Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei

Enzymes from the pentose phosphate pathway (PPP) are potential drug targets for the development of new drugs against Trypanosoma brucei, the causative agent of African sleeping disease: for instance, the 6-phosphogluconate dehydrogenase is currently studied actively for such purposes. Structural and functional studies are necessary to better characterize the associated enzymes and compare them to their human homologues, in order to undertake structure-based drug design studies on such targets. In this context, the crystal structure of 6-phosphogluconolactonase (6PGL) from T. brucei, the second enzyme from PPP, was determined at 2.1 Angstroms resolution. Comparison of its sequence and structure to other related proteins in the 6PGL family with a known structure (Thermotoga maritima Tm6GPL 1PBT and Vibrio cholerae Vc6PGL (1Y89), which have not been discussed in print), or in the glucosamine-6-phosphate-deaminase family (hexameric Escherichia coli 1DEA and monomeric Bacillus subtilis 2BKV), allowed the identification of the 6PGL active site. In addition to the analysis of the crystal structure, 3D NMR interaction studies and docking experiments are reported here. Key residues involved in substrate binding or in catalysis were identified.     

Three dimensional structure of bacterial pili

Crystallographic and associated biochemical and structural studies are in progress on the fiber-forming pilin proteins of the gonococcal pilus. Preparative scale purification procedures have been developed for the gonococcal pilin protein, which appear generally applicable to bacterial pilins. For three gonococcal pilin protein strains, we have obtained both reassembled pilus fibers and three-dimensional crystals. One needle-shaped crystal form of gonococcal C30 pilin diffracts beyond 3 Å resolution using synchrotron x-ray radiation. A diffraction data set to 3.5 Å resolution has been collected on these needle-shaped crystals (lattice spacings a=125.4(3) b=120.4(3), c=26.61(4) Å) in which the packing arrangement of the pilin subunits appears to resemble that seen in the pilus fibers using electron microscopy. X-ray diffraction data confirm our proposed model for the overall polypeptide fold of a pilin subunit, which is an antiparallel 4- helix bundle similar to tobacco mosaic virus coat protein and myohemerythrin.     

Dual subcellular localization of sialidase in cultured granule cells differentiated in culture.

A rapid small-scale procedure was set up to obtain highly purified preparations of lysosomes and plasma membranes from the homogenate of cerebellar granule cells differentiated in culture. It consisted in a centrifugation of the postnuclear fraction P2, on a Percoll gradient with formation of an upper and lower band. The upper band, upon centrifugation on 1 M sucrose, produced a light band lying on the top, that constituted the plasma membrane preparation. The upper band constituted the lysosome preparation. The plasma membrane preparation exhibited a 6-fold relative specific activity increase of Na+, K(+)-ATPase and 5'-nucleotidase, with negligible contamination by other subcellular markers; the lysosomal preparation exhibited a 30-fold relative specific activity increase of beta-galactosidase and beta-hexosaminidase, with virtually no contamination by other subcellular markers. Both the lysosome and plasma membrane preparations carried sialidase activity on MUB-NeuNAc and ganglioside GD1a. The sialidase activity on GD1a required the presence of Triton X-100 in both subcellular preparations; the sialidase activity on MUB-NeuNAc was markedly activated by albumin only in the lysosomes. The lysosomal sialidase had a unique optimal pH value, 3.9. The plasma membrane sialidase featured two values of optimal pH, one at 3.9, for both substrates and second at 5.4 and 6.0 for MUB-NeuNAc and GD1a, respectively. It is concluded that cerebellar granule cells differentiated in vitro possess one lysosomal sialidase and two plasma membrane sialidases, all of them active on ganglioside.     

Three dimensional structure and morphology of pelagic fish schools

In fish resource assessment, it is very important to know about the behaviour and form of fish schools. This paper describes the three‐dimensional (3D) morphology and internal structure of pelagic schools observed using vertical‐scanning multibeam sonar. The acoustic data were collected in waters off Venezuela, Senegal, and Mexico. The data were used to derive metrics of school location, density, shape and internal structure from a total of 668 schools: 257 from Mexico, 343 from Venezuela and 68 from Senegal. In general, school shapes were amoeboid‐like (e.g. spheres or ellipsoids) and not simply geometric. Also, the fish were patchily‐distributed, forming both nuclei (groups) and vacuoles (empty spaces) within the schools. The results support the hypothesis of ‘auto‐organization of the fish inside schools’, meaning that the distribution of fish within a school arises from the elementary reaction of the individuals.     

SARS病毒S蛋白三维结构预测

蛋白质结构类型识别方法可以在没有序列同源性的蛋白质之间检测有没有结构相似性。利用蛋白质结构类型识别方法预测了SARS病毒S蛋白N端区域的结构。模建的SARS病毒S蛋白N端区域是一个全折叠的结构。     

Diacylglycerol kinase from suspension cultured plant cells : characterization and subcellular localization

Diacylglycerol kinase (adenosine 5′-triphosphate:1,2-diacylglycerol 3-phosphotransferase, EC 2.7.1.107), purified from suspension cultured Catharanthus roseus cells (J Wissing, S Heim, KG Wagner [1989] Plant Physiol 90: 1546-1551), was further characterized and its subcellular location was investigated. The enzyme revealed a complex dependency on lipids and surfactants; its activity was stimulated by certain phospholipids, with phosphatidylinositol and phosphatidylglycerol as the most effective species, and by deoxycholate. In the presence of Triton X-100, used for its purification, a biphasic dependency upon diacylglycerol was observed and the apparent Michaelis constant values for diacylglycerol decreased with decreasing Triton concentration. The enzyme accepted both adenosine 5′-triphosphate and guanosine 5′-triphosphate as substrate and showed rather low apparent inhibition constant values for all nucleoside diphosphates tested. Diacylglycerol kinase is an intrinsic membrane protein and no activity was found in the cytosol. An investigation of different cellular membrane fractions confirmed its location in the plasma membrane.     

The fine structure of exfoliated cervical and vaginal cells.

In order to understand the means by which cellular aggregates were maintained in gynecologic samples, the fine structure of samples derived from a number of women of various ages was examined with special attention paid to the intercellular junctions. Most cells in the samples were squamous cells containing numerous intercellular fibrils and glycogen granules. Parabasal or intermediate cells were also seen as well as occasional endocervical cells. All of these cell types were often found as parts of aggregates and, while other cell junctions were present, desmosomes were the most prominent. It was concluded that desmosomes were probably responsible for maintaining the aggregated state of many of the cells found in gynecologic samples.     

Structural basis of motility in the microtubular axostyle: implications for cytoplasmic microtubule structure and function

The gross morphology of the protozoan microtubule axostyle of Saccinobaculus ambloaxostylus can now be described in macromolecular detail. The left-handed coil of the axostyle is seen to be dependent upon the asymmetry inherent in the constituent microtubules as expressed by the specific array of linkages between microtubules and by a possible tendency for microtubules to coil into left-handed helices. The laminated sheets of microtubules are not aligned parallel to the long axis of the organelle, but become increasingly tilted off-axis as one descends through the sheets of microtubules from the convex to the concave surface of the axostyle. Fine-structural analysis of the axostyle indicates similarities of the linkages to dynein. The potential loci of the force-generating protein(s) are discussed as well as implications of the axostyle's structure on general microtubule function.     

The fine structure of barley aleurone cells

Summary The ultrastructural morphology of both dry and water-imbibed barley aleurone cells is described. The aleurone cell is characterized by the presence of numerous aleurone grains and spherosomes. In addition, it contains organelles typical of other plant cells including structures similar to microbodies, and rough endoplasmic reticulum characterized by the presence of numerous polyribosomes. It is inferred that the morphological specialization of aleurone cells is related to their biochemical specialization.Work supported by National Science Foundation grant GB5863. The skillful technical assistance of Mrs. Janet Price is gratefully acknowledged.     

Qualitative and quantitative preservation of the fine structure of absorptive cells in cultured biopsies of human small-intestine

Summary The fine structure of the absorptive cells in human small-intestinal biopsies cultured for 6, 24, and 48 h was analyzed qualitatively and quantitatively. The findings show generally good preservation of the cultured absorptive cells and a normal distribution, size, and relative volume of their cell organelles, but there was a systematic decrease in the apical cell surface and an increase in the number of apical vesicles and tubules after culturing. Since the apical vesicles and tubules are thought to have a function in the transport of cell-coat material from the Golgi apparatus to the cell surface, these findings raise the question of whether a delayed transport or extrusion of cell surface material occurs.The diminished relative volume of the mitochondria and the increased signs of autophagy in some poorly preserved absorptive cells, are assumed to be an adaption to less favourable culture conditions.The authors acknowledge the help of Dr. A.S. Pena in the setting up of the organ culture technique, and also wish to thank Mrs. M.L. Bouwhuis for statistical advice and Mrs. M. de Gruil and Mr. L.D.C. Verschragen for technical assistance. The investigations were supported in part by the Foundation for Medical Research (FUNGO), which is subsidized by the Netherlands Organization for the Advancement of Pure Research (ZWO)     

Arachidonic acid channelling in the phospholipid fractions and subcellular compartments of cultured myocardial cells.

Arachidonic acid (AA) channeling in cultured heart cells was studied following pulse labelling for 1 h. AA was shown to be esterified immediately and equally distributed between the neutral lipids and phospholipids. A rapid constant flow to various phospholipid classes occurred thereafter, while the AA oxidation was only between 12%. The subcellular distribution of AA was studied by nitrogen cavitation followed by fractionation on 6.7% percoll in sucrose-EDTA. After 1 h pulse labeling and 2 h post-pulse incubation, most of the radioactivity was found in the sarcolemmal fraction with a much smaller amount in the mitochondrial fraction.     

Metabolic engineering of apoptosis in cultured animal cells: implications for the biotechnology industry

Animal cells have been widely used to obtain a wide range of products for human and animal healthcare applications. However, the extreme sensitivity of these cells in respect to changes experienced in their environment is evidenced by the activation of a gene-encoded program known as apoptosis, resulting in their death and destruction. From the bioprocess angle, losses in cell viability bring lower productivities and higher risks of product degradation. Consequently, many research efforts have been devoted to the development of apoptosis protective mechanisms, including the metabolic engineering of apoptosis pathways, that has proven effective in diminishing programmed cell death in a variety of biotechnological relevant cell lines. This review is focused especially in the encouraging initial results obtained with the over-expression of cloned anti-apoptosis genes, from both endogenous and viral origin interfering at mitochondrial and initiator caspases levels.     

Subcellular motility: A correlated light and electron microscopic study using cultured cells

To assess the possible role of filaments in subcellular motility, particular cultured cells were studied by light and electron microscopy. Motile cell margins always contained meshworks of ~50 Å diam. filaments. Organelles moved within cytoplasm occupied by a meshwork of 50–100 Å filaments and microtubules. When cells were treated with cytochalasin B, movements of cell margins stopped, but organelle movements continued; electron microscopically, while subplasmalemmal filaments had disappeared, subcortical filaments and microtubules remained. When cells were treated with hypertonic medium, organelle movements ceased but marginal movements continued; electron microscopically, although cell margins contained normal filament arrays, few subcortical filaments remained. It is concluded that while cell margins are moved by a meshwork of filaments, organelle movement is mediated by a subcortical meshwork of filaments and microtubules.     

Simulation of endo-PG digest patterns and implications for the determination of pectin fine structure

Novel stepwise approaches to the calculation of enzyme digest patterns are described and used in the validation of a computer simulation. Results obtained using the simulation show that, while a previously proposed model of endo-PG action captures some of the salient features of this enzymes behaviour, it is not sufficient to successfully predict experimental digest patterns from pectic substrates. Subsequently, it has been shown that a modified model incorporating existing information regarding subsite architecture and speculative site tolerances for esterified residues, goes someway towards improving the situation.     

Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 A resolution. Role of calcium in structure and activity.

The crystal structure of porcine pancreatic alpha-amylase (PPA) has been solved at 2.9 A resolution by X-ray crystallographic methods. The enzyme contains three domains. The larger, in the N-terminal part, consists of 330 amino acid residues. This central domain has the typical parallel-stranded alpha-beta barrel structure (alpha beta)8, already found in a number of other enzymes like triose phosphate isomerase and pyruvate kinase. The C-terminal domain forms a distinct globular unit where the chain folds into an eight-stranded antiparallel beta-barrel. The third domain lies between a beta-strand and a alpha-helix of the central domain, in a position similar to those found for domain B in triose phosphate isomerase and pyruvate kinase. It is essentially composed of antiparallel beta-sheets. The active site is located in a cleft within the N-terminal central domain, at the carboxy-end of the beta-strands of the (alpha beta)8 barrel. Binding of various substrate analogues to the enzyme suggests that the amino acid residues involved in the catalytic reaction are a pair of aspartic acids. A number of other residues surround the substrate and seem to participate in its binding via hydrogen bonds and hydrophobic interactions. The 'essential' calcium ion has been located near the active site region and between two domains, each of them providing two calcium ligands. On the basis of sequence comparisons this calcium binding site is suggested to be a common structural feature of all alpha-amylases. It represents a new type of calcium-protein interaction pattern.(ABSTRACT TRUNCATED AT 250 WORDS)