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PubMed1997

Tag games in yeast: the two-hybrid system and beyond.

The yeast Saccharomyces cerevisiae and the one- and two-hybrid systems are essential genetic tools for studying the macromolecular interactions that define all living organisms. Newly developed variations on this theme can now address an even bigger set of questions. Reverse one- and two-hybrid systems can identify factors that dissociate or abrogate defined macromolecular interactions. Different forms of three-hybrid systems can evaluate the complex interplay of proteins with RNAs, peptide ligands, small organic ligands or protein kinases. Finally, the ubiquitin-based split-protein sensor and the Sos recruitment systems promise to overcome some limitations of conventional two-hybrid systems.

Animals↗
PubMed2003

The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy.

The creation of structured shared data repositories for molecular data in the form of web-accessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the development of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.

Brain↗
PubMed2004

Automated sample mounting and alignment system for biological crystallography at a synchrotron source.

High-throughput data collection for macromolecular crystallography requires an automated sample mounting and alignment system for cryo-protected crystals that functions reliably when integrated into protein-crystallography beamlines at synchrotrons. Rapid mounting and dismounting of the samples increases the efficiency of the crystal screening and data collection processes, where many crystals can be tested for the quality of diffraction. The sample-mounting subsystem has random access to 112 samples, stored under liquid nitrogen. Results of extensive tests regarding the performance and reliability of the system are presented. To further increase throughput, we have also developed a sample transport/storage system based on "puck-shaped" cassettes, which can hold sixteen samples each. Seven cassettes fit into a standard dry shipping Dewar. The capabilities of a robotic crystal mounting and alignment system with instrumentation control software and a relational database allows for automated screening and data collection to be developed.

Chemistry Techniques, Analytical↗
PubMed1988

Macromolecular crowding extends the range of conditions under which DNA polymerase is functional.

The nick-translation reaction of E. coli DNA polymerase I (Pol I) was used as a model system to demonstrate the ability of macromolecular crowding to alter the response of an enzyme to a number of basic parameters, such as pH, temperature or inhibitors. In the presence of high concentrations of non-specific polymers, nick translation occurred under a variety of otherwise strongly inhibitory conditions. The conditions tested included a range of pH values or temperatures or inhibitory concentrations of urea, formamide or ethidium bromide. These crowding effects are accentuated at higher ionic strengths, suggesting their origin in increased binding between the polymerase and its DNA template-primer under crowded conditions. Kinetic measurements were consistent with such a mechanism.

DNA↗
PubMed2005

A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells.

Bacterial type IV secretion (T4S) systems mediate the transfer of macromolecular substrates into various target cells, e.g., the conjugative transfer of DNA into bacteria or the transfer of virulence proteins into eukaryotic host cells. The T4S apparatus VirB of the vascular tumor-inducing pathogen Bartonella henselae causes subversion of human endothelial cell (HEC) function. Here we report the identification of multiple protein substrates of VirB, which, upon translocation into HEC, mediate all known VirB-dependent cellular changes. These Bartonella-translocated effector proteins (Beps) A-G are encoded together with the VirB system and the T4S coupling protein VirD4 on a Bartonella-specific pathogenicity island. The Beps display a modular architecture, suggesting an evolution by extensive domain duplication and reshuffling. The C terminus of each Bep harbors at least one copy of the Bep-intracellular delivery domain and a short positively charged tail sequence. This biparte C terminus constitutes a transfer signal that is sufficient to mediate VirB/VirD4-dependent intracellular delivery of reporter protein fusions. The Bep-intracellular delivery domain is also present in conjugative relaxases of bacterial conjugation systems. We exemplarily show that the C terminus of such a conjugative relaxase mediates protein transfer through the Bartonella henselae VirB/VirD4 system into HEC. Conjugative relaxases may thus represent the evolutionary origin of the here defined T4S signal for protein transfer into human cells.

Amino Acid Sequence↗
PubMed2004

The yeast three-hybrid system as a tool to study caspases.

Caspases are cysteine proteases that play an essential role during apoptotic cell death and inflammation. They are synthesized as catalytically dormant proenzymes, containing an N-terminal prodomain, a large subunit (p20) containing the active site cysteine, and a small subunit (p10). The active enzymes function as tetramers, consisting of two p20/p10 subunit heterodimers. Both subunits contribute residues that are essential for substrate recognition. Activation of caspases culminates in the cleavage of a set of cellular proteins, resulting in disassembly of the cell or proinflammatory cytokine production. Inappropriate caspase activation contributes to or accounts for several diseases. The identification of caspase-interacting proteins that might act as activators, substrates, or inhibitors is therefore an attractive step in the development of novel therapeutics. However, caspase substrates and other proteins that bind specifically with the active heterodimeric p20/p10 form of caspases will escape detection in a classical two-hybrid approach with an unprocessed caspase precursor as bait. Alternatively, a number of so-called three-hybrid systems to analyze more complex macromolecular interactions have been developed. We describe the use of a three-hybrid approach adapted to the needs of caspases to detect and analyze the interaction of mature heteromeric caspases with protein substrates or inhibitors.

Animals↗
PubMed2003

Metal selectivity of Sargassum spp. and their alginates in relation to their alpha-L-guluronic acid content and conformation.

The discovery of a consistent and unusual enrichment in homopolymeric alpha-L-guluronic acid G-blocks in alginates extracted from a suite of Sargassum brown algae is described in this study. 1H NMR spectroscopy was used to characterize these alginates which display homopolymeric guluronic acid block (G-block) frequency values (F(GG)) between 0.37 and 0.81. The presence of these G-blocks results in an enhanced selectivity for cadmium or calcium relative to monovalent ions such as sodium and the proton as well as smaller divalent ions such as magnesium. Results of competitive exchange experiments for the Cd-Ca-alginate system yield selectivity coefficient, K*(Cd)Ca, values between 0.43 +/- 0.10 and 1.32 +/- 0.02 for a range in F(GG) of 0.23 to 0.81. In contrast to the Cd-Ca-alginate system, the Mg-Ca-alginate and Mg-Cd-alginate systems yielded maximum values of K*(Mg)Ca (18.0 +/- 1.4) and K*(Mg)Cd (16.0 +/- 0.9) for the alginates extracted from Sargassum fluitans (F(GG) = 0.81; Cuba) and Sargassum thunbergii (F(GG) = 0.75; Korea), respectively. Selectivity studies with mixed-metal pair alginate systems highlight the importance of the specific macromolecular conformation of the alginate polymer in determining metal binding behavior in multiple-metal systems. Furthermore, they demonstrate the importance of the conformation of the alginate as it occurs within the tissue of Sargassum in determining the metal binding behavior of this algal biosorbent. The unique composition of the alginates present in species of Sargassum may represent a distinct advantage over other brown algal species when considering their implementation for the strategic removal of toxic heavy metals from contaminated and industrial wastewaters.

Alginates↗
PubMed2004

Absorption enhancers in pulmonary protein delivery.

Extensive research efforts have been directed towards the systemic administration of therapeutic proteins and poorly absorbed macromolecules via various nontraditional, injection-free administration sites such as the lung. As a portal for noninvasive delivery, pulmonary administration possesses several attractive features including a large surface area for drug absorption. Nevertheless, achieving substantial bioavailability of proteins and macromolecules by this route has remained a challenge, chiefly due to poor absorption across the epithelium. The lungs are relatively impermeable to most drugs when formulated without an absorption enhancer/promoter. In an attempt to circumvent this problem, many novel absorption promoters have been tested for enhancing the systemic availability of drugs from the lungs. Various protease inhibitors, surfactants, lipids, polymers and agents from other classes have been tested for their efficacy in improving the systemic availability of protein and macromolecular drugs after pulmonary administration. The purpose of this article is to provide the reader with a summary of recent advances made in the field of pulmonary protein delivery utilizing absorption enhancers. This report reviews the various agents used to increase the bioavailability of these drugs from the lungs, their mechanisms of action and effectiveness, and their potential for toxicity.

Absorption↗
PubMed1986

Differential macromolecular leakage from the vasculature of tumors.

Tumor-induced neovascularization is essential for invasion, metastases, and exponential growth of solid tumors. The authors studied the differences in macromolecular leakage from the neovasculature of a fast-growing, early-metastasizing tumor, the Walker 256 carcinosarcoma, and a slow-growing, nonmetastasizing tumor, a rat chondrosarcoma. A 1-mm3 piece of the Walker 256 carcinoma or the chondrosarcoma was implanted in the cremaster muscle of rats. Five days after surgery the cremaster muscle with the implanted tumor was placed in a special bath containing Krebs solution such that the circulation and nerves from the animal to the cremaster were intact. Fluorescein isothiocyanate-labeled rat serum albumin (FITC-RSA) was injected (intra-arterially) into each rat to permit visualization of the vasculature by fluorescent microscopy. A closed-circuit television system was used to quantitate macromolecular leakage as a change in interstitial fluorescent intensity. Data are given as a relative fluorescent intensity (mean +/- standard error of the mean) in an area of the cremaster with tumor-induced neovascularization. These studies demonstrated that the vasculature induced by rapidly growing Walker 256 carcinosarcoma leak albumin freely when compared with the vasculature induced by the slow-growing chondrosarcoma. Furthermore, there was a significant increase in fluorescent intensity (albumin leakage) in the Walker tumor from 1 minute (24 +/- 3.0) to 30 minutes (49 +/- 5.6). In the normal cremaster area there was a significantly lower fluorescent intensity in the interstitium and a very slight increase with time (4 +/- 1.5 at 1 minute vs. 7 +/- 1.4 at 30 minutes). One interpretation of these data is that the mechanisms responsible for protein leakage from the vasculature of the Walker tumor may be involved in the fast growth and metastases of this tumor as compared with slower-growing tumors such as the chondrosarcoma.

Animals↗
PubMedDate not supplied

[The molecular factors of the cell adhesion of neural tissues and the Ca2+-independent adhesion system].

The review discusses various technical approaches to identification of plasma membrane and extracellular matrix proteins involved in cell adhesion. Physicochemical characteristics of macromolecular factors of the Ca2(+)-independent adhesion system in neural tissue cells are discussed alongside with the findings on their biosynthesis and expression on the cell surface at different stages of embryogenesis.

Animals↗
PubMed1994

Characterization of the Su antigen, a macromolecular complex of 100/102 and 200-kDa proteins recognized by autoantibodies in systemic rheumatic diseases.

The Su autoantigen was characterized biochemically using human and murine autoimmune sera and the clinical significance of anti-Su antibodies was studied in 236 Japanese and 160 American patients with systemic rheumatic diseases. Anti-Su in immunodiffusion (ID) was strongly associated with immunoprecipitation of one or more 100- to 102-kDa proteins by MRL/lpr mouse sera (27/32 of ID positive vs 4/20 of ID negative, P = 0.000016), and all four human anti-Su reference sera immunoprecipitated the 100/102-kDa protein(s). In addition, all sera immunoprecipitated a less efficiently labeled approximately 200-kDa protein that comigrated on sucrose density gradients with the 100/102-kDa proteins. Based on these data, a complex of the 100/102-kDa and 200-kDa proteins is likely to be the main target of anti-Su antibodies. Three of four anti-Su monospecific sera were negative for immunofluorescent antinuclear antibodies (ANA), suggesting anti-Su antibodies may be associated with a negative ANA in some cases. Autoantibodies to Su were detected frequently by immunoprecipitation in systemic lupus erythematosus (17-21%), scleroderma (13-20%), and overlap syndrome (22-40%) and were associated with autoantibodies to Ku.

Animals↗
PubMed2001

Modeling magnetization transfer using a three-pool model and physically meaningful constraints on the fitting parameters.

A model for water-macromolecular magnetization transfer is presented which addresses the mechanism of coupling between the hydrogen populations and the extraction of physically meaningful parameters from experimental magnetization transfer data. Both physical exchange between bulk-solvent and site-specific hydration-layer hydrogens and intermolecular magnetic dipolar coupling between these specific hydration-layer-solvent and macromolecular hydrogens are explicitly included, leading to a three-pool model for magnetization transfer. It is shown that the three-pool model is well approximated by a two-pool model for coupling between the bulk-solvent and macromolecular hydrogens when the dipolar-coupled solvent hydrogens are a small fraction of the total solvent, and the solvent-macromolecular coupling constant includes both dipolar magnetic, kappa(dip), and physical exchange, kappa(ex), coupling rates. The model is also extended to multiple solvent systems. The model results in a set of coupled equations that predict magnetization transfer spectra as a function of temperature and composition. Physically meaningful constraints on the coupling and relaxation parameters are established for systems in which magnetization transfer has been observed including solvated cross-linked proteins and lipid bilayers. Using parameter estimates based on these constraints, empirical magnetization transfer spectra are well predicted by the model. It is found that the degree of magnetization transfer becomes independent of kappa(dip) and kappa(ex) when these parameters become greater than about 50 s(-1). In the semi-rigid cross-linked protein systems where the mobility of the macromolecular matrix is insensitive to temperature, the magnitude of the observed magnetization transfer is consistent with being limited by the intermolecular dipolar coupling and spin-lattice relaxation in the bulk-solvent phase.

Journal Article↗
PubMed1988

Macromolecular changes accompanying immortalization and tumorigenic conversion in a human fibroblast model system.

Mutagenesis of a diploid human fibroblast strain, KD, with the chemical carcinogen 4 nitroquinolin-1-oxide led to the isolation of stably immortalized neoplastic substrains. Four of these transformed strains, HuT-11, -12, -13, and -14, have been characterized in great detail with regard to morphology and changes in gene expression from the parental KD strain. The HuT-11, -12 and -13 substrains are immortalized and non-tumorigenic, in contrast to HuT-14 which is both immortalized and tumorigenic. The HuT-14 substrain expresses a defective beta-actin as a consequence of a point mutation in 1 of the 2 functional beta-actin alleles. All 4 HuT strains have induced expression of the phosphoprotein plastin and 2 EGF-related polypeptides, and down-regulated expression of the transformation-sensitive tropomyosin isoforms. KD and HuT cells expressing high levels of exogenous mutant beta-actin after gene transfection show morphological alterations. HuT-12 transfectants with excessive mutant beta-actin expression exhibit an elevated tumorigenic potential and tropomyosin-isoform switching characteristic of the tumorigenic HuT-14 strain.

Actins↗
PubMed2001

Caveolar and intercellular channels provide major transport pathways of macromolecules across vascular endothelial cells.

Serum macromolecules are transported through the vascular endothelial layer to the interstitium via the caveolae and interendothelial clefts, but the nature of the permeability of these structures is unknown, and the manner of caveola-vesicle transport is controversial. We have developed a method of detecting macromolecular channels using an in situ HRP perfusion into arteries previously perfused with aldehyde and random conventional sectioning for electron microscopy. Using unbiased morphometry, 4.75% of the abluminal caveolae and 15.13% of the intercellular clefts were the tracer-positive in rat aortic endothelium. In rat aortas treated with N-ethylmaleimide, all caveolae and most free vesicles in the cytoplasm except those around the Golgi area were HRP-positive in the endothelial cells; 1.48% of abluminal caveolae were structurally recognized as caveolar channels through the endothelial layer in a plane of single section. The length density of the abluminal caveolae was decreased to about 80% to the physiological control level whereas the larger invaginations were more frequently observed. Moreover 96.17% of the intercellular clefts were HRP-positive. We suggest that a flexible channel-system functions extensively as a macromolecular transport pathway in the arterial endothelium in vivo because the tracer-labeled abluminal caveolae and intercellular clefts should be opened to the luminal surfaces methodologically. We therefore propose that caveolar channels, rather than transcytosis, provide a mechanism of caveola-vesicle transport in the endothelial cells, because free vesicles involved in transcytosis were few in number.

Animals↗