A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins

The three-dimensional structure of human angiogenin has been determined by X-ray crystallography and is compared here with an earlier model which predicted its structure, based on the homology of angiogenin with bovine pancreatic ribonuclease A. Comparison of the predicted model and crystal structure shows that the active-site histidine residues and the core of the angiogenin molecule, including most of the-strands and-helices, were predicted reasonably well. However, the structure of the surface loop regions and residues near the truncated C-terminus differs significantly. The C-terminal segment includes the active-site residues Asp-116, Gln-117, and Ser-118; Gln-117 in particular has been shown to be important in affecting the ribonucleolytic activity of angiogenin. Also, the orientation of one helix in the model differed from the orientation observed experimentally by about 20°, resulting in a large displacement of this chain segment. The difficulty encountered in predicting the surface loop regions has led to a new algorithm [Palmer and Scheraga (1991),J. Comput. Chem.,12, 505–526; (1992),J. Comput. Chem.,13, 329–350] for predicting the conformations of surface loops.     

Some improvements in the quality of NAA procedures and the reliability of the results

After considering the need for quality control in NAA, the concept of quality in NAA procedures themselves is discussed, and some important factors identified. Two approaches to improve quality are then described in more detail. The first concerns the unique ability of NAA using different isotopic reactions and different modes (INAA/RNAA) to provide independent data sets in the same laboratory, thus allowing internal validation or crosschecking. The second discusses the need for chemical yield measurements in RNAA and the advantages of the radioisotopic tracer technique. Some recent advances and further possibilities for this use of tracers are listed.     

Conformation of (2→1)-β-d-fructan in aqueous solution

The conformation and dilute solution properties of (2→1)-β-d-fructan in aqueous solution were studied by gel permeation chromatography, low-angle laser light-scattering photometry, viscometry, small-angle X-ray scattering and electron microscopy. Fractions covering a broad range of weight-average molecular weights (M_w) from 1.49 × 10⁴ to 5.29 × 10⁶ were obtained from a native sample by ultrasonic degradation and fractional precipitation. For M_w < 4 × 10⁴, the intrinsic viscosity [η] varies with M_w^0.71, indicating that the fructan chain behaves as a random coil expanded by an excluded-volume effect in this molecular weight region. For M_w > 10⁵, [η] exhibits an unusually weak dependence on M_w and finally becomes almost independent of molecular weight. This behaviour is interpreted in terms of a globular conformation of the high-molecular-weight fructan molecules. Small-angle X-ray-scattering measurements and electron microscopic observations support this interpretation of the values of [η] observed.     

PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM CLADISTIC ANALYSIS BASED ON MORPHOLOGICAL DATA1

A cladistic analysis was used to deduce the phylogenetic relationships within the colonial Volvocales. Forty-one pairs of characters related to gross morphology and ultrastructure of vegetative colonies as well as asexual and sexual reproduction were analyzed based on parsimony, using the PAUP 3.0 computer program, for 25 species belonging to nine volvocacean and goniacean genera of the colonial Volvocales. Chlamydomonas reinhardtii Dangeard was the outgroup. The strict consensus tree indicated the presence of two monophyletic groups, one composed of all the volvocacean species analyzed in this study and the other containing the goniacean species except for the four-celled species Gonium sociale (Dujardin) Warming. In addition, these two groups constitute a large monophyletic group, to which G. sociale is a sister group. A new combination Tetrabaena socialis (Dujardin) Nozaki et Itoh and a new family Tetrabaenaceae Nozaki et Itoh are thus proposed for G. sociale. In addition, the analysis suggests that the volvocacean genera Eudorina and Pleodorina are paraphyletic groups, respectively, and that the monotypic genus Yamagishiella has no autapomorphic characters and represents primitive features of the anisogamous and oogamous genera of the Volvocaceae. Phylogenetic relationships within the Volvocaceae and the Goniaceae, as well as the various modes of sexual reproduction exhibited by these organisms, are discussed on the basis of the analysis.     

Analysis of DNA polymerase activity in Petunia protoplasts treated with clastogenic agents

Clastogenic agents, i.e. agents that can induce chromosome or DNA breakage, have been shown to enhance the rale of direct gene transfer to protoplasts. The effect was analysed at the enzymatic level using protoplast homogenates as well as intact protoplasts. For that purpose existing procedures were modified to enable measurement of DNA polymerase in vivo. In the system used, external DNA was able to enter the cells without the addition of membrane-permeabilizing compounds. When comparing total DNA polymerase activity of protoplasts irradiated with X-rays or UV-light with that of untreated cells we did not observe significant differences. Incubation of protoplasts with high doses of bleomycin affected total DNA polymerase activity negatively. but dideoxythymidine triphosphate-sensitive activity was not influenced. We conclude that the DNA strand-breaks induced by low doses of X-rays. UV-light or bleomycin do not increase the total or the repair-DNA polymerase activity and. therefore. that the increase in the transformation rates after DNA strand-breaking is not preceded by enhanced DNA polymerase activity.     

The binding of zinc,but not cadmium,by phytic acid in roots of crop plants

Plant species adapted to soils enriched with heavy metals often accumulate these metals in their above or below ground organs. In this study, electron probe microanalysis of fractured, quench-frozen root specimens of common crop species shows that an appreciable quantity of Zn can be bound as Zn phytate (myo-inositolkis-hexaphosphate) within small vacuoles of cells in the root elongation zone of lucerne, soybean, lupins, tomato, rapeseed, cabbage, radish, maize and wheat exposed to high levels of Zn (80–300 M). Globular deposits of Zn phytate are most frequently observed in the endodermis of dicotyledonous species and in the pericycle of monocotyledonous species, but may also occur in the stele and inner cortex after prolonged exposure to toxic levels of Zn. The deposits could not be found in Zn-treated sunflower, field peas and Italian ryegrass. In three crop species, lucerne, soybean and maize, Zn-induced phytate globules were frequent, but exposure of roots to 30 M Cd did not induce the formation of Cd-containing globular deposits as observed inLemna minor (Van Steveninck et al., 1990a, 1992). Simultaneous Zn and Cd treatment induced the formation of Zn phytate globules as effectively as Zn alone, and Cd was not detected in the deposits.     

A new approach for rhizosphere research by X-ray microanalysis of microliter soil solutions

Lolium perenne growing with high root density on a fine nylon mesh (Kuchenbuch and Jungk, 1982) caused the development of element gradients in the rhizosphere below the mesh. Micro-liter soil solutions from 2-mg soil samples were sprayed onto Formvar-coated grids and analyzed by X-ray microanalysis in a transmission electron microscope. The results were comparable to those obtained by flame photometry and atomic absorption spectrometry (AAS) of conventional soil solutions from 1 g soil. X-ray microanalysis of micro-soil solutions allows the application of different extraction procedures to even small amounts of soil usually available from rhizosphere experiments. Information about soil buffering characteristics in the rhizosphere can thus be obtained. Aluminum accumulation in the rhizosphere of small segments of single Picea abies fine roots grown in undisturbed natural forest soil could be detected with this technique.     

The effects of continuous illumination on southern and northern Micrasterias strains

Different strains of Micrasterias (Chlorophyta, Conjugatophyceae); M. rotata (Grev.) Ralfs ex. Ralfs and M. denticulata Breb. ex. Ralfs var. angulosa (Hantzsch) W. & G. S. West from northern and southern Finland were treated with continuous illumination in order to study the cellular effects of the treatment and whether the tolerance to continuous light of the northern Finnish strains is related to the different daylenght conditions in northern and southern areas. During the growing season the Finnish strains normally live in long-day conditions or even in continuous light (between 60 and 70°N), and they also tolerated continuous illumination in the laboratory. Ultrastructural changes were found especially in the chloroplasts, where formation of calcium precipitates of different forms and sizes and also formation of plastoglobuli containing lipids appeared. However, even in 4-week treatments the ultrastructure of cells of these northern strains was not totally disrupted, contrary to what was found in southern M. torreyi , studied earlier. Southern and northern strains tolerated continuous illumination in different ways. They seem to differ from each other physiologically, and the differences are possibly located in their ionic metabolism and regulation. The injuries sustained during continuous illumination of Micrasterias may largely be caused by the accumulation of Ca²⁺ in cytoplasm and organelles, especially in the chloroplasts.     

Structural studies of reagents for peptide bond formation: Crystal and molecular structures of HBTU and HATU

Summary X-ray structure determinations of HBTU and HATU, well-known reagents for peptide bond formation, show that the solid-state structures of these compounds differ markedly from those commonly presented in the literature. The solid-state structures are isomers of the N,N,N',N'-tetramethyluronium salt formulation commonly written for HBTU and HATU. HBTU and HATU, obtained either directly from synthesis or from CH₃CN solution, crystallize as the guanidinium N-oxide isomers. Both compounds crystallize in nearly identical conformations, despite marked differences in crystal packing.