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At least 865 records · Page 48Linked to original sources
PubMed1999

Genetic and structural analyses of cytoplasmic filaments of wild-type Treponema phagedenis and a flagellar filament-deficient mutant.

Unique cytoplasmic filaments are found in the treponeme genus of spirochete bacteria. Their function is unknown, but their location underneath the periplasmic flagellar filaments (PFF) suggests a role in motility and/or cell structure. To better understand these unique structures, the gene coding for the cytoplasmic filaments, cfpA, was identified in various treponemal species. Treponema phagedenis cfpA was 2,037 nucleotides long, and the encoded polypeptide showed 78 to 100% amino acid sequence identity with the partial sequence of CfpA from T. denticola, T. vincentii, and T. pallidum subsp. pertenue. Wild-type T. phagedenis and a PFF-deficient isolate were analyzed by electron microscopy to assess the structural relationship of the cytoplasmic filaments and the PFF. The number of cytoplasmic filaments per cell of T. phagedenis (mean, 5.7) was compared with the number of PFF at each end of the cell (mean, 4.7); the results suggest that there is no direct one-to-one correlation at the cell end. Moreover, a structural link between these structures could not be demonstrated. The cytoplasmic filaments were also analyzed by electron microscopy at different stages of cell growth; this analysis revealed that they are cleaved before or during septum formation and before the nascent formation of PFF. A PFF-deficient mutant of T. phagedenis possessed cytoplasmic filaments similar to those of the wild type, suggesting that intact PFF are not required for their assembly and regulation. The extensive conservation of CfpA among pathogenic spirochetes suggests an important function, and structural analysis suggests that it is unlikely that the cytoplasmic filaments and the flagellar apparatus are physically linked.

Bacterial Proteins↗
PubMed1987

Structure of the cytoplasmic filament system in freeze-dried whole mounts viewed by HVEM.

Freeze-drying (FD) was used as an alternative to critical point-drying (CPD) for the preparation of whole mounts to study the cytoplasmic filament system in mammalian cultured cells by high voltage electron microscopy (HVEM). Rapid quenching methods such as plunging a grid into liquid propane cooled by LN2 or collision with a clean surface of a copper block cooled to LHe temperature were used to avoid ice crystal formation. For freeze-drying, a special apparatus was built that allowed the specimen to be kept at 145 K for 2-3 days at a vacuum of about 2 X 10(-7) Torr followed by gradual stepwise warming to room temperature. Purified skeletal muscle actin served as a test object for which the structure was known through independent techniques. PtK-1 cells, grown on gold grids and fixed in buffered glutaraldehyde, were used to study the structure of the cytoplasmic filament system. Under conditions that should avoid formation of ice crystals, the structure of actin fibres was as expected on the basis of previous studies, i.e. a tangle of independent uniform filaments about 7 nm thick, Using similar conditions, the cytoplasmic filaments of PtK-1 cells were equally distinct and evenly thick along their length and were usually associated with particles about 10 nm thick. On the other hand, when the sublimation time at the low temperature was cut short, both purified actin and the cytoplasmic filament system formed a network of tapering filaments devoid of particles, similar to that which has been described as a 'microtrabecular lattice'. We therefore conclude that when this structure is seen in FD preparations, it is probably the result of distortion produced by faulty FD procedure.

Actins↗
PubMed2003

Cytoplasmic polyhedrosis virus structure at 8 A by electron cryomicroscopy: structural basis of capsid stability and mRNA processing regulation.

The single-shelled cytoplasmic polyhedrosis virus (CPV) is a unique member of the Reoviridae. Despite lacking protective outer shells, it exhibits striking capsid stability and is capable of endogenous RNA transcription and processing. The 8 A three-dimensional structure of CPV by electron cryomicroscopy reveals secondary structure elements present in the capsid proteins CSP, LPP, and TP, which have alpha+beta folds. The extensive nonequivalent interactions between CSP and LPP, the unique CSP protrusion domain, and the perfect inter-CSP surface complementarities may account for the enhanced capsid stability. The slanted disposition of TP functional domains and the stacking of channel constrictions suggest an iris diaphragm-like mechanism for opening/closing capsid pores and turret channels in regulating the highly coordinated steps of mRNA transcription, processing, and release.

Animals↗
PubMed1977

[Ribonucleoproteins containing heterogeneous nuclear and messenger cytoplasmic RNA. Characteristics, structure and relations (author's transl)].

Following the study of Spirin, many authors have shown that cytoplasmic messenger RNA and heterogeneous nuclear RNA are complexed with specific proteins to form ribonucleoprotein particles (RNP). These RNP are heterogeneous in size and present a high protein to RNA ratio. Different observations suggest a polymeric structure for nuclear ribonucleoproteins but their protein composition is more clearly complex than that of cytoplasmic ribonucleoproteins. If we accept the following processing: heterogeneous nuclear RNP leads to free cytoplasmic RNP leads to polysomic RNP, the question arises as to what extent proteins originally present in nuclear RNP are conserved. Proteins more or less tightly bound to RNA have different roles: packing and protection of RNA, regulation during gene expression processing.

Animals↗
PubMed1984

Aldehyde dehydrogenase from human liver. Primary structure of the cytoplasmic isoenzyme.

Analysis of CNBr fragments and other peptides from human liver cytoplasmic aldehyde dehydrogenase enabled determination of the complete primary structure of this protein. The monomer has an acylated amino terminus and is composed of 500 amino acid residues, including 11 cysteine residues. No evidence of any microheterogeneity was obtained, supporting the concept that the enzyme is a homotetramer . The disulfiram-sensitive thiol in the protein, earlier identified through its reaction with iodoacetamide, is contributed by a cysteine residue at position 302, while the cysteine which in horse liver mitochondrial aldehyde dehydrogenase is reactive with coenzyme analogs appears to correspond to either Cys-455 or Cys-463. Analysis of glycine distribution and prediction of secondary structures to localize beta alpha beta regions typical for coenzyme-binding are not fully unambiguous, but suggest a short region around position 245 as a likely segment for this function. In this region, sequence similarities to parts of a bacterial aspartate-beta-semialdehyde dehydrogenase and a mammalian alcohol dehydrogenase were noted. Otherwise, no extensive similarities were detected in comparisons with characterized mammalian enzymes of similar activity or subunit size as aldehyde dehydrogenase (glyceraldehyde-3-phosphate dehydrogenase and glutamate dehydrogenase, respectively).

Aldehyde Dehydrogenase↗
PubMed1995

The Btk subfamily of cytoplasmic tyrosine kinases: structure, regulation and function.

The genetic defect associated with two closely related primary immunodeficiencies was recently identified as a deficiency of function of a new cytoplasmic tyrosine kinase, Bruton's tyrosine kinase (Btk). Btk and related genes expressed primarily in hematopoietic cells (Itk, Tec, Drsrc28C and Txk) comprise a new subfamily of cytoplasmic tyrosine kinases. These proteins share significant structural and sequence homology including an amino-terminal pleckstrin homology (PH) domain not present in other cytoplasmic tyrosine kinase subfamilies. This domain plays an essential role in regulation and function of the Btk subfamily proteins. Genetic evidence supports a critical role for Btk in B-lineage development. Additional studies demonstrate activation of these proteins in multiple hematopoietic signaling pathways including the B cell antigen receptor, several cytokine receptors, and a potential novel role in heterotrimeric G protein associated receptor signaling.

Agammaglobulinaemia Tyrosine Kinase↗
PubMed2004

The structure of the cytoplasmic domain of EpsL, an inner membrane component of the type II secretion system of Vibrio cholerae: an unusual member of the actin-like ATPase superfamily.

The type II secretion system (T2SS) is used by several Gram-negative bacteria for the secretion of hydrolytic enzymes and virulence factors across the outer membrane. In these secretion systems, a complex of 12-15 so-called "Gsp proteins" spans from a regulatory ATPase in the cytoplasm, via several signal or energy transducing proteins in the inner membrane and the pseudopilins in the periplasm, to the actual pore in the outer membrane. The human pathogen Vibrio cholerae employs such an assembly, called the Eps system, for the export of its major virulence factor, cholera toxin, from its periplasm into the lumen of the gastro-intestinal tract of the host. Here, we report the atomic structure of the major cytoplasmic domain of the inner membrane-spanning EpsL protein from V. cholerae. EpsL is the binding partner of the regulatory ATPase EpsE as well as of EpsM and pseudopilins, and is therefore a critical link between the cytoplasmic and the periplasmic part of the Eps-system. The 2.7A resolution structure was determined by a combination of Se-Met multiple anomalous dispersion (MAD) and multiple isomorphous replacement with anomalous scattering (MIRAS) phasing methods. The 28kDa cytoplasmic domain of EpsL (cyto-EpsL) consists of three beta-sheet-rich domains. With domains I and III similar to the RNaseH-fold, cyto-EpsL unexpectedly shows structural homology with the superfamily of actin-like ATPases. cyto-EpsL, however, is an unusual member of this superfamily as it misses the canonical actin domains 1B and 2B, which are common yet variable in this superfamily. Moreover, cyto-EpsL has an additional domain II, which has the topology of an SHS2-fold module. Within the superfamily this fold module has been observed only for domain 1C of the cell division protein FtsA, in which it mediates protein-protein interactions. This domain II displays great flexibility and contributes to a pronounced negatively charged canyon on the surface of cyto-EpsL. Functional data as well as structural homology and sequence conservation suggest that domain II interacts with EpsE, the major cytoplasmic binding partner of EpsL.

Actins↗
PubMed1983

Comparative structural analysis of cytoplasmic and chloroplastic 5S rRNA from spinach.

5S rRNAs from Spinacea oleracea cytoplasmic and chloroplastic ribosomes have been subjected to digestion with the single strand specific nuclease S1 and to chemical modification of cytidines by sodium bisulphite in order to probe the RNA structure. According to these data, cytoplasmic 5S rRNA can be folded as proposed in the general eukaryotic 5S rRNA structure (1) and 5S rRNA from chloroplastides is shown to be more related to the general eubacterial structure (2).

Base Sequence↗
PubMed2002

pH-dependent intramolecular binding and structure involving Cx43 cytoplasmic domains.

pH-induced closure of connexin43 (Cx43) channels involves interaction of the Cx43 carboxyl-terminal (Cx43CT) with a separate "receptor" domain. The receptor location and structure and whether the interaction is directly intramolecular are unknown. Here we show resonant mirror technology, enzyme-linked sorbent assays, and nuclear magnetic resonance (NMR) experiments demonstrating pH-dependent binding of Cx43CT to region 119-144 of Cx43 (Cx43L2), which we propose is the receptor. NMR showed that acidification induced alpha-helical order in Cx43L2, whereas only a minor modification in Cx43CT structure was detected. These data provide the first demonstration of chemically induced structural order and binding between cytoplasmic connexin domains.

Amino Acid Sequence↗
PubMed1998

Function of the KKXX motif in endoplasmic reticulum retrieval of a transmembrane protein depends on the length and structure of the cytoplasmic domain.

Transmembrane glycoproteins with type 1 topology can be retrieved to the endoplasmic reticulum (ER) by a retrieval signal containing a di-lysine (KK) motif near the C terminus. To investigate the structural requirements for ER retrieval, we have constructed mutants of the simian immunodeficiency virus (SIV) envelope (Env) protein with cytoplasmic tails of different lengths and containing a KK motif at the -3 and -4 positions. Such proteins were found to be retained intracellularly when the signal was located 18 amino acids or more away from the membrane spanning domain. The retrieval signal was found to be functional even when placed at the distal end of the wild-type SIV Env protein with 164 amino acids in the cytoplasmic tail, as shown by the lack of proteolytic processing and lack of cell surface expression of the mutant proteins. However, proteins with a cytoplasmic tail length of 13 amino acids or less having the di-lysine motif at the -3 and -4 positions were not retrieved to the ER since they were found to be processed and transported to the cell surface. The surface-expressed proteins were found to be functional in inducing cell fusion, whereas the proteins retained intracellularly were defective in fusion activity. We also found that the KK motif introduced near an amphipathic helical region in the cytoplasmic tail was not functional. These results demonstrate that the ability of the KK motif to cause protein retrieval and retention in the endoplasmic reticulum depends on the length and structure of the cytoplasmic domain. The ER retrieval of the mutant proteins was found to correlate with increased intracellular binding to beta COP proteins.

Cell Line↗
PubMed1996

Structure within eukaryotic cytoplasm and its relationship to glycolytic metabolism.

Taken together, the results reviewed here indicate that both structural proteins and enzymes exist in a relatively mobile, uncomplexed form and in a relatively immobile form, complexed with the matrix. The relative amounts of free and complexed forms of each protein are dependent upon the local concentrations of both small molecules and other macromolecules and hence may vary in time and space throughout the cell. Free and cytomatrix-bound enzymes exchange rapidly, while free and cytomatrix-bound structural proteins exchange more slowly. These two distinct time scales suggest that the slowly exchanging structural proteins form the core of fibrous structural elements--having many stabilizing intermolecular contacts with near neighbours--whereas the more rapidly exchanging enzymes adsorb to the surface of the structural elements and have fewer near neighbour contacts. The hierarchical nature of these associations is depicted schematically in Figure 3. Metabolism is proposed to proceed primarily via transport of small metabolites rather than by transport of enzymes, which may be organized in functional clusters to facilitate, metabolic regulation.

Cell Count↗
PubMed2001

A homologue of N-ethylmaleimide-sensitive factor in the malaria parasite Plasmodium falciparum is exported and localized in vesicular structures in the cytoplasm of infected erythrocytes in the brefeldin A-sensitive pathway.

N-Ethylmaleimide-sensitive factor (NSF) and its homologues play a central role in vesicular trafficking in eukaryotic cells. We have identified a NSF homologue in Plasmodium falciparum (PfNSF). The reported PfNSF gene sequence (GenBank accession number CAB10575) indicated that PfNSF comprises 783 amino acids with a calculated molecular weight of 89,133. The overall identities of its gene and amino acid sequences with those of rat NSF are 50.9 and 48.8%, respectively. Reverse transcription-polymerase chain reaction analysis and Northern blotting with total P. falciparum RNA indicated expression of the PfNSF gene. Polyclonal antibodies against a conserved region of NSF specifically recognized an 89-kDa polypeptide in the parasite cells. After homogenization of the parasite cells, approximately 90% of an 89-kDa polypeptide is associated with particulate fraction, suggesting membrane-bound nature of PfNSF. PfNSF was present within both the parasite cells and the vesicular structure outside of the parasite cells. The export of PfNSF outside of the parasite cells appears to occur at the early trophozoite stage and to terminate at the merozoite stage. The export of PfNSF is inhibited by brefeldin A, with 9 microM causing 50% inhibition. Immunoelectromicroscopy indicated that intracellular PfNSF was associated with organelles such as food vacuoles and that extracellular PfNSF was associated with vesicular structures in the erythrocyte cytoplasm. These results indicate that PfNSF expressed in the malaria parasite is exported to the extracellular space and then localized in intraerythrocytic vesicles in a brefeldin A-sensitive manner. It is suggested that a vesicular transport mechanism is involved in protein export targeted to erythrocyte membranes during intraerythrocytic development of the malaria parasite.

Amino Acid Sequence↗
PubMed2000

Structure of the cytoplasmic domain of p23 in solution: implications for the formation of COPI vesicles.

Coatomer, the coat protein complex of coat protein (COPI) vesicles, is involved in the budding of these vesicles. Its interaction with the cytoplasmic domains of some p24-family members, type I transmembrane proteins of the Golgi, has been shown to induce a conformational change of coatomer that initiates polymerization of the complex. From stoichiometrical data it is likely that interaction of coatomer with the small tail domains involves an oligomeric form of the p24 proteins. Here we present the structure of peptide analogs of the cytoplasmic domain of p23, a member of the p24 family, as determined by two-dimensional nuclear magnetic resonance spectroscopy in the presence of 2,2,2-trifluoroethanol. An improved strategy for structure calculation revealed that the tail domain peptides form alpha-helices and adopt a tetrameric state. Based on these results we propose an initial model for the binding of coatomer by p23 and the induced conformational change of coatomer that results in its polymerization, curvature of the Golgi membrane to form a bud, and finally a COPI-coated vesicle.

Amino Acid Sequence↗
PubMed2001

Solution structure of the cytoplasmic linker between domain III-S6 and domain IV-S1 (III-IV linker) of the rat brain sodium channel in SDS micelles.

The solution structure of the 36-mer peptide MP-5A in SDS micelles was investigated by CD and (1)H-NMR spectroscopies. The MP-5A was dissected from the cytoplasmic linker (K1482-A1517) connecting domain III-segment 6 (IIIS6) and domain IV-segment 1 (IVS1; III-IV linker) of the rat brain type IIA sodium channel. The molecular energy calculations including nuclear Overhauser effect and dihedral angle restraints gave a well-converged set of the structures of MP-5A for the region between I1488 and S1506. It was found that a large hydrophobic cluster is formed by I1488-F1489-M1490 (IFM motif), Y1497-Y1498, and M1501, which may be related to the fast inactivation process of the sodium channel. The solvent-accessible surface area of the IFM motif (195 A(2)), which is known to work essentially as an inactivation gate particle to occlude the ion permeation pore, gave the free energy (DeltaG) of stabilization of -3.9 kcal mol(-1) as a result of the hydrophobic interactions with its receptor. This value agreed well with the free energy of binding (inactivation) of -4.1 kcal mol(-1) calculated for the equilibrium between the open and the inactivated states of the sodium channels. It is concluded that the fast inactivation of the sodium channel is achieved by the environmental polarity-dependent conformational switching at the IFM motif, in response to the voltage-dependent activation and the movement of the S4 segments of the sodium channel.

Amino Acid Sequence↗
PubMed2004

Solution structure of the cytoplasmic domain of human CD99 type I.

Human CD99, which is encoded by the mic2 gene, is a ubiquitous 32 kDa transmembrane protein. Its major cellular functions are related to homotypic cell adhesion, apoptosis, vesicular protein transport, and differentiation of thymocytes or T cells. Recent reports have suggested that expression of a splice variant of CD99 increases the invasiveness of human breast cancer cells. In order to determine the structural basis of CD99 function, we have initiated structural studies on the human CD99 Type I cytoplasmic domain (hCD99cytoI) using circular dichroism and multi-dimensional NMR spectroscopy. The solution structure of hCD99cytoI shows that it has a hairpin shape anchored by two flexible loops. Consequently, hCD99cytoI does not have any regular secondary structural element; however, the NMR and CD data indicate that it possesses an intrinsic helical nature.

12E7 Antigen↗
PubMed1983

Crystallization-induced modification of cytoplasmic malate dehydrogenase structure and function.

In an effort to assess the effects of phase-state changes on protein conformations, we have compared several properties of cytoplasmic malate dehydrogenase in the crystalline and solution states. Two crystalline forms of the enzyme have been examined: one crystallized in the presence of nicotinamide adenine dinucleotide and the other in its absence. Though both forms catalyze cytoplasmic malate dehydrogenase's normal substrate conversions, they have specific activities 150-3000-fold less than the solution-state enzyme. These dramatic activity decreases cannot be accounted for by diffusion constraints imposed by the crystal lattice nor do they result from the manipulations necessary to crystallize or cross-link the enzyme. Further, crystal- and solution-state enzymes have different pH dependences of their enzymatic activities, have different sensitivities toward inactivation by the covalent inhibitor iodoacetate, and respond differently to nicotinamide adenine dinucleotide protection against this inactivation. Finally, crystals of the enzyme grown in the presence and absence of cofactor are also distinguishable from one another by using the same criteria. Taken together, these results suggest that crystallization perturbs the dynamics and, perhaps, the average conformation of cytoplasmic malate dehydrogenase.

Animals↗
PubMed1997

Probing the structure of the cytoplasmic domain of the aspartate receptor by targeted disulfide cross-linking.

Applying the technique of targeted disulfide cross-linking to the cytoplasmic domain of the aspartate receptor of Salmonella typhimurium indicates a generally alpha-helical conformation of the linker region, and a close juxtaposition and a parallel alignment at the interface between the two subunits in the linker region. This conclusion is supported by the results from the Fourier transform of the hydrophobicity values of the amino acid sequences. Aspartate binding in the periplasmic domain causes a closer juxtaposition of the two subunits in the cytoplasmic domain, as indicated by the more rapid disulfide cross-linking on addition of aspartate.

Amino Acid Sequence↗
PubMed1995

On the real structure of the cytoplasmic matrix: learning from the embedment-free electron microscopy.

The recent debate on the nature of the cytoplasmic matrix is reviewed on the basis of results obtained by electron microscopy of embedment-free materials, i.e., the critical point-dried whole mount-cell method, the polyethylene glycol (PEG)-embedding and subsequent de-embedding section method, and the freeze-etching method. Fine structural images obtained by these methods are carefully evaluated and close correspondence with electron microscopy regardless of these methods is demonstrated. Especially, 'novel' filamentous structures--the microtrabecular strands and the cross-linkers--correspond well to each other; they are structures which have been included in epoxy sections by conventional methods, but have been obscured simply because of a similar property of electron scattering between the filamentous structures and epoxy resin. Although this correspondence seems to support the existence of the microtrabeculae, the electron microscopy of serum albumin, when processed by the PEG-method, also exhibits filamentous networks resembling the microtrabecular lattice. This, together with the finding on the centrifugation of in situ cells, strongly suggests a possibility that most, if not all, microtrabecular strands and cross-linkers in cells without pretreatment by detergents do not represent actual in situ structures.

Animals↗