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At least 217 records · Page 12Linked to original sources
PubMed2000

Small GTPase Rac1: structure, localization, and expression of the human gene.

Rac1 is a member of the Rho family of small GTPases involved in signal transduction pathways that control proliferation, adhesion, and migration of cells during embryonic development and invasiveness of tumor cells. Here we present the complete structure of the human RAC1 gene and characterize its expression. The gene comprises 7 exons over a length of 29 kb and is localized to chromosome 7p22. The GC-rich gene promoter shows characteristics of a housekeeping gene and Northern blot studies revealed ubiquitous expression of two rac1 transcripts, 1.2 and 2.5 kb in size. The two transcripts are expressed in tissue-specific ratios, reflecting competition between two alternative polyadenylation sites. The RAC1 but not RAC2 gene contains an additional exon 3b that is included by alternative splicing into the variant Rac1b, a constitutively active mutant which induces the formation of lamellipodia in fibroblasts. These data indicate that the RAC1 gene encodes two signaling GTPases. The gene structure reported here will enable studies on the regulation of RAC1 expression during tumorigenesis and development.

5' Untranslated Regions↗
PubMed1997

Phosphorylation on histidine is accompanied by localized structural changes in the phosphocarrier protein, HPr from Bacillus subtilis.

The histidine-containing protein (HPr) of bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) serves a central role in a series of phosphotransfer reactions used for the translocation of sugars across cell membranes. These studies report the high-definition solution structures of both the unphosphorylated and histidine phosphorylated (P-His) forms of HPr from Bacillus subtilis. Consistent with previous NMR studies, local conformational adjustments occur upon phosphorylation of His 15, which positions the phosphate group to serve as a hydrogen bond acceptor for the amide protons of Ala 16 and Arg 17 and to interact favorably with the alpha-helix macrodipole. However, the positively charged side chain of the highly conserved Arg 17 does not appear to interact directly with phospho-His 15, suggesting that Arg 17 plays a role in the recognition of other PTS enzymes or in phosphotransfer reactions directly. Unlike the results reported for Escherichia coli P-His HPr (Van Nuland NA, Boelens R, Scheek RM, Robillard GT, 1995, J Mol Biol 246:180-193), our data indicate that phosphorylation of His 15 is not accompanied by adoption of unfavorable backbone conformations for active site residues in B. subtilis P-Ser HPr.

Bacillus subtilis↗
PubMed1990

Immunocytochemical analysis of P-fimbrial structure: localization of minor subunits and the influence of the minor subunit FsoE on the biogenesis of the adhesin.

Antibodies recognizing the non-adhesive minor P-fimbral subunit protein E and the P-fimbrial adhesin were used in an immunocytochemical analysis of P-fimbrial structure. It was demonstrated that P-fimbriae of the serotypes F71, F72 and F11 carry their adhesin in a complex with protein E. These complexes are commonly found at the tip of the fimbrial structure. In P-fimbriae of serotype F9, expressed by the uropathogenic Escherichia coli strain 21086, adhesin-protein E complexes are localized at the tips as well as along the shafts of the fimbriae. Protein E of F71 fimbriae (FsoE) plays a catalysing role in the biogenesis of the adhesin, but has no effect on the eventual localization of the adhesin.

Adhesins, Escherichia coli↗
PubMed1991

Immunogold fine structural localization of extracellular matrix components in aged human cornea. I. Types I-IV collagen and laminin.

Using the immunogold technique combined with cryoultramicrotomy and London Resin white (LR white) embedding, we studied the fine structural distribution of types I-IV collagen and laminin in corneal tissue from seven enucleated human eyes (age range, 63-78 years). Type II collagen was not identified in any corneal layer. Type I and type III collagen were distributed in a similar fashion in striated collagen fibrils in Bowman's layer and in the stroma. Type IV collagen was located only in the posterior non-banded region of Descemet's membrane. Laminin was identified in subepithelial anchoring plaques and the sub-endothelial region of Descemet's membrane in accordance with its recognized adhesive function.

Aged↗
PubMed2000

Selection criteria and preoperative investigation of patients with focal epilepsy who lack a localized structural lesion.

Children with medically resistant epilepsy are often referred for surgical evaluation. The absence of a specific focal lesion on MRI may render the work-up difficult. In response to the need to localize the primary area of epileptogenesis, surgery protocols are being developed which rely on clinical semiology, EEG and functional imaging data. In selected cases, intracranial EEG monitoring may be required. While testing more often depends on the convergence of modalities, it is possible to localize seizure origin in the majority of children, and fully excise the epileptogenic region. This review presents the etiology and preoperative modalities available for children with intractable, non-lesional epilepsy.

Brain↗
PubMed2001

[Structure, localization and physiologic role of pituitary adenylate cyclase activating polypeptide (PACAP)].

PACAP was isolated on the basis of its ability to stimulate adenylate cyclase in primary anterior pituitary cell culture from ovine hypothalami by Miyata et al. in 1989. This peptide is structurally related to the secretin family and shows a 67% sequence homology with vasoactive intestinal polypeptide (VIP). The amino acid sequence of PACAP has been highly preserved during the evolution that may be connected with its important physiological role. Similar to other "brain-gut peptides" PACAP is localized not only in the central but in the peripheral nervous system and in non-neural tissues as well. In addition to its hypophysiotropic effects in the hypothalamo-hypophysial system PACAP exerts its effects on water-salt balance, cardiovascular functions, gastrointestinal motility and secretion and also on the regulation of reproductive functions. PACAP has a role in certain neuro-immuno-endocrine processes, in the differentiation of the nervous system, and it has neuroprotective effects in the case of ischaemia and various toxic agents. Locally PACAP takes its effects as an auto- and paracrine hormone, a neurotransmitter or a neuromodulator in different organs. Besides VIP, PACAP plays an important role in the function of the photo-neuro-endocrine system.

Amino Acid Sequence↗
PubMed2005

Modified replica exchange simulation methods for local structure refinement.

Parallel tempering, also known as replica exchange molecular dynamics (REMD), has recently been successfully used to study the structure and thermodynamic properties of biomolecules such as peptides and small proteins. For large systems, however, applying REMD can be costly since the number of replicas needed increases as the square root of the number of degrees of freedom in the system. Often, enhanced sampling is only needed for a subset of atoms, such as a loop region of a large protein or a small ligand binding to a receptor. In such applications, it is often reasonable to assume a weak dependence of the structure of the larger region on the instantaneous conformation of the smaller region of interest. For these cases, we derived two variant replica exchange methods, partial replica exchange molecular dynamics (PREMD) and local replica exchange molecular dynamics (LREMD). The Hamiltonian for the system is separated, with replica exchange carried out only for terms involving the subsystem of interest while the remainder of the system is maintained at a single temperature. The number of replicas required for efficient exchange thus depends on the number of degrees of freedom in the fragment needing refinement rather than on the size of the full system. The method can be applied to much larger systems than was previously practical. This also provides a means to preserve the integrity of the structure outside the refinement region without introduction of restraints. LREMD takes this weak coupling approximation a step further, employing only a single representation of the large fragment that simultaneously interacts with all of the replicas of the subsystem of interest. This is obtained by combining replica exchange with the locally enhanced sampling approximation (LES), reducing the computational expense of replica exchange simulations to near that of a single standard molecular dynamics (MD) simulation. Use of LREMD also permits the use of LES without requiring the specification of a single temperature, a known difficulty for standard LES simulations. We tested these two methods on the loop region of an RNA hairpin model system and find significant advantages over standard MD and REMD simulations.

Algorithms↗
PubMed1996

Tetrameric (G4) acetylcholinesterase: structure, localization, and physiological regulation.

Acetylcholinesterase (AChE), a highly conserved enzyme in the animal kingdom, is distributed throughout a wide range of vertebrate tissues where it is expressed as multiple molecular forms comprising different arrangements of catalytic and structural subunits. The major AChE form in the CNS is an amphiphilic globular tetramer (G4 AChE) consisting of four identical catalytic subunits attached to cellular membranes by a hydrophobic noncatalytic subunit (P-subunit). This study focuses primarily on current data involving the structure of the G4 AChE P-subunit, the expression and regulation of G4 AChE during development and adulthood, and its role(s) in certain neurological disorders including Alzheimer's disease.

Acetylcholinesterase↗
PubMed1990

Structure, localization and function of FanF, a minor component of K99 fibrillae of enterotoxigenic Escherichia coli.

The DNA sequence of the K99 fanF gene, encoding FanF, was determined. An open reading frame of 999 bp was found. The primary structure of FanF was deduced and analysis revealed the presence of a signal sequence of 22 amino acid residues. The mature protein contains 311 amino acid residues (Mr 33,905 D). The amino acid sequence of FanF showed similarity with the K88ab major subunit FaeG. A specific mouse antiserum against FanF was prepared by constructing and purifying a hybrid Cro-LacZ-FanF protein. Minicell analysis, immunoblotting and immunoelectronmicroscopy revealed a pool of FanF in the periplasm of K99-producing cells and showed, furthermore, that FanF is a minor component of K99 fibrillae, present at the top and in or along the shaft of the K99 fibrillar structures. A fanF mutant plasmid was constructed. Cells harbouring this plasmid produced all K99-specific proteins, except FanF, but produced 0.1% of the K99 fibrillae relative to 'normal' K99-producing cells. Electron microscopic observations showed that cells defective in fanF produce only a few (apparently short) K99 fibrillae. FanF, therefore, was supposed to play a role in initiation and elongation of K99 fibrillae formation. Thin-layer chromatography experiments involving purified receptor material showed that FanF is not required for binding of K99 fibrillae to the ganglioside receptor. Fibrillae produced by an adhesion-negative strain carrying a mutation in the K99 major fibrillar subunit were shown to contain a normal amount of FanF.

Amino Acid Sequence↗
PubMed1995

Folding of the squash trypsin inhibitor EETI II. Evidence of native and non-native local structural preferences in a linear analogue.

A peptide, corresponding to the entire sequence of the squash trypsin inhibitor EETI II (Ecballium elaterium trypsin inhibitor) in which the six cysteines, engaged in three disulphide bridges in native EETI II, have been replaced by six serines, has been synthesised. CD, Fourier-transform infrared spectroscopy (FTIR) and 1H-NMR studies of this peptide revealed that some secondary structures present in native EETI II are still populated in the absence of disulphide bonds. Native-like secondary structures were observed for segments 10-15 (helix), 16-19 and 22-25 (reverse turns) but no native tertiary interaction was detected. However, a non-native local interaction between the aromatic ring of Phe26 and the amide group of Gly28 was observed. It is hypothesised that the 10-15, 16-19 and 22-25 native-like local conformations could play a major role in the early folding of EETI II.

Amino Acid Sequence↗
PubMed1995

The human type 1 inositol 1,4,5-trisphosphate receptor from T lymphocytes. Structure, localization, and tyrosine phosphorylation.

Inositol 1,4,5-trisphosphate receptors (IP3R) are intracellular calcium release channels involved in diverse signaling pathways. An IP3R is thought to play a role in mobilizing calcium required for activation of T lymphocytes. The IP3R is a tetrameric structure comprised of four approximately 300-kDa subunits encoded by a approximately 10-kilobase mRNA. In the present study we determined the structure of the human type 1 IP3R expressed in T lymphocytes (Jurkats). The IP3R in human T cells had a predicted molecular mass of 308 kDa and was most similar to the non-neuronal form of the rodent type 1 IP3R. Two putative tyrosine phosphorylation sites were identified, one near the amino terminus and one near the putative channel pore at the carboxyl terminus. During T cell activation the IP3R was tyrosine phosphorylated. A site-specific anti-IP3R antibody was used to localize the carboxyl terminus of the IP3R to the cytoplasm in T cells.

Amino Acid Sequence↗
PubMed1984

Type VI collagen. Studies on its localization, structure, and biosynthetic form with monoclonal antibodies.

Monoclonal antibodies were prepared by immunization with whole tissue and were selected for their reactivity with extracellular matrices in tissue immunofluorescence. Two such antibodies were used to isolate the corresponding antigen from pepsin extracts of human placental tissue by immunochromatography. In each case, polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate showed that the isolated material was composed of four polypeptides of Mr between 57,000 and 85,000 that were disulfide-bonded into a high molecular weight aggregate. Amino acid analyses showed that the isolated material was partly collagenous. The material was shown to be antigenically related to previously isolated peptic fragments of type VI collagen and it shared their unique structure as revealed by electron microscopy. Based on these findings, it was concluded that the isolated material was a form of type VI collagen. In immunofluorescence, the monoclonal antibodies localized type VI collagen throughout the connective tissue and in the extracellular matrix of cultured fibroblasts. Polypeptides presumably comprising the intact form of this collagen were isolated from cultures of metabolically radiolabeled fibroblast cell cultures using the two monoclonal antibodies. The isolated material consisted of two polypeptides of Mr 240,000 and 140,000 that were extensively disulfide cross-linked. Four additional monoclonal antibodies bound the same radioactive polypeptides from fibroblast cultures, but only one of them reacted with the fragments isolated from pepsin-digested placenta. Since all six antibodies were originally selected based on tissue immunofluorescence, and therefore react with the tissue form of the protein, the tissue form appears to be more similar to the polypeptides detected in fibroblast cultures than to the pepsin-resistant fragments. Since these monoclonal antibodies apparently recognize different parts of the molecule, they will be useful for further study of the structure and function of the intact form of type VI collagen.

Amino Acids↗
PubMed1978

Fine structural localization of potassium-stimulated rho nitrophenylphosphatase activity in denrites of the cerebral cortex.

A histochemical technique for the demonstration of K+-rho-nitrophenylphosphatase (K+-rhoNPPase) activity, a component of the Na+,K+-ATPase, has been applied at the fine structural level in the somatosensory cortex of the rat. Reaction product was consistenly found in dendrites and in association with the cytoplasmic aspect of the dendritic plasmalemma. Reaction product often filled portions of the tubular smooth endoplasmic reticulum in these processes. The results of these studies are interpreted to indicate that enzymatic activity is associated with large-and small-diameter dendrites. No convincing evidence of high activity was found in glial profiles. The importance of neurons and their dendrites in active transport of sodium and potassium ions in the cerebral cortex may be more significant than indicated by studies with isolated neurons and glia.

4-Nitrophenylphosphatase↗
PubMed2000

Correlation between 31P chemical shift tensor and local structure in lithium cyclohexaphosphates Li6P6O18 x 3H2O and Li6P6O18.

To understand the surprising behavior between the variations of the P'-P-P" angles and the correlated variations of the O'-P-O" ones, two lithium cyclohexaphosphate compounds Li6P6O18 x 3H2O and Li6P6O18 are studied by solid state nuclear magnetic resonance (NMR) spectroscopy. The two compounds exhibit the same [P6O18]6- ring anions but with 3m or 1 internal symmetry, respectively. Such symmetries induce local distortions that are exhibited by NMR spectroscopy. One-dimensional (1D) NMR gives information on structural sites of 7Li and 31P ions and the crystallographic non-equivalencies are observed. Nevertheless, in the anhydrous compound, X-ray diffraction and NMR results do not completely agree and some discrepancy exists between the number of sites observed with the first technique and the number of lines exhibited in the NMR spectra either for 7Li or 31P nuclei. This problem is elucidated by using 2D double quantum NMR spectroscopy coupled with theoretical considerations. We find that the 31P chemical shift tensor is dependent on the deviations of the O-P-O angles from those in the regular tetrahedron. Within the same empirical model, we suggest that the surprising behavior between the variations of the P'-P-P" and the ones of the O'-P-O" is related to the overall charge on the PO4 group. We also find the positions of the isotropic lines for 7Li essentially depend on the site co-ordination of this nuclei.

Crystallography, X-Ray↗
PubMed2005

Localization, structure and polymorphism of two paralogous Xenopus laevis mitochondrial malate dehydrogenase genes.

Two paralogous mitochondrial malate dehydrogenase 2 (Mdh2) genes of Xenopus laevis have been cloned and sequenced, revealing 95% identity. Fluorescence in-situ hybridization (FISH) combined with tyramide amplification discriminates both genes; Mdh2a was localized into chromosome q3 and Mdh2b into chromosome q8. One kb cDNA probes detect both genes with 85% accuracy. The remaining signals were on the paralogous counterpart. Introns interrupt coding sequences at the same nucleotide as defined for mouse. Restriction polymorphism has been detected in the first intron of Mdh2a, while the individual variability in intron 6 of Mdh2b gene is represented by an insertion of incomplete retrotransposon L1Xl. Rates of nucleotide substitutions indicate that both genes are under similar evolutionary constraints. X. laevis Mdh2 genes can be used as markers for physical mapping and linkage analysis.

Amino Acid Sequence↗
PubMed1992

Characterization and fine-structural localization of actin- and fibronectin-like proteins in planaria (Dugesia lugubris s.l.).

Actin- and fibronectin-like proteins were characterized in the planarian, Dugesia lugubris s.l., by sodium dodecyl sulphate polyacrylamide gel electrophoresis and immunoblotting analysis using antisera to vertebrate actin and fibronectin. These antisera recognized protein bands of 42 kDa and 220 kDa, respectively. In addition, the immunohistochemical distribution of both actin- and fibronectin-like material was examined by using immuno-electron microscopy. Actin-like protein was localized in myofibrils in various differentiation stages, and in the peripheral cytoplasm and lamellipodia of cells that were migrating. The fibronectin-like component was associated with the extracellular matrix in the fibrillar structures and with the surface of the migrating cells. Our data suggest that similar cellular and molecular mechanisms are involved in cell-matrix interactions and in the morphogenesis of living organisms at different evolutionary levels.

Actins↗
PubMed1981

Connective tissue components of the normal and fibrotic liver. I. Structure, local distribution and metabolism of connective tissue components in the normal liver and changes in chronic liver diseases.

The first part of this review describes the chemistry, the occurrence and the metabolism of extracellular connective tissue components in the liver. The normal liver contains typical connective tissue proteins (collagens, structural glycoproteins and proteoglycans) not only in vessel walls, perivascular areas and in the capsule, but they occur also in small amounts in the parenchyma, mainly in the space of Disse along the sinusoidal walls. The "interstitial" collagens type I and III represent the major amount of collagen in the normal as well as in fibrotic liver, showing a relative increase of type III in fibrosis. Basement membrane collagens type IV and V as well as the cysteine-rich collagenous components "7 S collagen" and "short chain collagen" have been shown to occur in extracts prepared after limited pepsin digestion. In the normal liver, basement membrane collagen can hardly be detected within the parenchyma by immunofluorescence microscopy; increased occurrence, however, can be shown along the sinusoids even in early stages of chronic liver diseases. The glycoprotein fibronectin was shown to be distributed very similarly to collagens type I and III, whereas the basement membrane specific glycoprotein laminin is restricted to vessel walls and the epithelial layer of bile ductuli in the normal liver but is also found in the parenchyma in fibrosis. Occurrence of proteoglycans is increased in fibrosis: a change in the composition of glycosaminoglycans from mainly heparan sulfate in the normal to dermatan- and chondroitin sulfate in the fibrotic liver was observed. It is not yet clear which cell type is mainly responsible for increased connective tissue synthesis in fibrosis. The occurrence of cells resembling smooth muscle cells ("myofibroblasts") in connective tissue septa of fibrotic livers and the fact that similar cells which actively synthesize collagen grow from explants of fibrotic livers may indicate the significance of this cell type in the process of liver fibrosis.

Basement Membrane↗
PubMedDate not supplied

Model of global spontaneous activity and local structured activity during delay periods in the cerebral cortex.

We investigate self-sustaining stable states (attractors) in networks of integrate-and-fire neurons. First, we study the stability of spontaneous activity in an unstructured network. It is shown that the stochastic background activity, of 1-5 spikes/s, is unstable if all neurons are excitatory. On the other hand, spontaneous activity becomes self-stabilizing in presence of local inhibition, given reasonable values of the parameters of the network. Second, in a network sustaining physiological spontaneous rates, we study the effect of learning in a local module, expressed in synaptic modifications in specific populations of synapses. We find that if the average synaptic potentiation (LTP) is too low, no stimulus specific activity manifests itself in the delay period. Instead, following the presentation and removal of any stimulus there is, in the local module, a delay activity in which all neurons selective (responding visually) to any of the stimuli presented for learning have rates which gradually increase with the amplitude of synaptic potentiation. When the average LTP increases beyond a critical value, specific local attractors (stable states) appear abruptly against the background of the global uniform spontaneous attractor. In this case the local module has two available types of collective delay activity: if the stimulus is unfamiliar, the activity is spontaneous; if it is similar to a learned stimulus, delay activity is selective. These new attractors reflect the synaptic structure developed during learning. In each of them a small population of neurons have elevated rates, which depend on the strength of LTP. The remaining neurons of the module have their activity at spontaneous rates. The predictions made in this paper could be checked by single unit recordings in delayed response experiments.

Cerebral Cortex↗