are 0.07 and 0.12 mM, respectively, and for hypoxanthine and NAD+ 0.29 and 0.16 mM, respectively.     

Size and shape of the multicatalytic proteinase from rat skeletal muscle

The multicatalytic proteinase from rat skeletal muscle, a non-lysosomal high molecular weight enzyme active at neutral to alkaline pH, has been examined in the electron microscope as well as by dynamic laser light scattering. Both methods reveal monodisperse particles. Electron micrographs show a cylinder-shaped complex with a diameter of 11 nm and a length of 16 nm in negatively stained, and a diameter of 9.6 nm and a length of 14.3 nm in freeze-dried, heavy metal replicated specimens. The molecule is composed of four rings or disks.     

Structure of the globular protein vicilin revealed by scanning tunnelling microscopy

Scanning tunnelling microscopy (s.t.m.) has been used to study the structure of the non-crystalline globular protein vicilin. Molecules were deposited on amorphous carbon substrates and imaged both in air and in vacuo without additional sample preparation. Current-voltage plots of an individual protein molecule are also reported. The s.t.m. images are compared with conventional transmission electron micrographs and with a model of vicilin based on small-angle synchrotron X-ray scattering data.     

Heavy riboflavin synthase from Bacillus subtilis. Particle dimensions, crystal packing and molecular symmetry

Heavy riboflavin synthase from Bacillus subtilis is an enzyme complex consisting of approximately three alpha-subunits (Mr 23.5 X 10(3)) and 60 beta-subunits (Mr 16 X 10(3)). The enzyme has been crystallized from phosphate buffer in a hexagonal crystal modification that belongs to space group P6(3)22. The asymmetric unit of the crystal cell contains ten beta-subunits. The structure of this unusual 10(6) Mr protein has been studied by small-angle X-ray scattering, electron microscopy of three-dimensional crystals, and crystallographic methods. The scattering curves can be interpreted in terms of a hollow sphere model with a ratio of inner and outer radius of 0.3:1. A diameter of 168 A was estimated from the scattering curves, in close agreement with electron microscopic studies. An aggregate with the stoichiometry beta 60, which was obtained by ligand-driven reaggregation of isolated beta-subunits, showed similar shape and dimensions, but a larger value for the ratio Ri/Ra. Electron micrographs of freeze-etched enzyme crystals showed approximately spherical molecules, which were arranged in hexagonal layers. The lattice constants found from the micrographs are in good agreement with the values derived from X-ray diffraction data. Rotation function calculations in Patterson space showed a set of peaks for 2-fold, 3-fold and 5-fold local rotation axes, accurately consistent with icosahedral symmetry and with the particle orientation A shown in the Appendix. The crystal packing can be described as follows: enzyme particles with icosahedral symmetry (point group 532) are located at points 32 of the hexagonal cell, corresponding to positions (0, 0, 0) and (0, 0, 1/2) on the 6-fold screw axes. From the data reported, it may be concluded that the enzyme structure can be described as an icosahedral capsid of 60 beta-subunits with the triangulation number T = 1. The alpha-subunits are located in the central core space of the capsid, but their spatial orientation is incompletely understood.     

Examination of subunit interaction in human ADH: carboxymethylation of the heterodimer beta 2 gamma 1.

Conflicting results have been obtained on whether the subunits of the human dimeric enzyme alcohol dehydrogenase interact kinetically. To examine this question, chemical modification by iodoacetate was used to selectively inactivate the beta 2 subunit of the heterodimeric isozyme beta 2 gamma 1. Subsequent studies of the modified beta 2 gamma 1 which, presumably, has only one functional active site per dimeric molecule, indicate that it is still active. Moreover, the properties of this hybrid are similar to those of the unmodified subunit. From these results, it is fair to conclude that the individual subunits of alcohol dehydrogenase contribute to the activity of the dimeric isozymes in an independent manner.     

Glutamine synthetase from a cyanobacterium, Phormidium lapideum: purification, characterization, and comparison with other cyanobacterial enzymes

Glutamine synthetase has been purified to homogeneity from cell extracts of a non-N2-fixing filamentous cyanobacterium, Phormidium lapideum. The subunit molecular weight of the enzyme was determined as about 59,000 by sodium dodecyl sulfate gel electrophoresis. Electron micrographs of the Phormidium enzyme revealed a two-layered structure of regular hexagons (12 subunits per molecule), which markedly resembles the three-dimensional polypeptide backbone structure of the Salmonella typhimurium glutamine synthetase established by X-ray crystallography (Almassy, Janson, Hamlin, Xuong, & Eisenberg (1986) Nature 323, 304-309). The N-terminal amino acid sequence of the Phormidium enzyme shows very high similarity with that of the enzyme from an N2-fixing cyanobacterium, Anabaena 7120; 18 residues are common in 23 residues compared. Strong immunocross-reactions between the antibody against the purified Phormidium glutamine synthetase and other cyanobacterial enzymes except the Anacystis enzyme were observed. The apparent Michaelis constants for NH3, L-glutamate, and ATP were determined to be 0.29, 7.4, and 1.7 mM, respectively. Divalent metal ions such as Mg2+ and Mn2+ activated the enzyme in the biosynthetic reaction, whereas various amino acids and glutamate analogs strongly inhibited the enzyme.     

Structure of animal ribosomes. VI. Adynamic model of ribosome structure]

A dynamic model for the structure of ribosomes is developed using X-ray small-angle scattering data and electron micrographs of ribosomes and polysomes. The large subunit has the shape of a conical frustum, and has a groove at its flat side. The small subunit consists of two semiparticles which are connected by a molecular strand; it may assume two conformations: a prolate P conformation and an oblate O conformation. Translocation of the ribosome along the mRNA in the elongation process of protein synthesis is accomplished by cyclic conformation transitions P-O-P-O in combination with the linking and rupturing of bonds. This mechanism is called "rack and roll" mechanism.     

Hemocyanin from the Australian freshwater crayfish Cherax destructor. Electron microscopy of native and reassembled molecules.

Examination and measurement of electron micrographs of negatively stained hemocyanin molecules from Cherax destructor show that the predominant aggregated forms, the 16S and 24S components, are typical structures for arthropod hexamers and dodecamers, respectively. In Cherax hemocyanin the hexamers are formed from the monomeric (Mr congruent to 75,000) subunits, M1 and M2, while the dodecamers contain in addition a dimeric (Mr congruent to 150,000) subunit, M3'. Studies of the composition of solutions of the subunits M1 and m2 to which calcium ions have been added at pH 7.8 show that, under these conditions, reassembly occurs to particles indistinguishable from native hexamers. It is noteworthy that dodecamers are not seen since this confirms the previous suggestion that incorporation of the dimeric subunit in the assembly process is necessary for their formation. The results obtained from Cherax hemocyanin are related to those of previous structural studies of arthropod hemocyanins. In particular, the possible controlling role of certain specific subunits in arthropod hemocyanin oligomers containing more than one kind of subunit is illustrated with a model for the Cherax dodecamer, in which the dimeric subunit is shared between the two halves of the molecule.     

Computer averaging of single molecules of alpha 2-macroglobulin and the alpha 2-macroglobulin/trypsin complex

From electron micrographs single molecules of alpha 2-macroglobulin in the "closed" form, the "open" form and as the trypsin complex have been computer averaged. The molecular images are discussed. Molecules of the electrophoretically fast migrating "F-form" have the "closed" form. In the case of the alpha 2-macroglobulin/trypsin complex the two attached trypsin molecules are located very near to each other and in the central part of the alpha 2-macroglobulin molecule.     

Architecture of peroxisomal alcohol oxidase crystals from the methylotrophic yeast Hansenula polymorpha as deduced by electron microscopy.

The architecture of alcohol oxidase crystalloids occurring in vivo in the peroxisomes of methylotrophic yeasts was deduced from electron micrographs of similar crystals of the Hansenula polymorpha enzyme grown in vitro. Three characteristic views of the crystal are observed, as well as single layers in the very early stages of crystal formation. The crystal is concluded to be cubical, with every octameric molecule making the same contacts with four neighbors in one plane, at right angles to its fourfold axis. The unit cell contains six octamers, in three mutually orthogonal orientations, and two large holes, which can accommodate other peroxisomal proteins involved in methanol metabolism. The crystal contains channels, connecting the holes, which allow the diffusion of relatively large molecules through the crystal. Crystal formation depends on just one contact per subunit, which may explain the fragility of the crystals.     

Investigation of the structure of nitrogenase by means of electron microscopy combined with optical diffraction]

Nitrogenase molecules are observed in electron micrographs as hepta or octa hedral rings about 100 angstrom in diameter and stick-like particle 95 angstrom wide and as long as 300 angstrom and more. The electron microscopy pattern was investigated by the optical diffraction technique. It is shown that the nitrogenase molecule has a cylindrical helical structure. The helical parameters of this structure have been determined. The molecule is composed of a family of discrete helixes (number of helixes 8), the spacing between the nearest subunits along the vertical axis being 25 angstrom and the period of the structure about 50 angstrom. It is supposed that the stick-like particle as a side-view projection of the polymerized round molecules. A hypothetic model of the protein is presented.