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PubMed1979

Substrate binding closes the cleft between the domains of yeast phosphoglycerate kinase.

Using small angle x-ray scattering from solutions of yeast phosphoglycerate kinase, we have measured the radius of gyration of the enzyme both in the presence and in the abscence of ligands. We find that the radius of gyration decreases by 1.09 +/- 0.34 A upon binding both substrates MgATP and 3-phosphoglycerate to form the ternary complex. Smaller decreases, at the limit of the precision of the measurement, were found for the separate binding of MgATP (0.30 +/- 0.50 A). Using computer modeling, it has been estimated that a substrate-induced cleft closure in phosphoglycerate kinase resulting from one lobe rotating 8-14 degrees relative to the other lobe lobe is consistent with this observed change in radius of gyration. We suggest, therefore, that the conformational change that results in the smaller radius of gyration for the ternary complex is a hinge motion of the two lobes which produces a closing of the cleft between the two lobes. The apparent similarity of the ligand-induced change in phosphoglycerate kinase to the cleft closure in hexokinase suggests that this kind of conformational change may prove to be a rather general kinase phenomenon (Bennett, W.S., and Steitz T.A. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4848-4852; Anderson, C.M., Zucker, F.H., and Steitz, T.A. (1979) Science 204, 375-380).

Adenosine Triphosphate↗
PubMedDate not supplied

[Internal structure of ribosomes using different types of emission].

A review is made of the experimental results obtained by the author and co-workers on the study of the structural organization of the RNA and the protein in ribosomes by the method of joint use of light, X-ray and neutron scattering and by the method of contrast variation in neutron scattering. Two rules are formulated for the folding of the ribonucleoprotein strand in ribosomes: (1) in each ribosomal subparticle the RNA is concentrated predominantly closer to the center of the particle whereas the protein has a more peripherical localization; (2) the compact ("crystallic") packing of hydrated RNA helices is an essential feature of the nucleus (nuclei) organization of the particles. An analysis of the experimental data on neutron scattering by ribosomal proteins has been done and the globulin conformation in solution of some of these proteins has been established. The widespread concept according to which the majority of ribosomal proteins on the ribosome and in solution are enlongated expanded structures is disputed. It is suggested that all, or almost all, ribosomal proteins are usual globular proteins recognizing the specific sequence of RNA on the periphery of the particles, and , hence, that the formation of functional centrers on the ribosome is, in principle, analogous to the formation of functional centers of other complex proteins with a quaternary structure.

Escherichia coli↗
PubMed1979

[Small angle X-ray scattering studies on the structure and symmetry of yeast pyruvate decarboxylase in solution].

The holo-enzyme of the pyruvate decarboxylase EC 4.1.1.1 isolated from brewer's yeast was studied by small-angle X-ray scattering. The point-group symmetry 222 deduced from electron microscopic investigations was confirmed for molecules in solution. The best approximation of the overall shape of the enzyme was reached by an homogeneous triaxial ellipsoid, with the half-axes of a = 2.47 nm, b = 5.08 nm and c = 8.0 nm. The ellipsoid is halved vertical to the a-axis, and both halves are turned from each other by about 30 degrees. As an explanation of the existence of four binding sites for Mg2+ and thiamine pyrophosphate on the dimeric molecule the hypothesis of a gene duplication is discussed.

Binding Sites↗
PubMed1977

Molecular structure of the K-region cis-dihydrodiol of 7,12-dimethylbenz[a]anthracene.

The molecular structure and conformation of the cis-5,6-dihydrodiol of 7,12-dimethylbenz[a]anthracene has been determined by an X-ray crystallographic analysis. The compound crystallizes in the space group P21/a with cell dimensions a equals 17.799(6), b equals 33.211(8), c equals 5.241(1) A, beta equals 91.88(2)degrees. There are two molecules, designated A and B in the asymmetrical unit, that are not related to each other by crystallographic symmetry. Their conformations are almost identical, and there are no significant differences in their bond lengths or angles. In both molecules the 5-hydroxyl group is equatorial while the 6-hydroxyl group is axial. This conformation is probably forced by steric hindrance between the hydroxyl group, 0-6, and the hydrogen atoms of the 7-methyl group. The molecules pack in the crystal by forming hydrogen bonds between the hydroxyl groups of adjacent molecules, A with A, B, with B, and A with B. The ring system of the cis-5,6-dihydrodiol is much more buckled than is that in 7,12-dimethylbenz[a]anthracene itself. The angle between the two outermost rings is 36 degrees, the deviation from planarity being primarily a consequence of the partial saturation in the ring containing the two hydroxyl groups. Extrapolation of these results to other dihydrodiol derivatives of carcinogenic hydrocarbons permits some predictions of preferred molecular geometry. Thus, the 8,9-dihydrodiol-10,11-epoxide of 7,12-dimethylbenz]a[anthracene, analogous to the biologically active 7,8-dihydrodiol-9,10-epoxide of benzo]a[pyrene, a mutagen that is believed to be an active intermediate in carcinogenesis by benzo]a[pyrene, should probably exist preferentially in a conformation bearing the8-hydroxyl group in the axial orientation.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1976

X-ray and functional studies of hemoglobins Nancy and Cochin-Port-Royal.

The mutations in hemoglobin Nancy beta145(HC2) Tyr leads to Asp and hemoglobin Cochin-Portal-Royal beta146(HC3) His leads to Arg involve residues which are thought to be essential for the full expression of allosteric action in hemoglobin. Relative to the structure of deoxyhemoglobin A, our x-ray study of deoxyhemoglobin Nancy shows severe disordering of the beta chain COOH-terminal tetrapeptide and a possible movement of the beta heme iron atom toward the plane of the porphyrin ring. These structural perturbations result in a high oxygen affinity, reduced Bohr effect, and lack of cooperatively in hemoglobin Nancy. In the presence of inositol hexaphosphate (IHP), the Hill constant for hemoglobin Nancy increases from 1.1 to 2.0. But relative to its action on hemoglobin A, IHP is much less effective in reducing the oxygen affinity and in increasing the Bohr effect of hemoglobin Nancy. This indicates that IHP does not influence the R in equilibrium T equilibrium as much in hemoglobin Nancy as in hemoglobin A, and this probably is due to the disordering of His 143beta which is known to be part of the IHP binding site. IHP is also known to produce large changes in the absorption spectrum of methemoglobin A, but we find that it has no effect on the spectrum of methemoglobin Nancy. In contrast to the large structural changes in deoxyhemoglobin Nancy, the structure of deoxyhemoglobin Cochin-Port-Royal differs from deoxyhemoglobin A only in the position of the side chain of residue 146beta. The intrasubunit salt bridge between His 146beta and Asp 94beta in deoxyhemoglobin A is lost in deoxyhemoglobin Cochin-Portal-Royal with the guanidinium ion of Arg 146beta floating freely in solution. This small difference in structure results in a reduced Bohr effect, but does not cause a change in the Hill coefficient, the response to 2,3-diphosphoglycerate, or the oxygen affinity at physiological pH.

Allosteric Site↗
PubMedDate not supplied

[Myelin].

The lipid and protein composition and the metabolic turnover of myelin in the C.N.S., are briefly reported. For a better understanding, it seemed useful to introduce some historical data on the discovery of myelin and to give a morphological description at structural and ultrastructural level.

Animals↗
PubMed1977

Structure and interactions of lipids in human plasma low density lipoproteins.

Temperature-dependent techniques (differential scanning calorimetry, polarizing microscopy, and x-ray scattering and diffraction techniques) were used to compare the properties of human plasma low density lipoproteins (LDL) with its extracted lipid classes. Three types of thermal transitions were characterized: (a) a reversible transition in intact LDL near body temperature associated with a liquid crystalline order-disorder phase change of cholesterol esters within the particles; (b) an irreversible high temperature transition (approximately 70-90 degrees) associated with LDL denaturation and release of cholesterol esters from the disrupted particles; and (c) low temperature transitions related to liquid crystalline and crystalline phase changes in these released esters. The temperature of the reversible transition in intact LDL varies among individual donors. Correlation analysis shows that the temperature of this transition negatively correlates with the amount of triglyceride relative to cholesterol ester in LDL. Studies on mixtures of cholesterol esters and triglycerides isolated from LDL show a similar effect, increasing amounts of triglycerides decreasing the temperature of the liquid leads to smectic liquid crystalline transition of the isolated esters. Thus, the amount of triglyceride in LDL influences the fluidity of the cholesterol esters in LDL. The enthalpy of the reversible transition in intact LDL is 0.69 cal/g of LDL cholesterol ester. This compares with 0.89 cal/g for the liquid leads to liquid crystalline transition of the cholesterol esters released from denatured LDL and 1.01 cal/g for the same transition in the extracted esters. Unlike the cholesterol esters released from denatured LDL, or isolated LDL esters, cholesterol ester in the intact LDL particle does not crystallize. These findings suggest that the behavior of cholesterol esters in intact LDL is constrained relative to their behavior when freed from the restrictions of the particle. These results together with experiments on partitioning of the individual lipid classes of LDL allow us to define the distribution and interaction of lipids in the intact LDL particle.

Calorimetry↗
PubMed1979

Small angle x-ray scattering from the inner and outer membranes from Escherichia coli.

Small angle X-ray data from purified forms of inner or cytoplasmic and outer membranes from Escherichia coli have been obtained and appear to be qualitatively similar. Transitory changes are apparent in the circularly averaged X-ray profiles from inner membranes. Such results could be due to the loss or denaturation of peripheral membrane proteins. Some partially dried forms of outer membrane are partly ordered and produce diffraction patterns which support an underlying bilayer structure. An extra light membrane fraction which results from membrane preparations utilizing a French pressure cell for spheroplast disruption has been characterized and shown to be similar to inner membrane. The purified membranes produce small angle X-ray diffraction patterns which are much different from those of lipid dispersions and the differences are attributable to the high protein content of the intact membranes. While the small angle X-ray region may be useful for characterizing the membrane preparations, the paucity of detail in the diffraction pattern suggest that it will be of little value in describing the complex underlying membrane structure.

Cell Membrane↗
PubMed1977

X-ray analysis of enzymically purified elastin from bovine ligamentum nuchae.

Insoluble elastin has been isolated from bovine ligamentum nuchae by treatment with quanidine and dithiothreitol followed by digestion with collagenase, purified by affinity chromatography. The preparation was subjected to both wide- and low-angle X-ray analysis. The wide-angle diffraction patterns of relaxed and stretched specimens showed only two broad diffraction rings, corresponding to spacings of 4.5 and 9.3 A. No significant reflections were visible in the low-angle diffraction pattern of unstretched specimens, but on stretching an equatorial reflection was produced, corresponding to spacings of between 45 and 50 A.

Animals↗
PubMed1977

The identification of particulate matter in biological tissues and fluids.

Sections, 1-2 micron thick, of Araldite embedded tissue were prepared to provide a link between optical and electron microscopy for the identification of crystals. This technique permits examination of individual particles by means of polarising light microscopy, electron microscopy, X-ray energy spectroscopy and electron diffraction. It provides a reliable method for routine and research studies. It has led to the positive identification of individual crystals of calcium pyrophosphate dihydrate and hydroxyapatite in synovial fluids. The method can be applied to the identification of other particulate matter in a variety of biological specimens.

Aged↗
PubMed1979

Silica and silicates in femoral lymph nodes of barefooted people in Ethiopia with special reference to elephantiasis of the lower legs.

Electron microscopy of femoral lymph nodes of barefooted Ethiopians show the presence of numerous particles of colloid-size and electron-density in the lysosomes of the macrophages in the gland. On diffraction analysis, the particles are found to be amorphous. Elemental microanalysis of the X-ray spectrum indicate the predominance of Si, Al and Fe. In elephantiasics some particles contain silicon alone, presumably silica. The distribution of the Al/Si ratios of the particles in subjects with elephantiasis of the lower legs show a difference from that of non-elephantiasics which is statistically "highly significant" at p less than 0.001. The importance of this as a possible aetiological factor in the disease is discussed. The hypothesis that the disease is discussed. The hypothesis that the disease is a silicosis of the peripheral lymphatics of the lower limbs is supported by the present study.

Aluminum↗
PubMed1977

Crystalloid nature of mineral deposits in Bowman's capsule of the human glomerulus. Study by X-ray microanalysis and electron microdiffraction.

Abnormal crystalline mineral deposits are often observed in the basement membrane of Bowman's capsule in the human glomerulus. The nature of these deposits has been the subject of much discussion. By means of electron probe microanalysis and electron diffraction techniques, we have identified these abnormal deposits as whitlockite (beta-calcium-orthophosphate).

Calcium Phosphates↗