Computing the geometry of a molecule in dihedral angle space using n.m.r.-derived constraints. A new algorithm based on optimal filtering.

We have developed a method based on optimal filtering to determine the three-dimensional structure of a protein from n.m.r.-derived constraints, using the dihedral angle internal representation of the molecule. It differs from currently proposed methods in that it directly produces estimates of errors on the parameters that are refined, hence providing an image of the minimum that has been found. A similar algorithm had already been proposed using cartesian co-ordinates as independent parameters, encoded in PROTEAN2. We found that using dihedral angles significantly reduces the computational burden of the technique, and provides better control over a priori informations that can be used, such as geometric restrictions for proline residues and informations from vicinal coupling constants. Performance of the method, encoded in FILMAN, is demonstrated by application to the folding of a ten-residue alanine polypeptide, to the geometric cyclization of an 11-residue peptide, as well as on the folding of a medium size protein, i.e. tendamistat. The validity of the error estimates on the dihedral angles produced by FILMAN is discussed.     

Chrysophycean scales as paleoindicators in the sediments of Hall Lake, Washington, U.S.A.

Twelve species of Mallomonas and ten species of other genera of Mallomonadaceae and Paraphysomonadaceae were found in sediments deposited in Hall Lake from about 1850 to the present. One Mallomonas species ( M. portue-ferreae peterfi & As-mund) was found that had not previously been reported from North America. The majority of the species have been described as either generally distributed or characteristic of acid or oligotrophic humic waters. M. heterospina Lund and M. multiunca Asmund, which were restricted to sediments deposited during the operation of a sawmill on the lake, have been collected from very eutrophic to dystrophic waters as well. On the whole the species composition indicates a change in the lake from oligotrophic to more eutrophic conditions.     

Biosynthesis of a 7-alpha-methoxycephalosporin. Incorporation of molecular oxygen.

A 7-alpha-methoxycephalosporin containing a carbamoyloxymethyl substituent at C-3 (cephamycin C) has been isolated from the extracellular fluid of an aqueous suspension of Streptomyces clavuligerus shaken in the presence of 18O2. The cephalosporin has been converted into its N-acetyl dimethyl ester and the distribution of 18O in the latter determined by chemical-ionization mass spectrometry. The results indicate that the oxygen atom of the methoxy group, as well as that linked to the exocyclic methylene group at C-3, is derived from molecular O2.     

Interactions between platelet-surface glycoproteins. Identification of glycoproteins capable of binding to platelet surfaces.

1. Platelets have been isolated from plasma and their surface glycoconjugates radioactively-labelled using galactose oxidase and NaB3H4. 2. Conditions have been defined for optimal labelling of glycoproteins and a membrane fraction enriched in plasma membrane has been prepared and characterized by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. 3. Desialylated glycoproteins that act as receptors to peanut agglutinin and lentil lectin have been purified from a detergent extract of plasma membrane. 4. Two glycosylated polypeptides that are able to bind to the surfaces of platelets have been identified and some characteristics of the binding have been investigated.     

Dynamin spirals.

Dynamin is an important component of membrane recycling at the plasma membrane and, potentially, within the cell. The role of dynamin in clathrin-mediated endocytosis has been based on numerous endocytosis assays, as well as on the discovery and gross characterization of the assembled spiral structure of dynamin. Recently, it has been shown that dynamin can also bind to liposomes and form helical tubes that constrict and vesiculate upon GTP addition. This suggests that dynamin is capable of and may be responsible for the pinching off of clathrin-coated vesicles from the plasma membrane during clathrin-mediated endocytosis.     

Species 7. Cisticola Brunnescens. Pl. VII.

This third species of Cloud-scraper was first named by Dr. von Heuglin in 1862 from an adult male in Summer dress obtained by himself in Abyssinia. Later (in 1869), not realizing their specific identity, von Heuglin gave examples of the same species in Winter and juvenile dresses with different specific names, viz. iodopyga and habessinica , but did not have to contend with the difficulty of separating ayresii from brunnescens because the former species does not occur in Abyssinia. Elsewhere, from Kenya Colony to South Africa, that has always been the difficulty, and wherever the two species were subsequently found they were more or less indiscriminately related to one another as forms or allies of ayresii (under that bird's wrong name terrestris) , until, in 1913 *, Roberts showed the differences between them in South Africa, and, in 1922†, van Someren the same for Kenya Colony.     

Two subforms of eukaryotic topoisomerase I. Purification and structure-function relationships.

A new method for isolation of eukaryotic topoisomerase I from calf thymus and from Jurkat-1 cells using HPLC has been developed. The method allows quantitative purification of high molecular weight topo I and two low molecular weight fractions differing by their isoelectric points. It has been suggested that these fractions be characterized as two subforms of the enzyme possessing structural and functional differences. The differences in their specific activities, sensitivity to camptothecin and in their proteolytic digestion maps have been demonstrated for the two enzymes.     

Morphological studies on the genusClematis linn. VIII. Floral and inflorescence anatomy inClematis patens with eight-sepaled flowers

The vascular anatomy of inflorescence axes and flowers ofClematis patens have been studied. The species shows a unique behaviour of the vascular bundles in the transition node from vegetative stem to pedicel: stelar bundles increase in number from six to eight as they ascend through the transition node so that the number of vascular bundles coincides with that of sepals. In the pedicel stele the resulting eight bundles are disposed opposite to eight sepals. respectively; each sepal receives its vascular supply from the bundle facing it. Morphological and anatomical evidence suggests that the calyx of eight sepals in this species should be interpreted as having consisted originally of four pairs of opposite organs, rather than as having been derived secondarily through chorisis of sepals from a calyx of four sepals as seen in most other species ofClematis.     

Histidyl-tRNA synthetase.

Histidyl-tRNA synthetase (HisRS) is responsible for the synthesis of histidyl-transfer RNA, which is essential for the incorporation of histidine into proteins. This amino acid has uniquely moderate basic properties and is an important group in many catalytic functions of enzymes. A compilation of currently known primary structures of HisRS shows that the subunits of these homo-dimeric enzymes consist of 420-550 amino acid residues. This represents a relatively short chain length among aminoacyl-tRNA synthetases (aaRS), whose peptide chain sizes range from about 300 to 1100 amino acid residues. The crystal structures of HisRS from two organisms and their complexes with histidine, histidyl-adenylate and histidinol with ATP have been solved. HisRS from Escherichia coli and Thermus thermophilus are very similar dimeric enzymes consisting of three domains: the N-terminal catalytic domain containing the six-stranded antiparallel beta-sheet and the three motifs characteristic of class II aaRS, a HisRS-specific helical domain inserted between motifs 2 and 3 that may contact the acceptor stem of the tRNA, and a C-terminal alpha/beta domain that may be involved in the recognition of the anticodon stem and loop of tRNA(His). The aminoacylation reaction follows the standard two-step mechanism. HisRS also belongs to the group of aaRS that can rapidly synthesize diadenosine tetraphosphate, a compound that is suspected to be involved in several regulatory mechanisms of cell metabolism. Many analogs of histidine have been tested for their properties as substrates or inhibitors of HisRS, leading to the elucidation of structure-activity relationships concerning configuration, importance of the carboxy and amino group, and the nature of the side chain. HisRS has been found to act as a particularly important antigen in autoimmune diseases such as rheumatic arthritis or myositis. Successful attempts have been made to identify epitopes responsible for the complexation with such auto-antibodies.     

Tuna cytochrome c at 2.0 A resolution. I.Ferricytochrome structure analysis.

The crystal structure of oxidized cytochrome c from tuna hearts has been solved by x-ray diffraction to a resolution of 2.0 A, using four isomorphous heavy atom derivatives. The crystals, space group P43, have 2 independent cytochrome molecules in the asymmetric repeating unit. No significant difference is seen between these 2 molecules, aside from conformations of a few surface side chains. The molecular folding observed is essentially that reported for tuna ferrocytochrome c. In particular, the ring of phenylalanine 83 lies against the heme group and closes the heme crevice, and is not swung out into the surroundings as had been believed from the 2.8 A horse ferricytochrome c structure.     

Morphological and biochemical correlates of skeletal muscle contractility in the cat. II. Physiological and biochemical studies.

Isometric twitch characteristics and biochemical parameters of isolated myosin and sarcoplasmic reticulum have been compared in three cat hind limb muscles. The fast twitch caudofemoralis and the slow twitch soleus are almost pure muscles as judged from histochemical studies. Isolated myosin from the caudofemoralis is not only 2- to 3-fold higher in its ATPase activities than that of the soleus, but also in non-dissociated forms has greater electrophoretic mobility than the soleus myosin. Purified myosins from fast muscles as well as soleus exhibited three light chains upon electrophoresis. However, the intact non-solubilized myosins differed in electrophoretic mobilities. The sarcoplasmic reticulum fraction isolated from caudfemoralis exhibits faster rates of Ca++ binding and uptake than soleus, and when fit to a two component model, the caudofemoralis SR exhibits a higher amount of a fast binding site than does soleus SR, features reflected in differences in the relaxation time of the two muscles. In contrast, the fast twitch tibialis anterior has been shown to be a gradient of fiber types and its isometric twitch may be separated by selective nerve stimulation, into a fast and a slow twitch component. Our findings that myosin fractions, as well as sarcoplasmic reticulum fractions isolated from these two components differ with respect to their biochemical characteristics add support to the possibility of a dual function in this muscle.     

Choline biosynthesis in sheep. Evidence for extrahepatic synthesis.

Three isomers of methylphytylbenzoquinone have been isolated from lipids of the unicellular alga Scenedesmus obliquus, the most abundant being 2-methyl-6-phytylbenzoquinone (65% of the total). The 2-methyl-3-phytyl and 2-methyl-5-phytyl isomers amounted to 8 and 27% respectively. Previously problems have been encountered in the separation of the 3-phytyl and the 6-phytyl isomers, but in the present study it was found that they separated readily as quinols. Phytyl plastoquinone was also found and the relevance of these compounds to the biosynthesis of alpha-tocopherol is discussed. As well as phylloquinone, a hydroxyphylloquinone was detected, and studies indicated that it is the 5' carbon atom to which the hydroxy group is attached. Such a compound has been found by workers using other unicellular algae.     

Sequence of lamprey vitellogenin. Implications for the lipovitellin crystal structure.

The amino acid sequence of lamprey vitellogenin has been predicted from the nucleotide sequence of cloned cDNA. The sites of proteolytic cleavage that produce the lipovitellin complex from the vitellogenin have been located by comparing the N-terminal sequences of two lamprey lipovitellin polypeptides with the predicted sequence. These results also confirm that the vitellogenin sequence derived here corresponds to the lipovitellin complex for which the crystal structure has been solved previously. Predictions of secondary structure indicate that the region most likely to correspond to the large alpha-helical domain of the crystallographic model consists of vitellogenin residues 300 to 600. Similar to the lipovitellins of Xenopus laevis, lamprey lipovitellin appears to lack approximately 200 C-terminal residues that are present in vitellogenin. However, the lamprey lipovitellin differs from those of Xenopus and chicken in two respects. First, most of the serine-rich domain that is present as the phosvitin polypeptide in the lipovitellins of the higher vertebrates appears to be lost in the maturation of lamprey vitellogenin to lipovitellin. Second, the domains that constitute the large lipovitellin-1 polypeptide in Xenopus and chicken are present in two polypeptides in lamprey, owing to an additional proteolytic processing event.     

Protein inhibitor of acid deoxyribonucleases. Improved purification procedure and properties.

A method is described for the extensive purification of acid deoxyribonuclease (acid DNase) and its specific inhibitor from beef liver, the existence of which had been only supported by indirect evidence. By the use of insolubilized acid deoxyribonuclease, eight other proteins interacting with the enzyme have been detected. One of them (molecular weight, 59,000) was identified as responsible for phosphodiesterase activity which is often a contaminant of DNase preparations. Acid DNase (free of phosphodiesterase) and its inhibitor have been obtained as homogeneous proteins, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The molecular weight of acid DNase and its inhibitor are, respectively, 26,500 and 21,500; those of other proteins range from 17,000 to 112,000. The properties of beef liver acid DNase are similar to those described for the enzymes extracted from other sources. The same alteration of DNase kinetics by this inhibitor, as that previously demonstrated with an impure protein has been confirmed; the sigmoidal shape observed at pH 5 for the plot of initial rate versus substrate concentration progressively disappears with increasing pH. We have also demonstrated that RNA, which inhibits the acid DNase through a competitive binding to the catalytic site, is able, like the substrate, to reverse the binding of inhibitor to the enzyme.     

The 22 S cylinder particles of Xenopus laevis. I. Biochemical and electron microscopic characterization

Supernatant fractions obtained after high speed centrifugation (1 h at 100 000 X g) of homogenates from whole ovaries, oocytes as well as from separated nuclei and ooplasms of Xenopus laevis contain distinct 22 S particles which have been purified and characterized by sucrose gradient centrifugation, ion exchange chromatography on DEAE-Sephacel and fast protein liquid chromatography (FPLC). The purity of the particle fraction has been assessed by electron microscopy as well as one- and two-dimensional gel electrophoresis. The particles appear as hollow cylinders of 10 nm outer diameter and 16 nm length, showing a composition of four stacked annuli which often reveal 6 symmetrically distributed granular subunits of approximately 3 nm diameter. Biochemically the particles are characterized by a group of 12 polypeptides with Mr values from 22 000 to 30 000 which in urea-denatured state markedly differ in their isoelectric values, ranging from pH 5.4 to ca. 8.2. Tryptic peptide mapping has demonstrated that all 12 major polypeptides are different. No evidence for association with nucleic acids has been found. The particles are very stable and resist treatments with low and high salt buffers, chelating agents, various non-denaturing detergents, and 3 M urea. They occur in relatively high concentrations both in the nucleus and in the cytoplasm. Structurally and compositionally identical cylinder particles have also been found in cultures of kidney epithelial cells of Xenopus and in human carcinoma (HeLa) cells, indicating that this is a rather widespread component of diverse cell types and species. The significance of this particle and its relationship to morphologically similar particles described in the literature is discussed.     

Glutamine synthetase. IX. Purification and characterization of the enzyme from sheep spleen.

Glutamine synthetase (L-glutamate: ammonia ligase (ADP-forming), EC 6.3.1.2) has been purified about 550-fold from sheep spleen. The subunit weight of the enzyme is estimated to be 48 000. Sedimentation coefficient determination by density gradient centrifugation gives a value of 15.0 S. The approximate molecular weight calculated from the S value is 378500. In addition, electron micrographs of the enzyme show an "H" shape. Hence, the protein appears to have eight subunits. In sheep spleen, the enzyme resides chiefly in the soluble fraction of the cell. The amino acid composition of the enzyme from spleen shows similarity to that from other sources. The enzyme activity is nearly five times as high in Mg2+ as in Mn2+. ATP inhibits the enzyme; the inhibition is competitive with respect to Mg2+ATP. A number of compounds, such as D-alanine, AMP, creatine phosphate, arsenite in combination with 2,3-dimercaptopropanol, and 2-amino-4-phosphonobutyrate, also inhibit the enzyme. The inhibition by the last compound is competitive with respect to glutamate. D-Glutamate and alpha-methyl-DL-glutamate can serve as substrates in the synthesis reaction, but N-methyl-DL-glutamate cannot. On the other hand, neither D-glutamine nor N-acetyl-L-glutamine can replace L-glutamine as a substrate in the gamma-glutamyl transfer reaction of the enzyme. Inhibition of Mn2+ and ATP and its reversal by Mg2+ have been discussed as a means of regulating the enzyme activity in mammalian tissues.     

The chemistry and biology of thymosin. I. Isolation, characterization, and biological activities of thymosin alpha1 and polypeptide beta1 from calf thymus.

A partially purified extract from thymus tissue termed thymosin Fraction 5 has been shown to reconstitute immunological deficiencies resulting from the lack of thymic function in several animal models, as well as humans with primary and secondary immunodeficiency diseases. Thymosin Fraction 5 consists of a family of polypeptides with molecular weights ranging from 1,000 to 15,000. Several of these polypeptides contribute individually to the biological activity of the parent compound. Two polypeptide components of thymosin Fraction 5, termed thymosin alpha1 and polypeptide beta1, have been characterized chemically and biologically. Thymosin alpha1 is a highly acidic molecule composed of 28 amino acid residues. This polypeptide has potent biological activity and has been found to be 10 to 1,000 times as active as thymosin Fraction 5 in one in vivo and several in vitro bioassay systems designed to measure differentiation and function of thymus-dependent lymphocytes (T cells). Polypeptide beta1, in contrast, is inactive in our bioassay systems, suggesting that it is not involved in thymic hormone action. Sequence analysis and homology studies have indicated that polypeptide beta1, although present in Fraction 5, does not contribute to the biological activity of thymosin Fraction 5.     

The mitochondrial genome of wild-type yeast cells. IV. Genes and spacers

The organization of the mitochondrial genome of wild-type Saccharomyces cerevisiae cells has been investigated further, by degrading mitochondrial DNA with micrococcal nuclease. Under the conditions used, this enzyme very strongly degrades the A + T-rich stretches (spacers) whereas it only inflicts a limited number of breaks into the G + C-rich stretches (genes). The macromolecular fragments derived from the “genes” have been separated from the oligonucleotides originating from the “spacers” by gel filtration, and both sorts of products have been investigated. It has been shown (a) that the spacers are very homogeneous in base composition and have a G + C content lower than 5% (mitochondrial DNA has a G + C content of 18%); (b) that the genes are very heterogeneous in base composition, the G + C content ranging from about 25% to 50%, when the average size of the fragments is 1·2 × 10⁵; smaller fragments, molecular weight 4 × 10⁴, having a G + C level as high as 65%, have been isolated in a yield of 10%; the average G + C content of genes is about 32%; (c) that genes and spacers are present in about equal amounts in the mitochondrial genome and that they have comparable average sizes.     

The evolutionary history of Drosophila buzzatii. XXIII. High content of nonsatellite repetitive DNA in D. buzzatii and in its sibling D. koepferae.

The frequency and types of repetitive nonsatellite DNA of two sibling species of the repleta group of Drosophila, D. buzzatii, and D. koepferae have been determined. For each species, the analysis is based on a sample of more than 100 clones (400 kb) obtained from genomic DNA. A theoretical model has been developed to correct for the presence of a mixture of repetitive and unique DNA in these clones. After correction, a high content of repetitive DNA has been demonstrated for both species (D. buzzatii, 19-26%; D. koepferae, 27-32%). The repetitive sequences have been classified according to their hybridization pattern when used as probes against genomic DNA and by their in situ hybridization signals on polytene chromosomes. Data suggest that the main nonsatellite component of these species is simpler and more repetitive than that of D. melanogaster, pointing to a wide variability in content and class size distribution of repetitive DNA among Drosophila species.     

Mycolic acids. A reinvestigation.

Mycolic acids derived from the cell walls of Mycobacterium bovis BCG, Mycobacterium bovis Bovinus I, Mycobacterium smegmatis, and Mycobacterium tuberculosis H37Rv have been fractionated as their p-bromophenacyl esters by a two-step high performance liquid chromatographic procedure: 1) adsorption chromatography on 10-micrometer particle size silica gel, and 2) reverse phase partition chromatography on a 10-micrometer particle size support containing a C18 bonded phase. This procedure has resulted in the isolation of approximately 24 mycolic acids from each bacterium (very likely homologs of various mycolate types) instead of the two to four that have previously been described. The implication of these results on the previously determined structures of these fatty acids is discussed.