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PubMed1998

Structure of an IkappaBalpha/NF-kappaB complex.

The inhibitory protein, IkappaBalpha, sequesters the transcription factor, NF-kappaB, as an inactive complex in the cytoplasm. The structure of the IkappaBalpha ankyrin repeat domain, bound to a partially truncated NF-kappaB heterodimer (p50/ p65), has been determined by X-ray crystallography at 2.7 A resolution. It shows a stack of six IkappaBalpha ankyrin repeats facing the C-terminal domains of the NF-kappaB Rel homology regions. Contacts occur in discontinuous patches, suggesting a combinatorial quality for ankyrin repeat specificity. The first two repeats cover an alpha helically ordered segment containing the p65 nuclear localization signal. The position of the sixth ankyrin repeat shows that full-length IkappaBalpha will occlude the NF-kappaB DNA-binding cleft. The orientation of IkappaBalpha in the complex places its N- and C-terminal regions in appropriate locations for their known regulatory functions.

Amino Acid Sequence↗
PubMed1988

Cytoplasmic membrane changes during adaptation of the fresh water cyanobacterium Synechococcus 6311 to salinity.

In this investigation, changes were characterized in cell structure and cytoplasmic membrane organization that occur when the freshwater cyanobacterium Synechococcus 6311 is transferred from 'low salt' (0.03 molar NaCl) to 'high salt' (0.5 molar NaCl) media (i.e. sea water concentration). Cells were examined at several time points after the imposition of the salt stress and compared to control cells, in thin sections and freeze fracture electron microscopy, and by flow cytometry. One minute after exposure to high salt, i.e. 'salt shock', virtually all intracellular granules disappeared, the density of the cytoplasm decreased, and the appearance of DNA material was changed. Glycogen and other granules, however, reappeared by 4 hours after salt exposure. The organization of the cytoplasmic membrane undergoes major reorganization following salt shock. Freeze-fracture electron microscopy showed that small intramembrane particles (diameter 7.5 and 8.5 nanometers) are reduced in number by two- to fivefold, whereas large particles, (diameters 14.5 and 17.5 nanometers) increase two- to fourfold in frequency, compared to control cells grown in low salt medium. The changes in particle size distribution suggest synthesis of new membrane proteins, in agreement with the known increases in respiration, cytochrome oxidase, and sodium proton exchange activity of the cytoplasmic membrane.

Cell Membrane↗
PubMed1975

Myxovirus-like structures in the glomerular endothelial cell cytoplasm in canine nephritis.

Electron microscopic examinations revealed the presence of myxovirus-like tubular structures, 200A in diameter, in the endothelial cytoplasm of the glomeruli in four dogs with chronic interstitial nephritis and in one healthy control dog. The structures were found inside the endoplasmic reticulum and in some longitudinal sections, the tubuli seemed to have a helical or spiral substructure. The morphology and cellular localization of the structures resembled those seen in systemic lupus erythematosus in man, and in cultures of cells from tissue infected with canine distemper. Precipitating canine distemper virus antibodies were not in evidence in dogs in which such structures were demonstrable by electron microscopy while these antibodies were found in other dogs.

Animals↗
PubMed1999

The cytoplasmic sites of the snRNP protein complexes are punctate structures that are responsive to changes in metabolism and intracellular architecture.

Five anti-Sm monoclonal antibodies, Y12, 7.13, KSm4, KSm6, and 128, stain similar discrete punctate structures distributed throughout the cytoplasm of hamster fibroblasts in addition to the expected intense nuclear staining. Several criteria suggest the cytoplasmic staining reflects the cytoplasmic pools of snRNP core proteins. The relative intensity of the cytoplasmic staining is similar to the 30% relative abundance of the cytoplasmic snRNP core proteins compared to the nuclear snRNP core proteins based on cell-fractionation studies. Moreover, the cytoplasmic staining is removed by the same extraction conditions that solubilize the pools of cytoplasmic snRNP core proteins. The cytoplasmic sites of staining are typically spherical but heterogeneous in diameter (0.2-0.5 microm). The larger particles greatly exceed the diameter of individual snRNP core particles and are likely to represent centers of many snRNP proteins or snRNP protein complexes. The staining, though punctate, is evenly dispersed throughout the cytoplasm with no evidence of major compartmentalization. The cytoplasmic staining pattern collapses into larger foci of intensely staining structures when cellular energy levels are depleted or when cells are exposed to hypertonic medium. Unlike the normal sites of snRNP protein cytoplasmic staining, these larger collapsed foci resist detergent extraction. These results suggest that the cytoplasmic staining identified with the anti-Sm monoclonal antibodies represents the large pools of snRNP core proteins in the cytoplasm.

Animals↗
PubMed1984

Three-dimensional approaches to the residual structure of histone-depleted HeLa cell nuclei.

Histone-depleted nuclei were prepared by high-salt extraction of interphase HeLa cell nuclei. A large amount of the nuclear DNA remained associated with a rapidly sedimenting residual nuclear structure including cytoplasmic (intermediate filament) and nuclear (matrix and lamina) proteins. Electron microscopy allowed detection in the insoluble structure of a residual nuclear envelope, nucleolar residues, and an intranuclear network whose correspondence with components of in situ fixed nuclei is discussed. Using three-dimensional electron microscopy, it is further demonstrated that the salt-insoluble structure remaining after histone depletion in 2 M NaCl is highly ordered. This is of the utmost importance when considering the roles reportedly ascribed to this structure in nuclear functions.

Cell Nucleolus↗
PubMed1971

Characterization of the genome of cytoplasmic polyhedrosis virus.

It is possible to oxidize in situ the 3'-terminals of the double-stranded ribonucleic acid (RNA) contained in structurally intact cytoplasmic polyhedrosis virus. The number of 3'-terminals subsequently found by reduction with tritiated sodium borohydride was equivalent to the number observed in RNA first isolated from the virus and then oxidized and reduced. The viral RNA appears to occur in 10 distinct polynucleotide segments present in equimolar amounts.

Borohydrides↗
PubMed1982

Chloroplastic and cytoplasmic valyl- and leucyl-tRNA synthetases from Euglena gracilis. Comparative study of their structural properties.

Chloroplastic and cytoplasmic valyl- and leucyl-tRNA synthetases purified from Euglena gracilis show a monomeric structure. The molecular weights of the two valyl-tRNA synthetases are identical (126,000) while those of the leucyl-tRNA synthetases are different (100 000 for the chloroplastic and 116 000 for the cytoplasmic enzyme). The tryptic maps and the amino acid compositions reveal differences between the chloroplastic valyl- and leucyl-tRNA synthetases and their cytoplasmic homologues. These results suggest that a chloroplastic aminoacyl-tRNA synthetase and its cytoplasmic counterpart are coded for by distinct genes.

Amino Acids↗
PubMed1990

Occurrence and developmental consequences of aberrant cellular organization in meiotically mature human oocytes after exogenous ovarian hyperstimulation.

The extent to which fertilization failure in in vitro inseminated human oocytes obtained from hyperstimulated ovaries was associated with alterations in cellular structure and cytoplasmic organization was examined by a combination of DIC, fluorescence, time-lapse video, and transmission electron microscopy. Detailed analysis of meiotically mature preovulatory (uninseminated) oocytes, and of oocytes that failed to fertilize in vitro, indicated that between 10% and 15% of grossly normal-appearing MII-stage oocytes displayed one of the following cellular perturbations: 1) a subtle change in organelle distribution, 2) a small region(s) of intracellular cytolysis, 3) a massive aggregation of SER tubules, 4) an accumulation of vesicles presumed to be of SER origin, 5) a change in the structural organization of the cortical cytoplasm and overlying plasma membrane, 6) a sudden and rapid internalization of perivitelline fluid by means of an apparently aberrant process of endocytosis, and 7) a premature and partial exocytosis of cortical granules. The description of these disorders is discussed with respect to the developmental consequences for the oocyte.

Cell Degranulation↗
PubMed2000

A structural basis for integrin activation by the cytoplasmic tail of the alpha IIb-subunit.

A key step in the activation of heterodimeric integrin adhesion receptors is the transmission of an agonist-induced cellular signal from the short alpha- and/or beta-cytoplasmic tails to the extracellular domains of the receptor. The structural details of how the cytoplasmic tails mediate such an inside-out signaling process remain unclear. We report herein the NMR structures of a membrane-anchored cytoplasmic tail of the alpha(IIb)-subunit and of a mutant alpha(IIb)-cytoplasmic tail that renders platelet integrin alpha(IIb)beta(3) constitutively active. The structure of the wild-type alpha(IIb)-cytoplasmic tail reveals a "closed" conformation where the highly conserved N-terminal membrane-proximal region forms an alpha-helix followed by a turn, and the acidic C-terminal loop interacts with the N-terminal helix. The structure of the active mutant is significantly different, having an "open" conformation where the interactions between the N-terminal helix and C-terminal region are abolished. Consistent with these structural differences, the two peptides differ in function: the wild-type peptide suppressed alpha(IIb)beta(3) activation, whereas the mutant peptide did not. These results provide an atomic explanation for extensive biochemical/mutational data and support a conformation-based "on/off switch" model for integrin activation.

Amino Acid Sequence↗
PubMed1999

Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.

The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme. Here, we have determined the crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase with the alternative substrate alpha-ketomalonate and the coenzyme analogue 1,4,5,6-tetrahydronicotinamide. Both subunits of the dimeric porcine heart, and from the prokaryotes Escherichia coli and Thermus flavus. However, large changes are noted around the active site, where a mobile loop now closes to bring key residues into contact with the substrate. This observation substantiates a postulated mechanism in which the enzyme achieves high levels of substrate discrimination through charge balancing in the active site. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by a conserved arginine in the active site loop. The enzyme must, however, also discriminate against smaller substrates, such as pyruvate. The structure shows in the closed (loop down) catalytically competent complex two arginine residues (91 and 97) are driven into close proximity. Without the complimentary, negative charge of the substrate side-chain of oxaloacetate or alpha-ketomalonate, charge repulsion would resist formation production of this catalytically productive conformation, hence minimising the effectiveness of pyruvate as a substrate. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.

Amino Acid Sequence↗
PubMed2005

The N-terminal Ac-EEED sequence plays a role in alpha-smooth-muscle actin incorporation into stress fibers.

We have previously shown that the N-terminal sequence AcEEED of alpha-smooth-muscle actin causes the loss of alpha-smooth-muscle actin from stress fibers and a decrease in cell contractility when introduced in myofibroblasts as a cell-penetrating fusion peptide. Here, we have investigated the function of this sequence on stress fiber organization in living cells, using enhanced green fluorescent protein (EGFP)-tagged alpha-smooth-muscle actin. The fusion peptide provokes the gradual disappearance of EGFP fluorescence of alpha-smooth-muscle actin from stress fibers and the formation of hitherto unknown rod-like structures. In addition to alpha-smooth-muscle actin, these structures contain cytoplasmic actins, gelsolin and cofilin but not other major actin-binding proteins. These rod-like structures are also visible in wild-type fibroblasts during normal cell spreading, suggesting that they represent a physiological step in the organization of alpha-smooth-muscle actin in stress fibers. Fluorescence-recovery-after-photobleaching experiments suggest that the fusion peptide reduces the dynamics of alpha-smooth-muscle actin and its incorporation in stress fibers. Here, we propose a new mechanism of how alpha-smooth-muscle actin is incorporated in stress fibers involving the sequence Ac-EEED.

Actins↗
PubMed1989

Cytoplasmic orientation and two-domain structure of the multidrug transporter, P-glycoprotein, demonstrated with sequence-specific antibodies.

The predicted cytoplasmic orientation and two-domain structure of the multidrug efflux pump P-glycoprotein were demonstrated with sequence-specific antibodies. We synthesized peptides corresponding to amino acid residues, Glu393-Lys408 (anti-P) and Leu1206-Thr1226 (anti-C) in P-glycoprotein from human mdr1 cDNA and used these peptides to produce polyclonal antibodies. From the primary structure of P-glycoprotein, and anti-C antibody is expected to recognize another position, Leu561-Thr581, in the duplicate structure of P-glycoprotein, but anti-P recognizes only one site. These antibodies bind to multidrug-resistant cells (KB-C2) with permeabilized plasma membrane but do not bind to nonpermeabilized KB-C2 cells or parental KB cells, supporting the predicted cytoplasmic orientation of these sequences. With immunoblotting of the membrane fractions from KB-C2 cells, a major 140-kDa polypeptide of the P-glycoprotein was detected with both anti-P and anti-C. Two minor polypeptides with molecular mass of 95 and 55 kDa were also detected. When membrane vesicles were digested mildly with trypsin, the amount of these two polypeptides increased. Anti-P detected only the 95-kDa polypeptide, and anti-C detected both 95- and 55-kDa polypeptides. Achromobacter lyticus protease I (lysyl endopeptidase) and Staphylococcus aureus V8 protease also produced two polypeptides with similar molecular weights. Absorption into lectin-agarose beads and labeling with [3H]glucosamine indicated that the 95-kDa polypeptide was glycosylated but that the 55-kDa polypeptide was not. These two polypeptides as well as P-glycoprotein were photoaffinity-labeled with a calcium channel blocker, [3H]azidopine, but most of the label was found in the 55-kDa polypeptide. The yield of labeled fragments from membrane vesicles photolabeled after digestion with trypsin was similar to that from membrane vesicles digested with trypsin after photolabeling. These data indicate 1) that the 95-kDa polypeptide is the fragment corresponding to the amino-terminal half of P-glycoprotein containing sugar chains; 2) that the 55-kDa polypeptide is the carboxyl-terminal half which was mainly labeled with [3H]azidopine; and 3) that P-glycoprotein has a relatively rigid structure with a small number of protease-sensitive sites and its global structure is not destroyed by tryptic cleavage.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2000

Consequences of phase separation in cytoplasm.

Solutions of structurally different macromolecules, when mixed, above certain concentrations, tend to phase separate. The high concentration and diversity of proteins present in the liquid phase of cytoplasm, together with the phenomena which accompany macromolecular crowding, appear to meet the requirements for multiphase separation. The resulting cytoplasmic phase compartments, bounded by interfaces and/or other intracellular surfaces, would provide a dynamic, three-dimensional organizational structure. Based on the known physicochemical properties of aqueous phase systems and the partitioning behavior of biomaterials in them, such an organization could account for numerous phenomena observed in cytoplasm, such as its microcompartmentation. Aqueous phase separation is an attractive model for the liquid phase of cytoplasm because it comprises not only a structure (phase compartments, interfaces) for constraining biomaterials but also a mechanism (partitioning) for translocating them to other sites.

Animals↗
PubMed1999

Identification of cation-independent mannose 6-phosphate receptor/insulin-like growth factor type-2 receptor as a novel target of autoantibodies.

Two human monoclonal autoantibodies, B-33 and B-24, were generated from the B cells of a patient with scleroderma. Both monoclonal antibodies (mAbs) were composed of mu and lambda chains, and recognized cytoplasmic vesicular structures by indirect immunofluorescence on Hep-2 cell line slides, although mAb B-24 showed an additional diffuse cytoplasmic staining pattern. By Western blot, mAb B-24 exhibited a polyreactive-like binding pattern, whereas mAb B-33 failed to recognize any electroblotted Hep-2 antigen. The polyreactive versus monospecific behaviour of mAbs B-24 and B-33 was further confirmed by enzyme-linked immunosorbent assay (ELISA) with a variety of foreign and autoantigens. The N-terminal sequence of a protein band isolated by affinity chromatography with mAb B-33 was identical to that of cation-independent mannose 6-phosphate receptor (CI-MPR), also known as the insulin-like growth factor type-2 receptor (IGF-2R). Immunofluorescence experiments on Hep-2 cell line slides demonstrated a striking co-localization between the staining pattern exhibited by these mAbs and the pattern obtained using a goat anti-CI-MPR serum, indicating the recognition by B-24 and B-33 of a structure located predominantly in late endosomes. Sequence analysis of the V-region gene segments of B-33 and B-24 showed both to be identical, except for the existence of a point mutation in B-33 located in the H-complementarity-determining region 3 (H-CDR3) (position 100D), which produces a non-conservative replacement of Gly by Ser. This single replacement appears to be responsible for the dramatic change in reactivity of human mAb B-33. The data shown here provide new evidence of the critical role played by the H-CDR3 region in distinguishing a polyspecific from a monospecific antibody. A population study demonstrated the existence of immunoglobulin G (IgG) reactivity against CI-MPR/IGF-2R in serum specimens from five individuals with different pathological conditions, thus indicating that this molecule is a potential target for the human autoimmune response.

Amino Acid Sequence↗
PubMed1981

Unusual structures in the epidermal Langerhans' cells of normal human skin.

Two unusual structures were found in the epidermal Langerhans' cells of normal human adult skin: (1) an intramitochondrial crystalline lattice structure composed of numerous electron-dense, fine particles approximately 90 A in diameter, with a lucent spacing of nearly 90 A; (2) bundles of unusual cytoplasmic tubular structures, approximately 120 A wide.

Cytoplasm↗
PubMed2002

Cytoplasmic peptide:N-glycanase (PNGase) in eukaryotic cells: occurrence, primary structure, and potential functions.

A cytoplasmic peptide:N-glycanase has been implicated in the proteasomal degradation of newly synthesized misfolded glycoproteins exported from the endoplasmic reticulum. The gene encoding this enzyme (Png1p) has been identified in yeast. Based on sequence analysis, Png1p was classified as a member of the 'transglutaminase-like superfamily' that contains a putative catalytic triad of amino acids (cysteine, histidine, and aspartic acid). More recent studies in yeast indicate that Png1p can bind to the 26S proteasome through its interaction with the DNA repair protein Rad23p. A mouse homologue of Png1p (mPng1p) bound not only to the Rad23 protein, but also to various proteins related to ubiquitin and/or the proteasome through an extended amino-terminal domain. This NH2 terminus of mPng1p, which is not found in yeast, contains a PUB domain predicted to be involved in the ubiquitin-related pathway. This review will focus on the primary structure and potential functions of the cytoplasmic PNGases.

Amidohydrolases↗