Elastic anisotropy of bivalve hinge-ligament

Compressive stress-strain properties of an elastic ligament of a bivalve, Pseudocardium sachalinensis were investigated in the swollen state in water. The ligament is a calcified tissue, composed of calcium carbonate and insoluble protein which is rich in methionine S-oxide residue [Kikuchi, Y. and Tamiya, N., J. Biochem. (Tokyo) 89, 1975-1976 (1981)]. X-ray diffraction study showed that calcium carbonate existed only in orthorhombic aragonite form, and that all the crystal c-axes of the unit cell orientate nearly in the growing direction of the ligament. The uniaxial compression modulus for the growing direction was appreciably larger than those for the other two directions, while the anisotropy of the modulus was absent for a decalcified ligament. Thus the mechanical anisotropy of the ligament could be explained by means of the uniaxially oriented structure of aragonite crystals being dispersed in a nearly isotropic protein matrix.

Three-dimensional structure of aspartate aminotransferase from Escherichia coli at 2.8 A resolution

The crystal structure of aspartate aminotransferase of Escherichia coli was determined by X-ray structure analysis at 2.8 A resolution. The structure was solved by the molecular replacement method and refined to an R-factor of 0.27, and it was found that the overall structure of AspAT of E. coli is similar to that of those of higher animals.

Crystallization and preliminary X-ray studies on human epidermal growth factor

Single crystals of human epidermal growth factor have been prepared from a polyethylene glycol solution and characterized by X-ray diffraction. The crystals grow in a space group of P2(1) with unit cell dimensions of a = 32.7, b = 32.5, c = 22.3 A, and beta = 96.9 degrees. They contain a single molecule per asymmetric unit and show better diffraction than 2.5 A.

Overproduction and preliminary X-ray characterization of aspartate aminotransferase from Escherichia coli

The aspartate aminotransferase of Escherichia coli was overproduced in cells after genetic manipulation, and was crystallized from a polyethylene glycol solution, pH 7.0. The crystals obtained were of good quality and had diffractions extending beyond 2.4 A. The space group and unit cell dimensions were determined with a precession camera and a four-circle diffractometer to be C222(1), and a = 157.1 A, b = 85.5 A, and c = 79.7 A, respectively. Only one protein subunit is contained in an asymmetric unit.

Single crystals of hydrogenase from Desulfovibrio vulgaris Miyazaki F

The hydrogenase solubilized from the particulate fraction from Desulfovibrio vulgaris Miyazaki F (IAM 12604) has been crystallized. Although the solubilized hydrogenase purified by the previous method (Yagi, T., Kimura, K., Daidoji, H., Sakai, F., Tamura, S., and Inokuchi, H. (1976) J. Biochem. (Tokyo) 79,661-671) revealed a single band upon disc electrophoresis, it could not be crystallized. The apparently homogeneous hydrogenase has been separated into three components of similar molecular weights by high performance liquid chromatography on DEAE-Toyopearl. Each hydrogenase component was successfully crystallized by means of the vapor diffusion method with polyethylene glycol or 2-methyl-2,4-pentanediol as a precipitating agent. Seeding procedure is necessary to grow an x-ray grade crystal. Preliminary x-ray experiments reveal that crystals grown from one component are in space group of P2(1)2(1)2(1) with a = 102.1(1), b = 126.8 (3), and c = 66.9(1) A. The unit cell volume of 8.66 X 10(5) A3 suggests that it contains one molecule/asymmetric unit (Vm = 2.43). The crystals grown from another component are in the same space group with a = 99.6(1), b = 126.8(3), c = 66.9(1) A, and the unit cell volume is 8.45 X 10(5) A3 (Vm = 2.37). The crystals diffract more than 2.5 A and are suitable for complete crystal analysis. Up to 4 A resolution native data have been collected on a diffractometer.

Crystallographic study of cytochrome c553 from Desulfovibrio vulgaris Miyazaki

Cytochrome c553 from the sulfate-reducing bacterium, Desulfovibrio vulgaris Miyazaki, has been crystallized. The combination of microdialysis and vapor diffusion allowed successful crystallization. The crystals were of good quality, and useful data were obtained that extended to the nominal resolution of 1.3 A. The space group is P4(3)2(1)2 with cell dimensions of a = b = 42.7 A, c = 103.4 A. More than twenty heavy-atom reagents were screened with the isomorphous replacement technique, and only the mersalyl derivative could be used for the phase determination. The single isomorphous replacement method combined with the anomalous scattering effect of the Hg-atom in mersalyl and the Fe-atom of the heme group was used for the phase determination.

Refined structure of cytochrome c3 at 1.8 A resolution

The structure of cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris Miyazaki has been successfully refined at 1.8 A resolution. The crystallographic R factor is 0.176 for 9907 significant reflections. The isotropic temperature factors of individual atoms were refined and a total of 47 water molecules located on the difference map were incorporated in the refinement. The four heme groups are closely packed, with adjacent pairs of heme planes being nearly perpendicular to each other. The fifth and the sixth ligands of the heme iron atoms are histidine residues with N epsilon 2-Fe distances ranging from 1.88 A to 2.12 A. The histidine co-ordination to the heme iron is different for each heme group. The heme groups are all highly exposed to solvent, although the actual regions exposed differ among the hemes. The four heme groups are located in different environments, and the heme planes are deformed from planarity. The differences in the heme structures and their environments indicate that the four heme groups are non-equivalent. The chemical as well as the physical properties of cytochrome c3 should be interpreted in terms of the structural non-equivalence of the heme groups. The characteristic secondary structural non-equivalence of the heme groups. The characteristic secondary structures of the polypeptide chain of this molecule are three short alpha-helices, two short beta-strands and ten reverse turns.

Studies on the phenotyping system of hyperlipoproteinemias. Evaluation of a new method by enzymic staining of lipids in serum lipoproteins separated by electrophoresis on agarose

A new electrophoresis of lipoproteins was examined as a means of defining hyperlipoproteinemia phenotypes. The serum lipoproteins of 119 patients with hyperlipoproteinemia whose serum total cholesterol (TC) concentration was more than 250 mg and/or whose triglyceride (TG) concentration exceeded 180 mg per 100 ml were determined by using a method of electrophoretic separation of lipoproteins on agarose and enzymic staining of each lipid component separately. Based on the lipoprotein-lipid profile with the acid of various parameters for distinction, i.e., Type II A, LDL-C greater than or equal to 180 mg/dl: Type IV, VLDL-TG greater than or equal to 130 mg/dl: type II B, LDL-C greater than or equal to 130 mg/dl, 119 patients were classified into Fredrickson's phenotypes of hyperlipoproteinemia. The percentages of phenotypes with those hyperlipoproteinemias were: type II A, 31.1%; II B, 33.6; IV, 29.4%; and V, 5.9% respectively. But types I and III were not observed in this survey. The characteristics of the lipoprotein profiles of each phenotype were clearly identified, and they were: type II A, high peak LDL-C and decrease of HDL-C fraction; II B, high peak of LDL-C and VLDL-TG; IV, high peak of VLDL-TG; V, prominence of chylomicrons and high VLDL-TG peak. The serial observations of the lipoprotein-lipid profiles were very useful for detecting the progressive changes in lipoproteins which occurred during the course of diseases, particularly in cases of secondary hyperlipoproteinemia. In conclusion, the new lipoprotein-lipid profile based on the agarose electrophoresis-enzymic staining method not only offers great help in classification of hyperlipoproteinemia but has contributed to therapeutic management.

On cytochrome c3 folding

The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki (DvM) is considered in detail by scrutinizing main chain folding together with the structure of the protein from D. desulfuricans Norway (DdN). The relative arrangement of the four heme groups in this molecule is similar to that of DdN and the disposition of alpha-carbon atoms of cysteine and histidine residues binding to heme groups is also similar. Structural differences between the two proteins occur in the shape of some specific loops of the chain on the molecular surface. As a result of a careful comparison of structures and sequences in both cytochromes c3, the reported sequence alignment of the cytochrome c3 family has been revised. Our new proposal of a sequence alignment based on the three-dimensional structures contains 24 evolutionarily conservative residues. All these conservative residues may play an important role in the folding pattern of cytochromes c3.

The structure of cytochrome c3 from Desulfovibrio vulgaris Miyazaki at 2.5 A resolution

The structure of tetraheme cytochrome c3 isolated from Desulfovibrio vulgaris Miyazaki has been determined at 2.5 A resolution by an X-ray diffraction method. Protein phases were computed by the multiple isomorphous replacement method using the native and four heavy atom derivatives, anomalous scattering measurements of the latter being considered. The mean figure of merit was 0.77. Four heme groups are exposed on the surface of the molecule. There are some short helical segments in the polypeptide chain, and hair-pin turns are often observed at glycine and alanine residues.

Molecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution

The crystal structure of Taka-amylase A was studied by an X-ray diffraction method at 3 A resolution. A total of 452 amino acid residues were found from the electron density map at the present stage. The four disulfide bonds and the branched carbohydrate were also located on the map. The difference electron density map of the maltotriose-soaked crystal showed that a maltose unit was bound in the active center left. The binding of iodine atoms to the enzyme was also studied.

Crystallographic data for cytochrome c3 from two strains of Desulfovibrio vulgaris, Miyazaki

Two crystalline forms of cytochrome c3 isolated from two strains of Desulfovibrio vulgaris, Miyazaki, tentatively designated as D. vulgaris, Miyazki F and D. vulgaris, Miyazaki K, have been found. Both belong to the orthorhombic system, space group P2(1)2(1)2(1), but have different cell dimensions; a=54.1, b=68.9 and c=35.0 A for D. vulgaris, Miyazaki F, and a=43.5, b=41.2, and c=62.9 A for D. vulgaris, Miyazaki K. The asymmetric unit of each crystal contains one molecule of cytochrome c3.