A distance geometry program for determining the structures of small proteins and other macromolecules from nuclear magnetic resonance measurements of intramolecular1H−1H proximities in solution

DISGEO is a new implementation of a distance geometry algorithm which has been specialized for the calculation of macromolecular conformation from distance measurements obtained by two-dimensional nuclear Overhauser enhancement spectroscopy. The improvements include (1) a decomposition of the complete embedding process into two successive, more tractable calculations by the use of “substructures”, (2) a compact data structure for storing incomplete distance information on a structure, (3) a more efficient shortest-path algorithm for computing the triangle inequality limits on all distances from this information, (4) a new algorithm for selecting random metric spaces from within these limits, (5) the use of chirality constraints to obtain good covalent geometry without the use ofad hoc weights or excessive optimization. The utility of the resultant program with nuclear magnetic resonance data is demonstrated by embedding complete spatial structures for the protein basic pancreatic trypsin inhibitor vs all 508 intramolecular, interresidue proton-proton contacts shorter than 4.0 Å that were present in its crystal structure. The crystal structure could be reproduced from this data set to within 1.3 Å minimum root mean square coordinate difference between the backbone atoms. We conclude that the information potentially available from nuclear magnetic resonance experiments in solution is sufficient to define the spatial structure of small proteins.     

Establishment and characterization of a new human hepatocellular carcinoma cell line

Summary A human hepatocellular carcinoma cell line (FOCUS—Friendship of China and United States) was derived from a patient with primary hepatocellular carcinoma. This cell line has been in continuous culture over an 18-mo period. The morphological and ultrastructural features of FOCUS are consistent with its neoplastic hepatocellular orgin. FOCUS cells contain aspartate aminotransferase and glucose-6-phosphatase activity. In addition, α₁-antitrypsin, fibrinogen, alpha fetoprotein, and carcinoembryonic antigens were detectble in the cytoplasm of the cultured cells by immunochemical staining techniques. The karyotype of the FOCUS cell is human in origin and it contains human DNA sequences as detected by molecular hybridization analysis. The FOCUS cells do not show evidence of density-dependent inhibition of growth under confluent conditions. Repeated growth curves over an 18-mo period were identical, revealing a doubling time of 42 to 48 h. The malignant potential of FOCUS cells was further demonstrated by their ability to lead to gross tumor formation after subcutaneous infection into nude mice. From one of the solid tumors grown in nude mice, recultured cell lines have been established and found to have properties identical to the original FOCUS cell line. This FOCUS cell line represents an additional model for further investigation of tumor specific antigens and the relationship between hepatitis B virus (HBV) and hepatocellular carcinoma. Preliminary molecular characterization has indicated the existence of integrated HBV sequences within the FOCUS genome.     

The binding of selenium to the lipids of two unicellular marine algae

Axenic cultures of the green algae $\text{Dunaliella}\text{primolecta}$ and red algae $\text{Porphyridium}\text{cruentum}$ were grown in the presence of sublethal quantities of selenite. All purified lipids from both algae were found to contain bound selenium, except for saturated hydrocarbons. Of the lipids which contain selenium, carotenoid pigments contain the greatest concentrations. Lipid-associated selenium is not metabolically incorporated. The selenium is probably non-covalently bound to the lipids.     

Effective cryoprotection of thylakoid membranes by ATP

Freezing of isolated spinach thylakoids in the presence of NaCl uncoupled photophosphorylation from electron flow and increased the permeability of the membranes to protons. Addition of ATP prior to freezing diminished membrane inactivation. On a molar basis, ATP was at least 100 times more effective in protecting thylakoids from freezing damage than low-molecularweight carbohydrates such as sucrose and glucose. The cryoprotective effectiveness of ATP was increased by Mg²⁺. In the absence of carbohydrates, preservation of thylakoids during freezing in 100 mM NaCl was saturated at about 1–2 mM ATP, but under these conditions membranes were not fully protected. However, in the presence of small amounts of sugars which did not significantly prevent thylakoid inactivation during freezing, ATP concentrations considerably lower than 0.5 mM caused nearly complete membrane protection. Neither ADP nor AMP could substitute for ATP. These findings indicate that cryoprotection by ATP cannot be explained by a colligative mechanism. It is suggested that ATP acts on the chloroplast coupling factor, either by modifying its conformation or by preventing its release from the membranes. The results are discussed in regard to freezing injury and resistance in vivo.Abbreviations CF₁ chloroplast coupling factor - Hepes 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid - PMS phenazine methosulfate - Tris 2-amino-2-(hydroxymethyl)-1,3-propandiol     

Evidence for lysosomal enzyme recognition by human fibroblasts via a phosphorylated carbohydrate moiety

Adsorptive endocytosis of five different lysosomal enzymes from various human and non-human sources was susceptible to inhibition by mannose and l-fucose, methyl α-d-mannoside, α-anomeric p-nitrophenyl glycosides of mannose and l-fucose, mannose 6-phosphate and fructose 1-phosphate. A few exceptions from this general scheme were observed for particular enzymes, particularly for β-glucuronidase from human urine. The inhibition of α-N-acetylglucosaminidase endocytosis by mannose, p-nitrophenyl α-d-mannoside and mannose 6-phosphate was shown to be competitive. The loss of endocytosis after alkaline phosphatase treatment of lysosomal enzymes supports the hypothesis that the phosphorylated sugars compete with a phosphorylated carbohydrate on the enzymes for binding to the cell-surface receptors [Kaplan, Achord & Sly (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 2026–2030]. Endocytosis of `low-uptake' forms of α-N-acetylglucosaminidase and α-mannosidase was likewise susceptible to inhibition by sugar phosphates and by alkaline phosphatase treatment, suggesting that `low-uptake' forms are either contaminated with `high-uptake' forms or are internalized via the same route as `high-uptake' forms. The existence of an alternative route for adsorptive endocytosis of lysosomal enzymes is indicated by the unaffected adsorptive endocytosis of rat liver β-glucuronidase in the presence of phosphorylated sugars and after treatment with alkaline phosphatase.     

The paramedial neurosecretory cells of the suboesophageal ganglion of the cricket,Teleogryllus commodus (Walk.)

Summary Ovariectomy, performed immediately after the final hatch, caused a reduction of stainable (neurosecretory?) material in the paramedial neurosecretory cells (PNC) (A-type) of the suboesophageal ganglion in 10 day-old females of Teleogryllus commodus (Walk.). A concomitant increase in nuclear volume and in the incorporation of ³⁵S-cysteine indicates increased synthesis of neurosecretory material. From these findings it is concluded that more stainable material is secreted in the cerebral neurohaemal organ after Ovariectomy. A functional relationship between the PNC and the ovaries is suggested.     

1H NMR studies at 360 Mhz of the methyl groups in native and chemically modified basic pancreatic trypsin inhibitor (BPTI)

In the ¹H NMR spectra obtained at 360 MHz after digital resolution enhancement, the multiplet resonances of the methyl groups in the basic pancreatic trypsin inhibitor (BPTI) were resolved. With suitable double irradiation techniques the individual methyl resonances were assigned to the different types of aliphatic amino acid residues. Furthermore, from pH titration and comparison of the native protein with chemically modified BPTI, the resonance lines of Ala 16 in the active site and Ala 58 at the C-terminus were identified. Potential applications of the resolved methyl resonances as natural NMR probes for studies of the molecular conformations are discussed.     

Xanthones et C-glucosides flavoniques du genre Gentiana (section Cyclostigma)

Xanthones with a uniform 1,3,7,8-oxidation pattern, the C-glycosides isoorientin and isovitexin, and in some cases mangiferin, were isolated from the aerial parts of G. nivalis, G. brachyphylla, G. favrati, G. rostani, G. utriculosa and G. schleicheri Kunz. The distribution of these compounds within the section Cyclostigma is given. Comparison of phenolic patterns in other sections of Gentiana is made.     

Zur Struktur von Reaktionszentren in phototrophen Bakterien: eine Standortbestimmung

Es ist gelungen, bakterielle Reaktionszentren-Komplexe (RC) ohne Lichtsammlerpigmente zu isolieren. Unsere Gruppe bearbeitet zur Zeit die Isolierung und Charakterisierung von Reaktionszentren aus Rhodospirillaceen. Bei phototrophen Bakterien sind 2 bis 4% des Bacteriochlorophylls mit einem Proteinkomplex assoziiert, in welchem sie durch aktinisches Licht oxidierbar sind und sich im Dunkeln wieder zurückreduzieren (P₈₇₀). Am besten untersucht sind RC-Komplexe von Rhodopseudomonas spheroides, R-26. Diese Mutante weist einen geringen Gehalt an Karotinoiden auf. Die RC-Komplexe werden mittels mild wirkender Detergenzien aus der Chromatophorenmembran solubilisiert. Sie enthalten je Mol RC 2 Mole BPhäo a, 4 Mole Bchl a, 1 Mol nichthämartig gebundenes Fe und 1 bis 2 Mole Ubichinon, die mit einem hydrophoben Trägerprotein assoziiert sind. Der Proteinanteil hat ein MW von etwa 7,5 10⁴ Dalton und ist aus drei verschiedenen Untereinheiten aufgebaut. Die größte der drei Untereinheiten kann vom Komplex wegdissoziieren, während die Pigmente an die beiden leichteren Untereinheiten gebunden bleiben und teilweise photochemische Aktivität bewahren. Die primäre, photochemische Reaktion ist ein lichtinduzierter Ladungstrennungsvorgang bei dem die RC-Bchl-Moleküle ein Elektron an einen Elektronenakzeptor abgeben. Als primäre Elektronenakzeptoren werden heute drei Möglichkeiten in Erwägung gezogen: Nichthäm-Eisen, Chinone und Ferrochinon-Komplexe. Es scheint, daß verschiedene Mikroorganismen ungleiche primäre Elektronenakzeptoren aufweisen. Energieübertragung in photosynthetischen Bakterienmembranen ist sehr wirkungsvoll. Weniger als 5% der absorbierten Photonen gehen als Fluoreszenzenergie verloren; der Rest führt zu Ladungstrennungen und Elektronentransport. Der hohe Wirkungsgrad muß durch charakteristische Strukturen, Umgebungsbedingungen und Interaktionen erklärt werden können. Interaktionen der Pigmentmoleküle untereinander, mit der Umgebung in der Chromatophorenmembran und mit den Trägerproteinen werden diskutiert als Standortbestimmung zur Beantwortung der Frage: Was macht die Bchl-Mole-küle des Reaktionszentrums geeignet, als Zentren des photochemischen Ladungstrennungsprozesses zu wirken? Ich danke den Mitarbeitern der Photosynthesegruppe Zürich für die kritischen Diskussionsbeiträge während des Kolloquiums über “Photosynthetische Membranen” an unserem Institut. Unsere Arbeit wird unterstützt durch den Schweizerischen Nationalfonds, NF-3.156-0.73, und die Fritz Hoffmann-La Roche-Stiftung.     

Protein synthesis in mouse embryos with experimentally produced asynchrony between chromosome replication and cell division

Summary The cleavage of fertilized mouse eggs was prevented during cytochalasin B incubation and consequently these eggs became tetraploid the following day during in vitro culture. When the eggs were cultured further in normal medium, they cleaved and gave rise to tetraploid blastocysts. Protein synthesis was analysed in these embryos at different developmental stages using two-dimensional polyacrylamide gel electrophoresis. The protein synthesis pattern of one-cell tetraploid eggs was intermediate between those of normal one- and two-cell embryos. Tetraploid two-cell embryos expressed protein sets equivalent to those of untreated four-cell embryos, and tetraploid four-cell embryos synthesized proteins similar to those of four- to eight-cell controls. At subsequent pre-implantation stages the asynchrony was no longer detectable. When fertilized eggs were cultured continuously in the presence of cytochalasin B, they became tetraploid, octoploid and more and more polyploid without cleavage occurring. The protein synthesis patterns expressed by these one-cell polyploid eggs did not resemble that of normal fertilized eggs, but were similar to those of cleaving control embryos and blastocysts of equivalent age and nuclear division. These results strongly suggest that in early mouse embryos stage-specific translation is temporally correlated with chromosome replication (karyokinesis) and independent of cell division (cytokinesis) or cell interaction.Some of these results were presented at the IX Congress of the International Society of Developmental Biologists in Basle, Switzerland, August 28–September 1, 1981