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At least 199 records · Page 11Linked to original sources
PubMed2004

pH-induced conformational transition of H. pylori acyl carrier protein: insight into the unfolding of local structure.

Acyl carrier protein (ACP) is a small acidic protein and its primary structure is highly conserved in various bacterial sources. Despite its small size, it interacts with diverse proteins associated with many biosynthetic pathways. The three-dimensional structure of H. pylori ACP and its structural characteristics were clarified using NMR and CD spectroscopy. H. pylori ACP consists of four helices connected by different sized loops. The helices correspond to residues L3-Q14 (alphaI), S36-G50 (alphaII), D56-E60 (alphaIII), and V65-K76 (alphaVI). The size of each helix differs slightly from that of homologous ACPs. However, H. pylori ACP showed a distinct pH-dependent conformational characteristic: at neutral pH, it adopts a partially unfolded structure, while it has a tight fold at pH 6. The chemical shift perturbation and (1)H-(15)N steady state NOE analysis at both pH 6 and 7 showed that the local change of structural components occurred mainly around loop II, and this change was reflected by the changes of the residues Ile 54 and Asp 56. Examination of the structure showed that the network of Glu 47, Ile 54, Asn 75, and Lys 76 is very important for the structural stability. The pH-dependent folding process shows a kind of cooperativity, since all the residues involved in the conformational transitions are contiguous and in spatial proximity.

Acyl Carrier Protein↗
PubMed1999

Is protein folding hierarchic? I. Local structure and peptide folding.

The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Nevertheless, we argue that both classes fold hierarchically and that folding begins locally. If this is the case, then the secondary structure of a protein is determined largely by local sequence information. Experimental data and theoretical considerations support this argument. Part I of this article reviews the relationship between secondary structures in proteins and their counterparts in peptides.

Computer Simulation↗
PubMed1998

Structural localization of the E3 glycoprotein in attenuated Sindbis virus mutants.

We have determined the three-dimensional structures of the wild-type Sindbis virus and two of its mutants that retain the E3 sequence within PE2. Using difference imaging between these mutants and the wild-type virus, we have assigned a location for the 64-amino-acid sequence corresponding to E3 in the mutant spike complex. In the wild-type virus, the spike is composed of an E1-E2 heterotrimer. The E3 protein was found to protrude midway between the center of the spike complex and the tips. Based on these results and the work of others, we propose a distribution for the functional domains of the spike proteins within the structure of wild-type Sindbis virus. Within the structure of the virus, the E1 domains form the central portion of the spike complex, while the tips are formed by the E2 domains that flare out from the center of the complex. The structural similarity between these Sindbis virus mutants and Ross River virus suggests that E3 may also be present in the latter, which is also a member of the Alphavirus genus.

Animals↗
PubMed1979

The fine structural localization of acid phosphatase in pore cells of embryonic and newly hatched Deroceras reticulatum (Pulmonata: Stylommatophora).

The fine structure of the pore cells in pre- and post-hatched Deroceras reticulatum is described. The cells have been divided into three main types on morphological grounds, one type being particulary rich in glycogen. Certain pore cells contain haemocyanin granules in grooves below cytoplasmic tongues, and in characteristic double-membrane-bounded vesicles within dilated cisternae of rough endoplasmic reticulum, as well as in other identified areas. All types of pore cells show fine fibres reminiscent of collagen associated with the basal lamina and pore complexes. In addition to acid phosphatase activity in lysosomes and Golgi elements, intra- and extracisternal activity has been demonstrated in association with the rough endoplasmic reticulum. The intracisternal activity is in close proximity to the Golgi apparatus and may represent enzyme that is about to enter the GERL system. Extracisternal activity may be associated with cellular lysis and death, or may represent local areas of degradation leading to cytodifferentiation. Remnants of lysed pore cells appear to be taken up by connective tissue amoebocytes.

Acid Phosphatase↗
PubMed1962

Fine structural localization of adenosinetriphosphatase activity in heart muscle myofibrils.

Activity of myofibrillar adenosinetriphosphatase was demonstrated histochemically at a fine structural level in isolated, unfixed or hydroxyadipaldehyde-fixed cardiac myofibrils in the rat, using a lead precipitation technique and either Ca(++) or Mg(++) as activating ion. Activity in relaxed myofibrils was found in the A band, but not the H, I, or Z bands. Deposits of final product frequently exhibited an axial periodicity of near 365 A, and bore a close relationship to filaments within the A band. Several patterns of distribution occurred in contracted myofibrils. In myofibrils which had shortened to the point of disappearance of the I band, final product was distributed throughout the sarcomere, except for the unreactive Z band. A second type of distribution occurred in strongly contracted fibers in which there was intensification of activity in the center of the sarcomere. These findings are discussed in the light of the recent morphological evidence and it is suggested that the distribution of final product is consistent with localization of enzyme activity to the cross-bridges between the thick and thin filaments.

Actin Cytoskeleton↗
PubMed2005

Modeling the local structure and energetics of protozeolitic nanoclusters in hydrothermally stable aluminosilicate mesostructures.

The density functional theory (DFT) method is used to investigate the structure and bonding of silica and aluminosilicate nanoclusters containing five- and six-membered oxygen rings. The clusters, which are derived from the BEA zeolite structure, are considered as models of the protozeolitic clusters that are incorporated into the pore walls of steam stable aluminosilicate mesostructures assembled from zeolite seeds. Two locally different Brønsted acid sites in the aluminosilicate structure are identified for the adsorption of a water molecule. The sterically more open acid site is favored for water binding. The stability of the aluminosilicate structure in the presence of H2O molecule is studied by breaking an Al-O bond and inserting a water molecule into the five-membered ring structure. We find that an excitation energy at least 18 times larger than the room-temperature thermal energy is needed to break the stable five-membered ring structure, implying a high hydrothermal stability and acidity for this aluminosilicate structure.

Journal Article↗
PubMed1985

Human osteogenic sarcoma: fine structural localization of alkaline phosphatase.

The localization of alkaline phosphatase in eight osteogenic sarcomas of osteoblastic. chondroblastic, and fibroblastic type was investigated at the fine structural level using beta-glycerophosphate as substrate and lead as capturing ion. Final product marking localization of alkaline phosphatase was deposited over plasma membranes and associated subplasmalemmal vesicles and vacuoles in various types of osteoblastlike, chondroblastlike, and fibroblastlike cells as well as certain multinucleated giant cells. Presence of L-homoarginine or L-tetramisole in the incubation medium, and incubation at 65 degrees C, prevented the deposition of final product, suggesting that the enzyme studied was "bone specific." The evidence obtained was compatible with the notion that the different cells showing presence of reaction product were functionally and histogenetically closely related and all were likely to be capable of bone production.

Adolescent↗
PubMed2001

Nucleotide binding induces global and local structural changes of myosin head in muscle fibres.

Thermal stability and internal dynamics of myosin heads in fiber bundles from rabbit psoas muscle has been studied by electron paramagnetic resonance (EPR) spectroscopy and differential scanning calorimetry (DSC). Using ADP, ATP and orthovanadate (V(i)), three intermediate states of the ATP hydrolysis cycle were simulated in glycerinated muscle fibers. DSC transitions contained three overlapping endotherms in each state. Deconvolution showed that the transition temperature of 58.4 degrees C was almost independent of the intermediate state of myosin, while nucleotide binding shifted the melting temperatures of 54.0 and 62.3 degrees C, and changed the enthalpies. These changes suggest global rearrangements of the internal structure in myosin head. In the presence of ADP and ADP plus V(i), the conventional EPR spectra showed changes in the ordering of the probe molecules, suggesting local conformational and motional changes in the internal structure of myosin heads. Saturation transfer EPR measurements reported increased rotational mobility of spin labels in the presence of ATP plus orthovanadate corresponding to a weakly binding state of myosin to actin.

Adenosine Diphosphate↗
PubMed1981

Fine structural localization of adenosine triphosphatase activities in the saccus vasculosus of the rainbow trout, Salmo gairdneri Richardson.

The following characteristics of the adenosine triphosphatases (ATPase) in the saccus vasculosus were studied in Salmo gairdneri Richardson: 1) distributional pattern, 2) cytochemical properties in relation to different substrates, inhibitors, pH and bivalent metal ions, and 3) ultrastructural localization. Ultracytochemical studies using modifications of the Washstein-Meisel technique showed that within the pH range 7.1-8.0 several Mg++ or Ca++-activated ATPase are localized on the intracellular surface of membranes and in the cytoplasm of ependymal coronet cells and tanycytes ("supporting cells", "Zwischenzellen", glial cells"). The high ATPase activity at the level of the specialized luminal plasma membranes of coronet cell globules and of tanycyte microvilli is discussed in relation to phenomena of active transport and a possible resulting transfer of low-molecular weight substances into and/or from the cerebrospinal fluid (CSF). The localization of ATPase on the specialized membranes of primary vesicles is considered in connection with available structural and enzyme-cytochemical data on a possible function of these cell organelles in storage and release of substances (including Ca++ ions?). The cytoplasmic ATPase activity in coronet cells is ascribed to microtubules and/or possible existing contractile proteins/filaments, presumably concerned with internal transport or motility processes. In tanycytes ATPase activity is believed to be associated with the characteristic microfilamentous system of still unknown function. The ATPase activity in the (9 + 0) ciliary apparatus of globules could not be interpreted in terms of motility. The present study provides further support to the proposed hypothesis of the transport function of the saccus vasculosus, and an extension of the concept in the sense that not only the principal coronet cells, but also the tanycytes of this circumventricular organ are involved in CSF-homeostasis.

Adenosine Triphosphatases↗
PubMed1984

Local structural changes in tropomyosin detected by a trypsin-probe method.

Structural changes in tropomyosin from rabbit skeletal muscle were studied by the tryptic digestion method, which is an application of the quantitative enzyme-probe method recently developed by Ueno and Harrington [Ueno, H., & Harrington, W.F. (1984) J. Mol. Biol. 173, 35-61]. Effects of ionic strength, temperature, and an interchain disulfide bond at Cys-190 on the structure of tropomyosin were examined. A region of high susceptibility to trypsin was found to be localized in the middle portion of the molecule, and its susceptibility increased on lowering ionic strength and/or raising temperature. With the introduction of a disulfide bond at Cys-190, cleavage on the N-terminal side of Cys-190 was accelerated. The results suggest that skeletal muscle tropomyosin is flexible in the middle of the molecule in contrast to the flanking N- and C-terminal trypsin-resistant segments.

Animals↗
PubMed2004

Combining evolutionary and structural information for local protein structure prediction.

We study the effects of various factors in representing and combining evolutionary and structural information for local protein structural prediction based on fragment selection. We prepare databases of fragments from a set of non-redundant protein domains. For each fragment, evolutionary information is derived from homologous sequences and represented as estimated effective counts and frequencies of amino acids (evolutionary frequencies) at each position. Position-specific amino acid preferences called structural frequencies are derived from statistical analysis of discrete local structural environments in database structures. Our method for local structure prediction is based on ranking and selecting database fragments that are most similar to a target fragment. Using secondary structure type as a local structural property, we test our method in a number of settings. The major findings are: (1) the COMPASS-type scoring function for fragment similarity comparison gives better prediction accuracy than three other tested scoring functions for profile-profile comparison. We show that the COMPASS-type scoring function can be derived both in the probabilistic framework and in the framework of statistical potentials. (2) Using the evolutionary frequencies of database fragments gives better prediction accuracy than using structural frequencies. (3) Finer definition of local environments, such as including more side-chain solvent accessibility classes and considering the backbone conformations of neighboring residues, gives increasingly better prediction accuracy using structural frequencies. (4) Combining evolutionary and structural frequencies of database fragments, either in a linear fashion or using a pseudocount mixture formula, results in improvement of prediction accuracy. Combination at the log-odds score level is not as effective as combination at the frequency level. This suggests that there might be better ways of combining sequence and structural information than the commonly used linear combination of log-odds scores. Our method of fragment selection and frequency combination gives reasonable results of secondary structure prediction tested on 56 CASP5 targets (average SOV score 0.77), suggesting that it is a valid method for local protein structure prediction. Mixture of predicted structural frequencies and evolutionary frequencies improve the quality of local profile-to-profile alignment by COMPASS.

Algorithms↗
PubMedDate not supplied

[Local structure of cytochrome c from horse heart in solution. Conformational analysis using data of two-dimensional nuclear Overhauser effect spectroscopy].

Using the earlier suggested method the calculation of the backbone conformations of horse heart cytochrome c in oxidized (ferricytochrome c) and reduced (ferrocytochrome c) states has been performed by the two-dimensional nuclear Overhauser effect spectroscopy data. For both protein forms the secondary structure elements have been revealed and the conformations of the irregular polypeptide chain segments have been analysed. The similarity of the secondary structures of ferri- and ferrocytochrome c in solution was established from the comparison of their conformations. Small differences between the conformations of two molecule forms are shown to be localized within the polypeptide chain fragments situated in the spatial structure near the heme crevice. The comparison of the dihedral phi and psi angles in the calculated conformations of horse cytochrome C with the corresponding characteristics of X-ray structures of tuna ferri- and ferrocytochrome c made for the oxidized and reduced protein forms using the quantitative criteria testifies the similarity of their conformations in solution and crystal. In is shown that the conformational changes of the separate amino acid residues which take place as the result of the "solution-to-crystal" transition occur on the surface fragments of protein globule and do not lead to essential alterations of the secondary molecule structure.

Amino Acids↗
PubMed1986

Human osteogenic sarcoma: fine structural localization of adenosine triphosphatase.

The localization of ATPases in 7 osteogenic sarcomas of osteoblastic, chondroblastic and fibroblastic type was investigated at the fine structural level using two types of substrates: one with lead as capturing ion and one with strontium (the latter presumed to reveal sites of Na+-K+-dependent transport ATPase). Reaction product with the lead-ATP medium was located on the plasma membrane and the membranes bordering subjacent vesicles and vacuoles in all the various types of osteoblastlike and fibroblastlike cells and also in types 1 and 3 chondroblastlike cells, and multinucleated giant cells believed to be neoplastic. Furthermore, deposits of reaction product were demonstrated in lysosomelike organelles in all the aforementioned cells. Except in the case of chondroblastlike cells, precipitates marking the localization of enzyme were confined to areas of the plasma membrane where adjacent cells were closely applied (the free surface lacked precipitates). In chondroblastlike cells the reaction product was usually deposited along the whole plasma membrane. Presence of L-Homoarginine or L-Tetramisole in the incubation medium in concentrations that have been shown to completely abolish alkaline phosphatase activity did not affect the occurrence of the reaction product with ATP as substrate indicating that the enzyme hydrolysing ATP was substrate-specific. Reaction product marking sites of Na+-K+-dependent ATPase was confined to plasma membranes and lysosomes of cells in vessel walls. The observations strengthen the notion obtained in studies on the localization of alkaline phosphatase, namely that osteoblastlike, chondroblastlike, and fibroblastlike cells in osteogenic sarcomas are histogenetically related to one another and to those multinucleated giant cells that presumably are of a neoplastic nature.

Adenosine Triphosphatases↗
PubMed1999

Hot-spot mutants of p53 core domain evince characteristic local structural changes.

Most of the oncogenic mutations in the tumor suppressor p53 map to its DNA-binding (core) domain. It is thus a potential target in cancer therapy for rescue by drugs. To begin to understand how mutation inactivates p53 and hence to provide a structural basis for drug design, we have compared structures of wild-type and mutant p53 core domains in solution by NMR spectroscopy. Structural changes introduced by five hot-spot mutations (V143A, G245S, R248Q, R249S, and R273H) were monitored by chemical-shift changes. Only localized changes are observed for G245S, R248Q, R249S, and R273H, suggesting that the overall tertiary folds of these mutant proteins are similar to that of wild type. Structural changes in R273H are found mainly in the loop-sheet-helix motif and the loop L3 of the core domain. Mutations in L3 (G245S, R248Q, and R249S) introduce structural changes in the loop L2 and L3 as well as terminal residues of strands 4, 9, and 10. It is noteworthy that R248Q, which is often regarded as a contact mutant that affects only interactions with DNA, introduces structural changes as extensive as the other loop L3 mutations (G245S and R249S). These changes suggest that R248Q is also a structural mutant that perturbs the structure of loop L2-L3 regions of the p53 core domain. In contrast to other mutants, replacement of the core residue valine 143 to alanine causes chemical-shift changes in almost all residues in the beta-sandwich and the DNA-binding surface. Long-range effects of V143A mutation may affect the specificity of DNA binding.

Binding Sites↗
PubMed1985

Chromosomal localization, structure, and expression of the human alpha-fetoprotein gene.

By in situ hybridization of cloned human alpha-fetoprotein cDNA to human mitotic chromosome preparations, the alpha-fetoprotein gene was localized within the q11-22 region on the long arm of human chromosome 4. In addition, the human alpha-fetoprotein gene was isolated from a genomic phage library. The gene is split into 15 exons and 14 introns, and the entire structure is contained within two large (9.5 and 9.0) and two small (0.3 and 0.25 kb) EcoRI fragments of contiguous chromosomal DNA. The structure of alpha-fetoprotein and its gene is very similar to the corresponding structures of serum albumin, indicating a common evolutionary origin of these two serum proteins. However, the two genes are differentially expressed during normal development and under certain pathological conditions such as hepatomas, germ-cell tumors, or ataxia-telangiectasia. The molecular basis of this differential gene expression remains to be understood.

Chromosome Mapping↗
PubMed1978

Fine structural localization of alkaloid synthesis in endoplasmic reticulum of submerged Claviceps purpurea.

Acetyl coenzyme A (CoA) carboxylase (EC 6.4.1.2), an enzyme catalyzing the synthesis of malonyl-CoA, was cytochemically localized in endoplasmic reticulum (ER) of sclerotia-like cells of submerged Claviceps purpurea Tul. producing clavine alkaloids. The enzymic activity was structurally bound in unit membranes of ER strands which, later on, evolved into vacuoles containing lipoprotein material. The reaction product was absent from ER in nonvacuolized filamentous hyphae and ovoid asexual spores containing numerous lipid globules; it was also absent from ER in the mycelium of submerged C. purpurea strain producing no alkaloids. In view of our previous morphogenetic observations and the available biochemical evidence, the observed localization of acetyl-CoA carboxylase was assumed not to coincide with fatty acid biosynthesis but to represent sites of alkaloid synthesis.

Acetyl-CoA Carboxylase↗
PubMed2005

Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme.

pFGE is the paralog of the formylglycine-generating enzyme (FGE), which catalyzes the oxidation of a specific cysteine to Calpha-formylglycine, the catalytic residue in the active site of sulfatases. The enzymatic activity of sulfatases depends on this posttranslational modification, and the genetic defect of FGE causes multiple sulfatase deficiency. The structural and functional properties of pFGE were analyzed. The comparison with FGE demonstrates that both share a tissue-specific expression pattern and the localization in the lumen of the endoplasmic reticulum. Both are retained in the endoplasmic reticulum by a saturable mechanism. Limited proteolytic cleavage at similar sites indicates that both also share a similar three-dimensional structure. pFGE, however, is lacking the formylglycine-generating activity of FGE. Although overexpression of FGE stimulates the generation of catalytically active sulfatases, overexpression of pFGE has an inhibitory effect. In vitro pFGE interacts with sulfatase-derived peptides but not with FGE. The inhibitory effect of pFGE on the generation of active sulfatases may therefore be caused by a competition of pFGE and FGE for newly synthesized sulfatase polypeptides.

Alanine↗
PubMed1983

Structural localization of the proteins of the head to tail connecting region of bacteriophage phi 29.

The head to tail connector of bacteriophage phi 29 has been studied to locate its two structural proteins (p10 and p11). Treatment with trypsin led to proteolysis of p10 while p11 remained intact. Computer filtration of electron micrographs of crystals of trypsinized necks showed a change in the external 12-fold area of the neck when compared with control necks. Proteolized necks completely released p10 after treatment with low concentrations of an ionic detergent. The resulting structures, containing p11, showed similarity with the central area of the neck (seen in front view) and accounted for the lower collar and the axial extension of the neck (seen in side view). These results, together with the differences found in the proteolysis of p10 in necks with and without appendages, lead to a model for the neck region of phi 29 in which p10 makes the upper collar (and the external 12-fold area of the neck seen in front view), while p11 forms the lower collar and the axial extension (the inner region of the neck seen in front view).

Bacillus subtilis↗