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PubMed2004

25 Angstrom resolution structure of a cytoplasmic dynein motor reveals a seven-member planar ring.

Dyneins form one of the three major families of cytoskeleton-based motor proteins that together drive most of the visible forms of cell and organelle movement. We present here a 3D reconstruction of a cytoplasmic dynein motor domain obtained by electron microscopy, at 25 Angstrom resolution. This work demonstrates a basic motor architecture of a flat, slightly elliptical ring composed of seven densities arranged around a partially enclosed central cavity. We have used specific Fab tags to localize the microtubule-binding domain; the connecting stalk emerges at one end of the motor's long axis. Through proposed fitting of representative AAA domain structures, we show that the nucleotide catalytic P-1 domain is likely located at the opposite end of the motor. Thus mechanisms that couple nucleotide hydrolysis with microtubule binding must be propagated around a ring structure, in a manner clearly distinct from kinesin or myosin-mediated movements. Analysis of the Fab tagged datasets reveals classes of particles with stalks protruding at distinct angles from the motor. There is a approximately 40 degrees variation in microtubule-binding stalk angle that may reflect linkage to dynein's mechanochemical cycle. Overall, the work provides sufficient resolution to begin the mapping of landmark features onto a dynein motor, and provides a foundation for understanding the mechanics of dynein movement.

Antibodies↗
PubMed1987

Structure of purified cytoplasmic cofactor from Methanobacterium thermoautotrophicum.

The reduction of methylcoenzyme M to methane is known to require a heat stable and oxygen sensitive cofactor. Recently it has been shown that the active site of this cofactor is 7-mercaptoheptanoylthreonine phosphate. The present study shows that in the complete structure of this cofactor 7-mercaptoheptanoylthreonine phosphate is linked by pyrophosphate to two N-acetyl-glucosamine residues and an unidentified terminal group R with m/z 214. By fast-atom-bombardment mass spectrometry the intact cofactor, isolated as the mixed disulfide with 2-mercaptoethanol, was shown to have a molecular weight of 1084.5. The pyrophosphate bond is quite labile and undergoes hydrolysis or prolonged storage. This lability of the pyrophosphate bond may explain why the intact cofactor has not been isolated until now.

Euryarchaeota↗
PubMed2001

Probing the dark state tertiary structure in the cytoplasmic domain of rhodopsin: proximities between amino acids deduced from spontaneous disulfide bond formation between cysteine pairs engineered in cytoplasmic loops 1, 3, and 4.

To probe proximities between amino acids in the cytoplasmic domain by using mutants containing engineered cysteine pairs, three sets of rhodopsin mutants have been prepared. In the first two sets, a cysteine was placed, one at a time, at positions 311-314 in helix VIII, while the second cysteine was fixed at position 246 (set I) and at position 250 (set II) at the cytoplasmic end of helix VI. In the third set, one cysteine was fixed at position 65 while the second cysteine was varied between amino acid positions 306 and 321 located at the cytoplasmic end of helix VII and throughout in helix VIII. Rapid disulfide bond formation in the dark was found between the cysteine pairs in mutants A246C/Q312C,A246C/K311C and in mutants H65C/C316, H65C/315C and H65C/312C. Disulfide bond formation at much lower rates was found in mutants A246C/F313C, V250C/Q312C, H65C/N310C, H65C/K311C, H65C/F313C, and H65C/R314C; the remaining mutants showed no significant disulfide bond formation. Comparisons of the results from disulfide bond formation in solution with the distances observed in the rhodopsin crystal structure showed that the rates of disulfide bond formation in most cases were consistent with the amino acid proximities as revealed in crystal structure. However, deviations were also found, in particular, in the set containing fixed cysteine at position Cys246 and cysteines at positions 311-314. The results implicate significant effects of structural dynamics on disulfide bond formation in solution.

Amino Acid Sequence↗
PubMed2001

Solution structures of the cytoplasmic linkers between segments S4 and S5 (S4-S5) in domains III and IV of human brain sodium channels in SDS micelles.

The two cytoplasmic linkers connecting segment S4 and segment S5 (S4-S5 linker) of both domain III (III/S4-S5) and IV (IV/S4-S5) of the sodium channel alpha-subunit are considered to work as a hydrophobic receptor for the inactivation particle because of the three hydrophobic amino acids of Ile-Phe-Met (IFM motif) in the III-IV linker of the sodium channel alpha-subunit. To date, the solution structures of the peptides related to III/S4-S5 (MP-D3: A1325-M1338) and IV/S4-S5 (MP-D4: T1648-L1666) of human brain sodium channels have been investigated using CD and (1)H NMR spectroscopies. SDS micelles were employed as a solvent. The micelles mimic either biological membranes or the interior of a protein and can be a relevant environment at the inactivated state of the channels. It was found that the secondary structures of both MP-D3 and MP-D4 assume alpha-helical conformations around the N-terminal half-side of the sequences, i.e. the residues between V1326 and L1331 in MP-D3 and between L1650 and S1656 in MP-D4. Residue A1329 in MP-D3, which is considered to interact with F1489 of the IFM motif, was found to be located within the alpha-helix. Residues F1651, M1654, M1655, L1657 and A1669 in MP-D4, which also play an important role in inactivation, formed a hydrophobic cluster on one side of the helix. This cluster was concluded to interact with the hydrophobic cluster due to the III-IV linker before the inactivation gate closes.

Amino Acid Motifs↗
PubMed1986

Formation of nucleus-like structure in the cytoplasm of lambda-DNA-injected fertilized eggs and its partition into blastomeres during early embryogenesis in Xenopus laevis.

The fate of bacteriophage lambda-DNA was examined after injection into the fertilized eggs of Xenopus laevis. Injection of a large amount of lambda-DNA (ca. 24 ng) into a fertilized Xenopus egg induced the formation around the injected DNA of a giant nucleus-like structure which was surrounded by an apparently normal bilayered nuclear membrane with nuclear pore complexes. Southern blot analysis revealed the persistence of injected lambda-DNA until the blastula stage. The nucleus-like structure was partitioned into blastomeres during cleavage through a process of nuclear fission, and was maintained in a group of extraordinarily large blastomeres until the blastula stage.

Animals↗
PubMed2002

Solution structures of the cytoplasmic tail complex from platelet integrin alpha IIb- and beta 3-subunits.

Integrin adhesion receptors constitute a cell-signaling system whereby interactions in the small cytoplasmic domains of the heterodimeric alpha- and beta-subunits provoke major functional alterations in the large extracellular domains. With two-dimensional NMR spectroscopy, we examined two synthetic peptides [alphaIIb((987)MWKVGFFKRNR) and beta3((716)KLLITIHDRKEFAKFEEERARAKWD)] encompassing the membrane-proximal regions of the cytoplasmic domain motifs from the platelet integrin complex alphaIotaIotabbeta3. These membrane-proximal regions contain two conserved motifs, represented by (989)KVGFFKR in the alphaIIb-subunit, and (716)KLLITIHDR in the beta3-subunit. The dimer interaction consists of two adjacent helices with residues V990 and F993 of the alphaIotaIotab-subunit heavily implicated in the dimer interfacial region, as is I719 of beta3. These residues are situated within the conserved motifs of their respective proteins. Further structural analysis of this unique peptide heterodimer suggests that two distinct conformers are present. The major structural difference between the two conformers is a bend in the beta3-peptide between D723 and A728, whereas the helical character in the other regions remains intact. Earlier mutational analysis has shown that a salt bridge between the side chains of alphaIotaIotab(R955) and beta3(D723) is formed. When this ion pair was modeled into both conformers, increased nuclear Overhauser effect violations suggested that the more bent structure was less able to accommodate this interaction. These results provide a molecular level rationalization for previously reported biochemical studies, as well as a basis for an atomic level understanding of the intermolecular interactions that regulate integrin activity.

Amino Acid Motifs↗
PubMed1982

The structure of the cytoplasmic matrix preserved by freeze-drying and freeze-substitution.

This paper reports a study of the cytoplasmic matrix in whole cultured cells examined by high voltage electron microscopy. In order to acquaint ourselves with the influence of preparation procedures on the morphology depicted, PtK2 cells were prepared for examination by first freezing in propane at -185 degrees C and then drying while maintained at -95 degrees C. Other cells of the same type were first fixed with glutaraldehyde and OsO4 and then frozen dried. Others were prepared by freeze-substitution and eventually dried by the critical-point method from CO2. And finally, some were preserved by conventional techniques of glutaraldehyde and OsO4 followed by dehydration in alcohol and critical-point drying. The observations are presented in stereo images. The morphologies after these various procedures are quite similar. All show the characteristic three-dimensional lattice or meshwork of slender filaments called microtrabeculae. In cells rapidly frozen and then dried from the frozen state, there is less evidence of shrinkage and probable change in the trabecular structure than in cells first fixed with glutaraldehyde and then frozen dried. The differences we relate to the demonstrable failure of glutaraldehyde to penetrate the cell quickly and fix instantly any component that is in active motion. Other differences that can be observed between all four types of preparation are not recognizably striking and are thought to reflect as much as anything morphological diversity in the original cells. In some instances, the amorphous ice of the initial freezing at -185 degrees C was allowed to crystallize at -80 degrees C. The small crystals that form push aside the microtrabeculae and leave obvious imprints on the structure. The essential message from these experiments is that the cytomatrix is structured.

Animals↗
PubMed1977

Transformations in the structure of the cytoplasmic ground substance in erythrophores during pigment aggregation and dispersion. I. A study using whole-cell preparations in stereo high voltage electron microscopy.

Pigment migration in cultured erythrophores of the squirrel fish Holocentrus ascensionis, after manipulation with K+, epinephrine, 3',5'-dibutyryl cyclic adenosine monophosphate, theophylline, and caffeine, is essentially identical to that observed in this chromatophore in situ. For such observations, the erythrophores are dissociated from the scales with hyaluronidase and collagenase, and allowed to spread on an amorphous collagen substrate, where they resemble the discoid erythrophore in situ. In this state, they are readily fixed by glutaraldehyde and osmium tetroxide, and are then critical-point dried for whole-cell viewing in the high voltage electron microscope. The organization and fine structure of the erythrophore cytoplast was stereoscopically examined after fixation of the pigment granules in four experimental states: pigment dispersed, pigment aggregated, pigment aggregating, and pigment dispersing. In the dispersed cell, granules are contained in an extensive three-dimensional lattice composed of radially oriented microtubules and a network of fine filaments 3-6 nm in diameter (microtrabeculae), whereas in the aggregated cell, the microtrabecular system is absent, and the majority of the microtubules appear displaced into the cortices on the cytoplasmic surface of the plasma membrane. In cells fixed while aggregating, few microtrabeculae are observed, although formless thickenings are observed in the cortices, on granules, and between clumped granules. In dispersing cells, the microtrabecular system is reformed from material stored in the cortices and with the granules in the centrosphere. These observations suggest that the granules are suspended in a dynamic microtrabecular system that withdraws during pigment aggregation and is restructured during pigment dispersion. The microtubules guide linear granule motion not by defining physical channels, but by a recognizable affinity of microtubules, microtrabeculae, and granules for one another.

Animals↗
PubMed1996

Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA.

Comparative modeling of secondary structure is a proven approach to predicting higher order structural elements in homologous RNA molecules. Here we present the results of a comprehensive comparison of newly modeled or refined secondary structures for the cytoplasmic large subunit (23 S-like) rRNA of eukaryotes. This analysis, which covers a broad phylogenetic spectrum within the eukaryotic lineage, has defined regions that differ widely in their degree of structural conservation, ranging from a core of primary sequence and secondary structure that is virtually invariant, to highly variable regions. New comparative information allows us to propose structures for many of the variable regions that had not been modeled before, and rigorously to confirm or refine variable region structures previously proposed by us or others. The present analysis also serves to identify phylogenetically informative features of primary and secondary structure that characterize these models of eukaryotic cytoplasmic 23 S-like rRNA. Finally, the work summarized here provides a basis for experimental studies designed both to test further the validity of the proposed secondary structures and to explore structure-function relationships.

Base Sequence↗
PubMed1971

Proteins of a polyhedral cytoplasmic deoxyvirus. 3. Structure of frog virus 3 and location ov virus-associated adenosine triphosphate phosphohydrolase.

The adenosine triphosphatase associated with frog virus 3 shows high specificity for ATP or deoxyadenosine triphosphate and appears to be distinct from the corresponding activity in host cells, poxvirus, or reovirus. The enzyme activity is probably integrated into virus particles since it is firmly associated with subviral particles produced when approximately 50 to 60% of the outer viral protein is removed by detergent treatment. The occurrence of adenosine triphosphatase activity within three unrelated viruses suggests that adenosine tryphosphatase might be a necessary function for most viruses that replicate in the cell cytoplasm.

Adenosine Triphosphatases↗
PubMed1975

Synaptic fine structure and nuclear, cytoplasmic and extracellular networks: The stereoframework concept.

When certain intracellular and extracellular localities known to be rich in protein complexes are fixed and processed for electron microscopy, they show a reticulate precipitate which represents three-dimensional framework of material that forms the wall of polygonal lacunae. This is referred to as a stereoframework. Examples of a stereoframework described her include the presynaptic dense projections, cleft substance, postsynaptic density, the cytonet, coats of coated vesicles, reticulosomes, 'microfilamentous' network of growth cones, the glycocalyx of gut microvilli, blood plasma, precipitates of the Golgi apparatus, the chromatin of nuclei and the nuclear pore complex. The stereoframeworkappears most electron-dense when it has a very close mesh, e.g. as in the case of the dense projections. The stereoframework is assumed to have no direct relationship with themolecular architecture of the protein complexes in vivo and so can be regarded as a denaturization and precipitation artifact. This being so, attempts to elucidate the substructure of the above entities simply by inspection are fruitless. Furthermore, evidence is given that stereoframework precipitation can distort or completely obliterate organelles occupying the same locality, for example this could apply to structures such as actin filaments (perhaps running into the locality marked by a dense projection), microtubules(running into the presynaptic bag), smooth ER, tenuous connections between synaptic vesicles and the presynaptic membrane, structures within the nuclear pore complex and chromosome substructures in the nucleus. Finally it is suggested that the flat shape of synaptic vesicles (at inhibitory synapses) may be a distortion effect imposed upon the synaptic vesicles not as a result of osmotic effects, but as a conformation to the shape of a stereoframework which has been precipitated from protein complexes in the vicinity ofthe synaptic vesicles.

Animals↗
PubMed1995

Genomic structure of a cytoplasmic dynein heavy chain gene from the nematode Caenorhabditis elegans.

We report the cloning and sequencing of genomic DNA encoding a cytoplasmic dynein heavy chain from the nematode Caenorhabditis elegans. In a contiguous stretch of 35,103 bp of DNA from the left arm of linkage group I, we have found a gene that is predicted to encode a protein of 4,568 amino acids. This gene is composed of 15 exons and 14 relatively short introns, and it has significant homology to the other dynein heavy chains in the databases. The deduced molecular mass of the derived polypeptide is 512,624 Da. As with other dynein heavy chains that have been sequenced to date, it contains four GXXGXGK(S/T) motifs that form part of a consensus sequence for the nucleotide triphosphate-binding domains. Comparison of the axonemal and cytoplasmic dynein heavy chains shows that regions of homology among all dyneins are clustered in the carboxyl terminal two-thirds of the polypeptide, whereas the amino terminal one-third of the heavy chains may contain domains that specify functions that differ between the axonemal and cytoplasmic forms of the dynein heavy chain.

Animals↗
PubMed1975

[Fibrillar and tubular fine structures in the cytoplasm of Entamoeba histolytica (author's transl)].

The electron-microscopical study of conventional fixed and contrasted Entamoeba histolytica-trophozoites from Diamonds monoxenic TTY-medium revealed "thick fibrils" in the vesicular cytoplasm of the parasites. They are 9-14 nm in diameter and are therefore considered to be myosin-like filaments, that are spread mainly in the tail or the uroid of the moving ameba. No association with microfilaments (MF) or other organelles could be observed. During the same investigation microtubules (MT) of variable length are described having a diameter of 35 nm, surrounded by a 19-25 nm wide capsule. They are distributed singly or in bundles with a maximal diameter of 350 nm. Some of the MT were coiled up to a helical shape.

Animals↗