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At least 1,009 records · Page 56Linked to original sources
PubMed2003

Glycation and post-translational processing of human interferon-gamma expressed in Escherichia coli.

Until recently, nonenzymatic glycosylation (glycation) was thought to affect the proteins of long living eukaryotes only. However, in a recent study (Mironova, R., Niwa, T., Hayashi, H., Dimitrova, R., and Ivanov, I. (2001) Mol. Microbiol. 39, 1061-1068), we have shown that glycation takes place in Escherichia coli as well. In the present study, we demonstrate that the post-translational processing (proteolysis and covalent dimerization) observed with cysteineless recombinant human interferon-gamma (rhIFN-gamma) is tightly associated with its in vivo glycation. Our results show that, at the time of isolation, rhIFN-gamma contained early (but not advanced) glycation products. Using reverse phase high performance liquid chromatography in conjunction with fluorescence measurements, enzyme-linked immunosorbent assay, and mass spectrometry, we found that advanced glycation end products arose in rhIFN-gamma during storage. The latter were identified mainly in the Arg/Lys-rich C terminus of the protein, which was also the main target of proteolysis. Mass spectral analysis and N-terminal sequencing revealed four major (Arg140/Arg141, Phe137/Arg138, Met135/Leu136, and Lys131/Arg132) and two minor (Lys109/Ala110 and Arg90/Asp91) cleavage sites in this region. Tryptic peptide mapping indicated that the covalent dimers of rhIFN-gamma originating during storage were formed mainly by lateral cross-linking of the monomer subunits. Antiviral assay showed that proteolysis lowered the antiviral activity of rhIFN-gamma, whereas covalent dimerization completely abolished it.

Amino Acid Sequence↗
PubMed1993

The mechanism of equilibrium binding of microtubule-associated protein 2 to microtubules. Binding is a multi-phasic process and exhibits positive cooperativity.

The mechanism of binding of microtubule-associated protein 2 (MAP2) to taxol-stabilized microtubules (MTs) was examined through Scatchard analysis of equilibrium binding and by immunoelectron microscopy. We demonstrate the following. 1) Binding is a cooperative process as indicated by sigmoidal binding curves, prominent humps in Scatchard plots, and an all-or-none response in binding during ligand titrations. At high tubulin/MAP2 ratios, the Kd for noncontiguous binding (5-25 microM) is estimated to be 100-1500 times greater than that predicted for contiguous binding, suggesting a high degree of cooperativity. 2) Cooperativity is indicated independently by a highly clustered or patchy distribution of MAP2 on MTs as revealed by immunoelectron microscopy. 3) The binding of truncated constructs of mouse MAP2 protein suggests that a domain of MAP2 conferring cooperativity is located in or near the MT binding site near the carboxyl terminus. We speculate that in the cell, cooperativity may generate MTs with uniform biochemical properties and contribute to the segregation of MAPs in neuronal cell processes.

Animals↗
PubMed2006

Mapping ground water vulnerability to pesticide leaching with a process-based metamodel of EuroPEARL.

To support EU policy, indicators of pesticide leaching at the European level are required. For this reason, a metamodel of the spatially distributed European pesticide leaching model EuroPEARL was developed. EuroPEARL considers transient flow and solute transport and assumes Freundlich adsorption, first-order degradation and passive plant uptake of pesticides. Physical parameters are depth dependent while (bio)-chemical parameters are depth, temperature, and moisture dependent. The metamodel is based on an analytical expression that describes the mass fraction of pesticide leached. The metamodel ignores vertical parameter variations and assumes steady flow. The calibration dataset was generated with EuroPEARL and consisted of approximately 60,000 simulations done for 56 pesticides with different half-lives and partitioning coefficients. The target variable was the 80th percentile of the annual average leaching concentration at 1-m depth from a time series of 20 yr. The metamodel explains over 90% of the variation of the original model with only four independent spatial attributes. These parameters are available in European soil and climate databases, so that the calibrated metamodel could be applied to generate maps of the predicted leaching concentration in the European Union. Maps generated with the metamodel showed a good similarity with the maps obtained with EuroPEARL, which was confirmed by means of quantitative performance indicators.

Adsorption↗
PubMed1999

Learning process by goldfish and its use of a local site as a map.

The issue we address is whether an animal knows or understands the significance of learning. We constructed an animal's own conceptualization via resolving a paradox underlying the process of learning. We found a kind of self-similar pattern in the behavior of goldfish resolving a paradoxical experimental problem. The pattern can be considered as a solution to the paradox in the experiment. An animal's own learning should be revised through solving paradoxes. The dualism of mechanistic thinking and vitalism can thus be avoided.

Animals↗
PubMed1985

Microtubule-associated protein 1B: identification of a major component of the neuronal cytoskeleton.

The major nontubulin proteins in purified brain microtubules are high molecular weight species traditionally classified into two groups known as microtubule-associated proteins 1 and 2 (MAP 1 and MAP 2). In an earlier study, we found that MAP 1 consisted of a complex of polypeptides and we characterized the highest molecular weight species--MAP 1A--with the use of a monoclonal antibody. In the current report, we describe four monoclonal antibodies raised against electrophoretically purified MAP 1B. All of the antibodies reacted exclusively with this protein. Together with peptide mapping, these results indicated that MAP 1B was structurally distinct from the other MAPs. Another distinctive property of MAP 1B was that most of it remained soluble during microtubule polymerization, resulting in an extreme underestimate of its abundance in the brain. Immunofluorescence microscopy of rat brain sections and cultured rat brain cells indicated that compared to MAP 1A and MAP 2, MAP 1B was particularly prominent in axonal as well as dendritic processes. Together, these data indicate that MAP 1B is a major, previously undescribed component of the neuronal cytoskeleton.

Animals↗
PubMed2005

Development of a kinetic analysis technique for PACS management and a screening examination in dynamic radiography.

The purpose of this study was to develop a method of kinetic analysis for picture archiving and communication system (PACS) management and computer-aided diagnostic application in dynamic chest radiography. The main analytical technique used in this study was a new algorithm that converts dynamic radiographs into a color-static image. The algorithm is a visualization technique for kinetic information that uses the intensity-density transformation and the direction classification in optical flow. The image made by the new algorithm was defined as a "kinetic map," and, by analysis using the kinetic map, a patient collation system and nodule detection system were constructed. By analysis that used an artificial neural network of certain feature vectors as kinetic map similarity, the collation system obtained good identification performance. Temporal subtraction processing between a current-status map with simulated nodule and previous-status map detected the region of abnormality as the simulated nodule. It is expected that our method of analysis will be useful as a screening examination for risk management and computer-aided diagnostic application in dynamic chest radiography.

Adult↗
PubMed2003

Optimization of protease-inhibitor interactions by randomizing adventitious contacts.

Polypeptide protease inhibitors are often found to inhibit targets with which they did not coevolve, as in the case of high-affinity inhibition of bacterial subtilisin by the leech inhibitor eglin c. Two kinds of contacts exist in such complexes: (i) reactive site loop-active site contacts and (ii) interactions outside of these that form the broader enzyme-inhibitor interface. We hypothesized that the second class of "adventitious" contacts could be optimized to generate significant increases in affinity for a target enzyme or discrimination of an inhibitor for closely related target proteases. We began with a modified eglin c, Arg-42-Arg-45-eglin, in which the reactive site loop had been optimized for subtilisin-related processing proteases of the Kex2/furin family. We randomized 10 potential adventitious contact residues and screened for inhibition of soluble human furin. Substitutions at one of these sites, Y49, were also screened against yeast Kex2 and human PC7. These screens identified not only variants that exhibited increased affinity (up to 20-fold), but also species that exhibited enhanced selectivity, that is, increased discrimination between the target enzymes (up to 41-fold for furin versus PC7 and 20-fold for PC7 versus furin). One variant, Asp-49-Arg-42-Arg-45-eglin, exhibited a Ki of 310 pM for furin and blocked furin-dependent processing of von Willebrand factor in COS-1 cells when added to the culture medium of the cells. The exploitation of adventitious contact sites may provide a versatile technique for developing potent, selective inhibitors for newly discovered proteases and could in principle be applied to optimize numerous protein-protein interactions.

Amino Acid Substitution↗
PubMed2005

Multilevel regulation of protein-protein interactions in biological circuitry.

Protein-protein interactions are central to biology and, in this 'post-genomic era', prediction of these interactions has become the goal of many computational efforts. Close inspection of even relatively simple biological regulatory circuitry reveals multiple levels of control of the contributing protein interactions. The fundamental probability that an interaction will occur under a given set of conditions is difficult to predict because the relationship between structure and energy is not known. Layered on this basic difficulty are allosteric control mechanisms involving post-translational modification or small ligand binding. In addition, many biological processes involve multiple protein-protein interactions, some of which may be cooperative or even competitive. Finally, although the emphasis in predicting protein interactions is based on equilibrium thermodynamic principles, kinetics can be a major controlling feature in these systems. This complexity reinforces the necessity of performing detailed quantitative studies of the component interactions of complex biological regulatory systems. Results of such studies will help us to bridge the gap between our knowledge of structure and our understanding of functional biology.

Allosteric Site↗
PubMed2006

Prions: protein only or something more? Overview of potential prion cofactors.

Transmissible spongiform encephalopathies (TSEs) in humans and animals are attributed to protein-only infectious agents, called prions. Prions have been proposed to arise from the conformational conversion of the cellular protein PrP(C) into a misfolded form (e.g., PrP(Sc) for scrapie), which precipitates into aggregates and fibrils. It has been proposed that the conversion process is triggered by the interaction of the infectious form (PrP(Sc)) with the cellular form (PrP(C)) or might result from a mutation in the gene for PrP(C). However, until recently, all efforts to reproduce this process in vitro had failed, suggesting that host factors are necessary for prion replication. In this review we discuss recent findings such as the cellular factors that might be involved in the conformational conversion of prion proteins and the potential mechanisms by which they could operate.

Animals↗
PubMed2004

Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles.

Gene expression profiles from the anterior cingulate cortex (ACC) of human, chimpanzee, gorilla, and macaque samples provide clues about genetic regulatory changes in human and other catarrhine primate brains. The ACC, a cerebral neocortical region, has human-specific histological features. Physiologically, an individual's ACC displays increased activity during that individual's performance of cognitive tasks. Of approximately 45,000 probe sets on microarray chips representing transcripts of all or most human genes, approximately 16,000 were commonly detected in human ACC samples and comparable numbers, 14,000-15,000, in gorilla and chimpanzee ACC samples. Phylogenetic results obtained from gene expression profiles contradict the traditional expectation that the non-human African apes (i.e., chimpanzee and gorilla) should be more like each other than either should be like humans. Instead, the chimpanzee ACC profiles are more like the human than like the gorilla; these profiles demonstrate that chimpanzees are the sister group of humans. Moreover, for those unambiguous expression changes mapping to important biological processes and molecular functions that statistically are significantly represented in the data, the chimpanzee clade shows at least as much apparent regulatory evolution as does the human clade. Among important changes in the ancestry of both humans and chimpanzees, but to a greater extent in humans, are the up-regulated expression profiles of aerobic energy metabolism genes and neuronal function-related genes, suggesting that increased neuronal activity required increased supplies of energy.

Animals↗
PubMed2005

14-3-3 proteins: a number of functions for a numbered protein.

Many signal transduction events are orchestrated by specific interactions of proteins mediated through discrete phosphopeptide-binding motifs. Although several phosphospecific-binding domains are now known, 14-3-3s were the first proteins recognized to specifically bind a discrete phosphoserine or phosphothreonine motif. The 14-3-3 proteins are a family of ubiquitously expressed, exclusively eukaryotic proteins with an astonishingly large number of binding partners. Consequently, 14-3-3s modulate an enormous and diverse group of cellular processes. The effects of 14-3-3 proteins on their targets can be broadly defined using three categories: (i) conformational change; (ii) physical occlusion of sequence-specific or structural protein features; and (iii) scaffolding. This review will describe the current state of knowledge on 14-3-3 proteins, highlighting several important advances, and will attempt to provide a framework by which 14-3-3 functions can be understood.

14-3-3 Proteins↗
PubMed1990

Structural analysis of the receptors for granulocyte colony-stimulating factor on neutrophils.

We investigated granulocyte colony-stimulating factor (G-CSF) receptors on neutrophils from three patients with chronic myelogenous leukemia (CML) in the chronic phase, in comparison with four normal volunteers. Because we experienced some difficulties in radioiodinating intact recombinant human G-CSF, we developed a new derivative of human G-CSF termed YPY-G-CSF. It was easy to iodinate this protein using the lactoperoxidase method because of two additional tyrosine residues, and its radioactivity was higher than that previously reported. The biological activity of YPY-G-CSF as G-CSF was fully retained. Scatchard analysis demonstrated that CML neutrophils had a single class of binding sites (1400 +/- 685/cell) with a dissociation constant (Kd) of 245 +/- 66 pM. The number of sites and Kd value of CML neutrophils were not significantly different from those of normal neutrophils (p greater than 0.9). Cross-linking studies revealed two specifically labeled bands of [125I]YPY-G-CSF-receptor complexes with apparent molecular masses of 160 and 110 kd on both normal and CML neutrophils. This is the first report describing two receptor proteins on neutrophils. According to the analyses of the proteolytic process of these cross-linked complexes and proteolytic mapping, we assume that alternative splicing or processing from a single gene may generate two distinct receptor proteins that bind specifically to G-CSF but have different fates in intracellular metabolism.

Adult↗
PubMed1997

Distribution mapping of ciliary beat frequencies of respiratory epithelium cells using image processing.

Through their rapid periodic actions, the cilia of the human respiratory tract play an important role in clearing inhaled noxious particles. An automated method is developed, based on an image-processing technique, to measure and analyse objectively and quantitatively, ciliary beat frequency (CBF). Microscopic ciliary images are transformed into digitised grey images through an image grabber inside a PC, and signals are extracted from these, based on an image-subtraction algorithm, and are processed through power spectrum analysis using a fast Fourier transform (FFT). By means of the FFT power spectrum, maximum peak frequencies are detected as CBFs in each partitioned block for the entire digitised field. Using these CBFs, distribution maps are composed in various resolutions, showing visually the spatial distribution of CBFs through cells and in a single cell. To measure CBF variations quantitatively, phenylephrine hydrochloride is used, and the changes in CBF influenced by its concentration and duration are observed.

Cell Culture Techniques↗
PubMed1995

The nucleolar architecture of polymerase I transcription and processing.

The nucleolus, the site of transcription and processing of the major ribosomal genes, generally reveals three distinct ultrastructural components in conventional thin-section electron micrographs (fibrillar centres, dense fibrillar component and granular component). We show here that different parts of the transcription and transcript processing pathway can be mapped to the different nucleolar components in pea root cells. This study shows the full three-dimensional arrangement of the different domains by in situ hybridization and confocal microscopy, and their correspondence with the major ultrastructural components of the nucleolus is revealed by parallel serial section electron microscopy. The active rDNA is widely dispersed in discrete foci, the larger of which, at least, correspond to well-defined fibrillar centres. A probe to the external transcribed spacer (ETS) sequence of the pre-rRNA transcripts labels clearly demarcated regions surrounding the foci of rDNA, and which we show correspond to the dense fibrillar component. Finally, a probe to the entire 45S transcript shows a higher concentration in regions corresponding to the granular component, surrounding the dense fibrillar component labelled by the ETS probe. The changes in structure that occur with heat shock show that nucleolar organization is dynamic and dependent upon transcriptional activity. These results show that the various RNA processing events are spatially highly organized and suggest a vectorial or radial model of transcription and transcript processing, where nascent and newly completed transcripts occupy zones surrounding the genes, which are in turn surrounded by regions containing the older more mature transcripts.

Cell Nucleolus↗
PubMed2006

Viral modulators of cullin RING ubiquitin ligases: culling the host defense.

Cullin RING ubiquitin ligases (CRULs) are found in all eukaryotes and play an essential role in targeting proteins for ubiquitin-mediated destruction, thus regulating a plethora of cellular processes. Viruses manipulate CRULs by redirecting this destruction machinery to eliminate unwanted host cell proteins, thus allowing viruses to slip past host immune barriers. Depending on the host organism, virus-modified CRULs can perform an amazing range of tasks, including the elimination of crucial signal transduction molecules in the human interferon pathway and suppression of virus-induced gene silencing in plants. This Perspective summarizes recent advances in our understanding of how viral proteins manipulate the function of CRULs.

Animals↗
PubMed1997

Localization of antigenic sites on Der p 2 using oligonucleotide-directed mutagenesis targeted to predicted surface residues.

BACKGROUND: Understanding the molecular nature of allergen-antibody interactions is important to understanding the mechanism of conventional immunotherapy as well as to designing alternative immunotherapeutic strategies. Many important allergens have been cloned and expressed, making it possible to apply recombinant DNA techniques to dissect antigenic determinants. OBJECTIVE: The aim of this study was to use predictive algorithms and site-directed mutagenesis to investigate monoclonal antibody and IgE antibody epitopes of the major house dust mite allergen Der p 2. METHODS: Computer algorithms were used to assess the primary amino acid sequence of Der p 2 and to identify regions of hydrophilic and flexible sequence. Subsequently, site-directed mutagenesis was used to generate amino acid substitutions at hydrophilic residues at positions 44-46 and at position 100. The variants were tested in a competitive inhibition ELISA with four group 2-specific murine monoclonal antibodies and with human IgE antibody from mite allergic patients. RESULTS: Conservative amino acid substitutions at position 44-46 did not distinguish IgE antibody epitopes, but did suggest that these residues are involved in the epitope defined by one monoclonal antibody, 15E11. Non-conservative substitution of proline at this position reduced binding to all four monoclonal antibodies, as well as IgE antibody, by 50-80%. Point mutants at position 100 mapped the epitopes of two monoclonal antibodies, 7A1 and 13A4, previously shown to bind the same region of Der p 2. In addition, the two variants tested at this position showed distinct inhibition curves with these two monoclonal antibodies indicating differences in fine specificity. CONCLUSIONS: Using predictive algorithms, in the absence of tertiary structural information, we have been able to localize important B cell determinants on Der p 2. The results suggest that it is possible to modulate antibody recognition of allergens using site-directed mutagenesis and that this approach may provide a new strategy for allergen specific immunotherapy.

Antibodies, Monoclonal↗
PubMed1994

Glycosylation of two recombinant human uterine tissue plasminogen activator variants carrying an additional N-glycosylation site in the epidermal-growth-factor-like domain.

Recombinant human uterine tissue plasminogen activator (tPA) glycosylation mutants carrying an additional N-glycosylation site in the epidermal-growth-factor-like domain due to the replacement of either Tyr67 by Asn (YN-tPA) or Gly60 by Ser (GS-tPA) were expressed in mouse epithelial cells (C127) in the presence of [6-3H]glucosamine. Glycopeptides comprising individual glycosylation sites were isolated and oligosaccharides attached were liberated by treatment with endo-beta-N-acetylglucosaminidase H or peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F. Oligosaccharide alditols obtained after reduction were either directly characterized by high-pH anion-exchange chromatography (high-mannose and hybrid-type glycans) or preparatively subfractionated after enzymic desialylation and separation from sulphated asialooligosaccharides (complex-type sugar chains). Individual (sub)fractions of glucans were studied by methylation analysis, liquid secondary-ion mass spectrometry and, in part, by exoglycosidase digestion, whereas corresponding deglycosylated peptides were identified by amino acid analysis and N-terminal amino acid sequencing. The results revealed that Asn117 of YN-tPA carried exclusively high-mannose-type glycans with five to nine mannose residues similar to wild-type tPA expressed in this cell line [Pfeiffer, G., Schmidt, M., Strube, K.-H. & Geyer, R. (1989) Eur. J. Biochem. 186, 273-286]. In contrast, Asn117 of GS-tPA carried only small amounts (about 25%) of high-mannose and hybrid-type species and predominantly complex-type sugar chains (about 75%) which were partially incomplete and mostly devoid of fucose. Newly introduced N-glycosylation sites at Asn67 (YN-tPA) or Asn58 (GS-tPA) as well as those at Asn184 and Asn448 were solely substituted by complex-type glycans. Each carbohydrate attachment site displayed a peculiar oligosaccharide pattern with regard to branching and substitution by Gal alpha 3-residues, sulphate groups, intersecting GlcNAc and lactosamine repeats. Our study clearly demonstrates that creation of a new glycosylation site at Asn58 influenced the oligosaccharide processing and, hence, the glycosylation pattern at Asn117, whereas introduction of a new site at Asn67 did not. The relative amounts of complex-type glycans at Asn117 of GS-tPA correlated with the degree of carbohydrate substitution of Asn58. Therefore, it can be concluded that the presence of a sugar chain at the position and not the Gly to Ser mutation itself is responsible for the observed alteration of GS-tPA glycosylation.

Amino Acid Sequence↗
PubMed2003

Depicting the MM3 potential energy surfaces of trisaccharides by single contour maps: application to beta-cellotriose and alpha-maltotriose.

The adiabatic potential energy surfaces (PES) of two trisaccharides (beta-cellotriose and alpha-maltotriose) were obtained using the MM3 force field. Each PES can be described by a single 3D contour map for which the energy is plotted against the two psi glycosidic angles. Given the usually small variations of the phi glycosidic torsional angle in the low-energy regions of disaccharide maps (at least with MM3), it is valid to leave both phi glycosidic angles to relax in the process of building the conformational map of trisaccharides. The surfaces are those expected from the map of disaccharides containing the same linkages and monosaccharide units (i.e., beta-cellobiose and alpha-maltose), with second-order factors altering the 'symmetry' of both linkages. A large low-energy region appears for beta-cellotriose, comprising four minima in close proximity, with barriers between them below 0.6 kcal/mol. On the other hand, for alpha-maltotriose a main global minimum is observed, with several surrounding local minima. The surfaces obtained agree with single-crystal X-ray data on these trisaccharides and derivatives. A reduction of the linkage flexibilities is observed when passing from the disaccharides to the trisaccharides. Furthermore, the linkage closer to the reducing end appears to be less flexible than the linkage closer to the non-reducing end.

Carbohydrate Conformation↗