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PubMed1995

Mapping light-dependent structural changes in the cytoplasmic loop connecting helices C and D in rhodopsin: a site-directed spin labeling study.

All 20 single cysteine substitution mutants in the sequence Y136-M155 of bovine rhodopsin have been prepared and modified with a sulfhydryl-specific nitroxide reagent. This sequence contains the C-D interhelical loop, a transducin interaction site. The accessibilities of the attached nitroxides to collisions with paramagnetic probes in solution were determined, and the electron paramagnetic resonance spectra were analyzed, both in the dark and after photoexcitation. Accessibility data show that the rhodopsin polypeptide crosses an aqueous/hydrophobic boundary near V138 and H152. The nitroxide mobilities inferred from the spectra are consistent with a model where the C helix extends to at least residue C140, with much of the helix surface in contact with protein rather than lipid near the cytoplasmic surface of the membrane. Upon photoexcitation, electron paramagnetic resonance spectral changes are observed at sites on the putative C helix surface that are in contact with the protein and at specific sites in the C-D interhelical loop. A simple interpretation of these results is that photoexcitation involves a rigid body movement of the C helix relative to the others in the helix bundle.

Amino Acid Sequence↗
PubMed1993

The primary structure of rat brain (cytoplasmic) dynein heavy chain, a cytoplasmic motor enzyme.

Overlapping cDNA clones encoding the heavy chain of rat brain cytoplasmic dynein have been isolated. The isolated cDNA clones contain an open reading frame of 13,932 bp encoding 4644 aa (M(r), 532,213). The deduced protein sequence of the heavy chain of rat brain dynein shows significant similarity to sea urchin flagellar beta-dynein (27.0% identical) and to Dictyostelium cytoplasmic dynein (53.5% identical) throughout the entire sequence. The heavy chain of rat brain (cytoplasmic) dynein contains four putative nucleotide-binding consensus sequences [GX4GK(T/S)] in the central one-third region that are highly similar to those of sea urchin and Dictyostelium dyneins. The N-terminal one-third of the heavy chain of rat brain (cytoplasmic) dynein shows high similarity (43.8% identical) to that of Dictyostelium cytoplasmic dynein but poor similarity (19.4% identical) to that of sea urchin flagellar dynein. These results suggested that the C-terminal two-thirds of the dynein molecule is conserved and plays an essential role in microtubule-dependent motility activity, whereas the N-terminal regions are different between cytoplasmic and flagellar dyneins.

Amino Acid Sequence↗
PubMed2006

The Drosophila rhodopsin cytoplasmic tail domain is required for maintenance of rhabdomere structure.

The ninaE-encoded Rh1 rhodopsin is the major light-sensitive pigment expressed in Drosophila R1-6 photoreceptor cells. Rh1 rhodopsin localizes to and is essential for the development and maintenance of the rhabdomere, the specialized membrane-rich organelle that serves as the site of phototransduction. We showed previously that the vertebrate bovine rhodopsin (Rho) is expressed and properly localized in Drosophila photoreceptor cells. Drosophila photoreceptors expressing only Rho have normal rhabdomere structure at young ages, but the rhabdomeres are not maintained and show extensive disorganization by 7-10 days of age. A series of Rho-Rh1 opsin chimeric rhodopsins were used to identify Rh1 domains required for maintenance of rhabdomeric structure. The results show that the Rh1 rhodopsin cytoplasmic tail domain, positioned to interact with cytoplasmic structural components, plays a major role in promoting rhabdomeric organization.

Amino Acid Motifs↗
PubMed1985

Cytoplasmic motions, rheology, and structure probed by a novel magnetic particle method.

The motions of magnetic particles contained within organelles of living cells were followed by measuring magnetic fields generated by the particles. The alignment of particles was sensed magnetometrically and was manipulated by external fields, allowing non-invasive detection of particle motion as well as examination of cytoplasmic viscoelasticity. Motility and rheology data are presented for pulmonary macrophages isolated from lungs of hamsters 1 d after the animals had breathed airborne gamma-Fe2O3 particles. The magnetic directions of particles within phagosomes and secondary lysosomes were aligned, and the weak magnetic field produced by the particles was recorded. For dead cells, this remanent field was constant, but for viable macrophages, the remanent field decreased rapidly so that only 42% of its initial magnitude remained 5 min after alignment. A twisting field was applied perpendicular to the direction of alignment and the rate at which particles reoriented to this new direction was followed. The same twisting was repeated for particles suspended in a series of viscosity standards. Based on this approach, the low-shear apparent intracellular viscosity was estimated to be 1.2-2.7 X 10(3) Pa.s (1.2-2.7 X 10(4) poise). Time-lapse video microscopy confirmed the alignment of ingested particles upon magnetization and showed persistent cellular motility during randomization of alignment. Cytochalasin D and low temperature both reduced cytoplasmic activity and remanent-field decay, but affected rheology differently. Magnetic particles were observed in association with the microtubule organizing center by immunofluorescence microscopy; magnetization did not affect microtubule distribution. However, both vimentin intermediate filaments and f-actin reorganized after magnetization. These data demonstrate that magnetometry of isolated phagocytic cells can probe organelle movements, rheology, and physical properties of the cytoskeleton in living cells.

Animals↗
PubMed1984

Chemical synthesis of the 5'-terminal part bearing cap structure of messenger RNA of cytoplasmic polyhedrosis virus (CPV): m7G5'pppAmpG and m7G5'pppAmpGpU.

The 5'-terminal structures of mRNA bearing the so-called 'cap' from cytoplasmic polyhedrosis virus (CPV), m7G5' pppAmpG and m7G5' pppAmpGpU, were first chemically synthesized. S,S-Di(4-methoxyphenyl) N6-benzoyl-2'-O-methyladenosine 5'-phosphorodithioate ((ArS) 2pAbmz) was prepared by phosphorylation of the 5'-hydroxyl group of N6-benzoyl-2'-O-methyladenosine with S,S-di(4-methoxyphenyl) phosphorodithioate by TPS. By the triester approach using (ArS) 2pAbmz as starting material, the protected dinucleotide and trinucleotide bearing 5'-phosphate group were synthesized. The protective groups of the dinucleotide and trinucleotide were removed to obtain pAmpG and pAmpGpU, respectively. By the reaction of a capping agent ((PhS) ppm7G) with pAmpG and pAmpGpU in the presence of silver nitrate or iodine. The 5'-terminal structure of the messenger RNA strand of CPV which was labelled isotopically, was confirmed completely as m7G5' pppAmGpU by cochromatography with the materials chemically synthesized here.

Chemical Phenomena↗
PubMed1980

[Effect of the unsaturation of lipids fatty acids on the structure and function of the cytoplasmic membranes of E. coli].

The results presented in this paper establish relationships between structural, morphological and functional properties of cytoplasmic membrane vesicles isolated from an E. coli unsaturated fatty auxotroph. The membranes were isolated from cells grown in the presence of either oleic, linolenic or elaidic acids. High-angle X-ray diffraction studies show that order-disorder transitions induced by temperature variation sand associated with the hydrocarbon chains of the lipids are a function of the fatty acid composition of the membranes. In some cases, "cocrystallization" of various lipid species takes place within a single type of ordered domains. In other cases, there is a segregation of various lipid species into more than one distinct type of ordered domain. The various order-disorder transitions observed, induce morphological changes in the hydrophobic core of the membranes which can be detected by freeze-fracture electron microscopy. A random distribution of particles on the fracture faces is observed when the hydrocarbon chains of the lipids are disordered. Upon ordering of the hydrocarbon chains, particles are excluded from the ordered domains and as a consequence, smooth areas and areas with dense ly packed particles are observed. Discontinuities in the rate of energy-dependent beta-galactoside uptake as a function of temperature correlate with the order-disorder transitions observed. The increased slope of the Arrhenius representation in the temperature region of the transition is associated with the segregation of the carrier proteins excluded from the ordered membrane domains and their subsequent aggregation in the membrane domains containing the disordered lipids.

Cell Membrane↗
PubMed1976

Serial liver biopsy observations in hepatitis B antigen carriers by light and electron microscopy.

Liver morphology and function were restudied after an interval of 1 1/2-2 years in 21 Chinese men with hepatitis B antigen (HBsAg). Antigenemia and mild liver histopathology disappeared in one individual who developed antibody to HBsAg(Anti-HBsAg). 20 subjects who were chronic carriers of HBsAg had mild histological abnormalities which were usually persistent and were more commonly lobular than portal. Particularly striking were focal necrosis, eosinophilic bodies, ground-glass cytoplasmic change, and, by electron microscopy, microtubular structures within cytoplasmic membranous cysternae. Interval development of chronic aggressive hepatitis was observed in only one subject. This study suggests that the great majority of HBsAg carriers have a good prognosis at least over a 1 1/2-2-year period, and that liver biopsy is most indicated in those with persistent liver function abnormalities.

Adult↗
PubMed1988

Freeze-fracture study of the trophozoite and the cyst of Entamoeba histolytica.

The fine structure of the trophozoite and cyst of Entamoeba histolytica from the stool of a patient was compared using the freeze-fracture method. The intramembranous particles (IMP's) were heterogeneously distributed on the plasma membrane of the trophozoite and their density was 1139 +/- 105/micron 2 on the P face. Particle-rich depressions and linear particle arrays, reported by other investigators on cultured trophozoites, were also observed on the P face while on the E face such special particle arrangement was not recognized. Particle-free, small protrusions were frequently observed on the P face of the trophozoite membrane. The existence of these protrusions is a new finding. In the cyst, the IMP's were also distributed heterogeneously on both the P and E faces of the plasma membrane. The density of the IMP's, however, was much lower than in the trophozoite: 6 +/- 2/micron 2 on the P face and averaging less than 1/micron 2 on the E face. In freeze-fracture images, the plasma membrane of the cyst showed a variety of configurations from smooth to uneven or ridged surfaces. These morphological alterations of the plasma membrane may be attributed to the aging of the cyst. The thick wall of the cyst had a filamentous tri- or tetra-lamellar structure. The cytoplasm of the cyst was similar in structure to that of the trophozoite and the diameter of the nuclear pores was equal in both trophozoites and cysts.

Adult↗
PubMed2006

Cytoplasmic lipid droplets: rediscovery of an old structure as a unique platform.

Cytoplasmic lipid droplets (LDs) exist in virtually any kind of cell. They have a core of lipid esters covered by the surface phospholipid monolayer. A number of proteins related to various cell functions are present in LDs and/or LD-rich subcellular fractions, suggesting that LDs are an independent organelle that is engaged in various cellular activities. Furthermore, a recent study suggested that LDs are a platform where the proteasomal and autophagic pathways converge. The molecular composition and architecture of LDs are discussed here, with special reference to the technical difficulties encountered when analyzing this unique organelle.

Animals↗
PubMed1996

Structure-activity relationship of cytoplasmic 5'-nucleotidase substrate sites.

Various 5'-nucleotidases (EC 3.1.3.5) exist in vertebrate tissues. The sequence and cDNA cloning of the membrane-bound ecto-5'-nucleotidase (e-N) and one of the cytosolic isoenzymes, IMP-preferring (c-N-II), but not the cytosolic AMP-preferring form (c-N-I), have been reported. While c-N-II has a broad tissue distribution, c-N-I is found only in vertebrate heart. The published data on substrate specificity involve mainly the naturally occurring nucleoside monophosphates, without a systematic structure-activity relationship study. In the present study we have used a series of AMP and IMP analogues to examine the structure-activity relationship for c-N-I and c-N-II in detail. The rank order of activity of the test compounds differed substantially between c-N-I and c-N-II. c-N-I and c-N-II varied with respect to the following interactions with substrate: (1) hydrogen-bond formation with the substituent in the 6-position of the purine ring (a donor-type with c-N-I and an acceptor-type with c-N-II); and (2) hydrophobic attraction of the 6-position unsubstituted purine ring (more pronounced with c-N-I than with c-N-II). No better substrate than 5'-AMP was found for c-N-I. We propose that c-N-I functions as an AMP-binding protein in the myocardial cell with an important role during ischaemic ATP breakdown when AMP accumulates rapidly.

5'-Nucleotidase↗
PubMed1996

M-phase-specific phosphorylation and structural rearrangement of the cytoplasmic cross-linking protein plectin involve p34cdc2 kinase.

Plectin, a widespread and abundant cytoskeletal cross-linking protein, serves as a target for protein kinases throughout the cell cycle, without any significant variation in overall phosphorylation level. One of the various phosphorylation sites of the molecule was found to be phosphorylated preferentially during mitosis. By in vivo phosphorylation of ectopically expressed plectin domains in stably transfected Chinese hamster ovary cells, this site was mapped to the C-terminal repeat 6 domain of the polypeptide. The same site has been identified as an in vitro target for p34cdc2 kinase. Mitosis-specific phosphorylation of plectin was accompanied by a rearrangement of plectin structures, changing from a filamentous, largely vimentin-associated state in interphase to a diffuse vimentin-independent distribution in mitosis as visualized by immunofluorescence microscopy. Subcellular fractionation studies showed that in interphase cells up to 80% of cellular plectin was found associated with an insoluble cell fraction mostly consisting of intermediate filaments, while during mitosis the majority of plectin (> 75%) became soluble. Furthermore, phosphorylation of purified plectin by p34cdc2 kinase decreased plectin's ability to interact with preassembled vimentin filaments in vitro. Together, our data suggest that a mitosis-specific phosphorylation involving p34cdc2 kinase regulates plectin's cross-linking activities and association with intermediate filaments during the cell cycle.

Amino Acid Sequence↗
PubMed2006

A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs.

Mitochondrial tRNAs (mtRNAs) often lack domains and posttranscriptional modifications that are found in cytoplasmic tRNAs. These structural and chemical elements normally stabilize the folding of cytoplasmic tRNAs into canonical structures that are competent for aminoacylation and translation. For example, the dihydrouridine (D) stem and loop domain is involved in the tertiary structure of cytoplasmic tRNAs through hydrogen bonds and a Mg2+ bridge to the ribothymidine (T) stem and loop domain. These interactions are often absent in mtRNA because the D-domain is truncated or missing. Using gel mobility shift analyses, UV, circular dichroism and NMR spectroscopies and aminoacylation assays, we have investigated the functional folding interactions of chemically synthesized and site-specifically modified mitochondrial and cytoplasmic tRNAs. We found that Mg2+ is critical for folding of the truncated D-domain of bovine mtRNAMet with the tRNA's T-domain. Contrary to the expectation that Mg2+ stabilizes RNA folding, the mtRNAMet D-domain structure was unfolded and relaxed, rather than stabilized in the presence of Mg2+. Because the D-domain is transcribed prior to the T-domain, we conclude that Mg2+ prevents misfolding of the 5'-half of bovine mtRNAMet facilitating its correct interaction with the T-domain. The interaction of the mtRNAMet D-domain with the T-domain was enhanced by a pseudouridine located in either the D or T-domains compared to that of the unmodified RNAs (Kd=25.3, 24.6 and 44.4 microM, respectively). Mg2+ also affected the folding interaction of a yeast mtRNALeu1, but had minimal effect on the folding of an Escherichia coli cytoplasmic tRNALeu. The D-domain modification, dihydrouridine, facilitated mtRNALeu folding. These data indicate that conserved modifications assist and stabilize the formation of the functional mtRNA tertiary structure.

Aminoacylation↗
PubMed2005

Limkain b1, a novel human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes.

Detection of self-reactive antibodies has an established role in the diagnosis and monitoring of many human autoimmune diseases. Autoantibodies with restricted reactivity to cytoplasmic compartments and structures are an occasional incidental finding following routine examination of serum for antinuclear antibody reactivity. A prerequisite for rational exploitation of self-reactive antibodies, in either clinical or research settings, is the establishment of the molecular identity of the target autoantigen(s). Here we report on the identification of a novel autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (PMP-70) and/or PXF (PEX19). Immunoscreening a HeLa cell cDNA expression library with a human autoimmune serum identified two clones that encode fragments of limkain b1 (LKAP). We demonstrate that mouse polyclonal antibodies raised against a bacterially expressed fragment of limkain b1 mark the same cytoplasmic structures as human serum, as does an EGFP:LKAPCT429 fusion protein expressed in HeLa cells. An immunoblot screen against a bacterially expressed MBP:LKAPCT429 fusion protein substrate, using a cohort of 16 additional human sera that display Hep 2 cell cytoplasmic staining patterns similar to the prototype serum, identified three additional sera reactive to limkain b1. This is the first report establishing the molecular identity of a peroxisomal autoantigen. Preliminary results suggest that limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures.

ATP-Binding Cassette Transporters↗
PubMed1992

Assessing hydrophobic regions of the plasma membrane H(+)-ATPase from Saccharomyces cerevisiae.

The hydrophobic, photoactivatable probe TID [3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine] was used to label the plasma membrane H(+)-ATPase from Saccharomyces cerevisiae. The H(+)-ATPase accounted for 43% of the total label associated with plasma membrane protein and incorporated 0.3 mol of [125I]TID per mol of 100 kDa polypeptide. The H(+)-ATPase was purified by octyl glucoside extraction and glycerol gradient centrifugation, and was cleaved by either cyanogen bromide digestion or limited tryptic proteolysis to isolate labeled fragments. Cyanogen bromide digestion resulted in numerous labeled fragments of mass less than 21 kDa. Seven fragments suitable for microsequence analysis were obtained by electrotransfer to poly(vinylidene difluoride) membranes. Five different regions of amino-acid sequence were identified, including fragments predicted to encompass both membrane-spanning and cytoplasmic protein structure domains. Most of the labeling of the cytoplasmic domain was concentrated in a region comprising amino acids 347 to 529. This catalytic region contains the site of phosphorylation and was previously suggested to be hydrophobic in character (Goffeau, A. and De Meis, L. (1990) J. Biol. 265, 15503-15505). Complementary labeling information was obtained from an analysis of limited tryptic fragments enriched for hydrophobic character. Six principal labeled fragments, of 29.6, 20.6, 16, 13.1, 11.4 and 9.7 kDa, were obtained. These fragments were found to comprise most of the putative transmembrane region and a portion of the cytoplasmic region that overlapped with the highly labeled active site-containing cyanogen bromide fragment. Overall, the extensive labeling of protein structure domains known to lie outside the bilayer suggests that [125I]TID labeling patterns cannot be unambiguously interpreted for the purpose of discerning membrane-embedded protein structure domains. It is proposed that caution should be applied in the interpretation of [125I]TID labeling patterns of the yeast plasma membrane H(+)-ATPase and that new and diverse approaches should be developed to provide a more definitive topology model.

Amino Acid Sequence↗
PubMed1994

[Fine structural studies on the cytoplasmic membrane morphology of transitional cell carcinoma in men].

Transitional cell carcinomas (TCC) in the human urinary bladder were observed on the fine morphological behaviour of the plasma membrane, with special references to the morphological differences in various grades of TCC utilizing thin sections and freeze fracture replica electron microscopically. The purpose of this study is to clarify the characteristic differences between various grades of human TCC as a indicator suggestive of the TCC malignancy using electron microscopic techniques. (1) The asymmetric unit membrane seen on the luminal membrane of the superficial cells was unique in all of TCC G1 and some TCC G2 cases. In other TCC G2 and TCC G3, there observed the symmetric unit membrane. Fusiform vesicles directly beneath the luminal plasma membrane were recognized only in TCC G1. (2) Microvilli (MV) seen on the luminal plasma membrane in TCC G1 were found to have the same appearance and distribution as on the normal bladder epithelium. As the grades increased in severity, there were less MV being shorter and club-like-forms. Even deformed with bleb formation microvilli were more apparent in TCC G3 cases than in TCC G2. (3) There was no difference observed between the junctional complex of the superficial cells of the all TCC grades and normal cells. As the cellular malignancies develop, however, the interdigitation structures and desmosomal appearances situated between neighboring intermediate cells tended to decrease. (4) Intracytoplasmic tonofilaments proliferation was obvious in TCC G2, but not in G3. (5) With increasing severity of TCC grades, intramembranous particles showed significant decrease in number as seen on freeze-fracture replica. In conclusion, these results suggest that fine structural observation may prove to be a useful parameter to know the grades of TCC in human bladder tumors.

Carcinoma, Transitional Cell↗
PubMed1990

Vaults. II. Ribonucleoprotein structures are highly conserved among higher and lower eukaryotes.

Vaults are cytoplasmic ribonucleoprotein structures that display a complex morphology reminiscent of the multiple arches which form cathedral vaults, hence their name. Previous studies on rat liver vaults (Kedersha, N. L., and L. H. Rome. 1986. J. Cell Biol. 103:699-709) have established that their composition is unlike that of any known class of RNA-containing particles in that they contain multiple copies of a unique small RNA and more than 50 copies of a single polypeptide of 104,000 Mr. We now report on the isolation of vaults from numerous species and show that vaults appear to be ubiquitous among eukaryotes, including mammals, amphibians (Rana catesbeiana and Xenopus laevis), avians (Gallus Gallus), and the lower eukaryote Dictyostelium discoideum. Electron microscopy reveals that vaults purified from these diverse species are similar both in their dimensions and morphology. The vaults from these various species are also similar in their polypeptide composition; each being composed of a major polypeptide with an approximate mass of 100 kD and several minor polypeptides with molecular masses similar to those seen in the rat. Antibodies raised against rat vaults recognize the major vault protein of all species including Dictyostelium. Vaults therefore appear to be strongly conserved and broadly distributed, suggesting that their function is essential to eukaryotic cells.

Animals↗
PubMed1989

The cell walls of Chara aspera Willd. (Charophyta) vegetative cells.

The ultrastructure of the vegetative cell walls of the charophyte Chara aspera Willd was studied with TEM. Thallus cells, rhizoid bulbil and rhizoidal node cells were investigated. The internodal cells transverse walls contained plasmodesmata. The longitudinal walls of the internodal cells were uniform, fibrillar, with two thin structurally distinct layers with different structure facing the cytoplasm. The outermost layers of internodal, cortical and rhizoid bulbil cells were composed of randomly orientated fibrils. The longitudinal walls of the cortical cells were helicoidal in structure. In the rhizoid bulbil cell walls, six different layers could be distinguished, but their occurrence seemed to depend on the fixation, staining and cutting procedures. A middle lamella and osmophilic deposits were found in the wall between rhizoidal node cells. The cytoplasmic structure of the internodal and cortical cells was not found to differ from other species of Chara. Charasomes were observed only in cortical cells.

Cell Wall↗