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At least 1,369 records · Page 76Linked to original sources
PubMed2003

RVP-net: online prediction of real valued accessible surface area of proteins from single sequences.

SUMMARY: RVP-net is an online program for the prediction of real valued solvent accessibility. All previous methods of accessible surface area (ASA) predictions classify amino acid residues into exposure states and named them buried or exposed based on different thresholds. Real values in some cases were generated by taking the mid points of these state thresholds. This is the first method, which provides a direct prediction of ASA without making exposure categories and achieves results better than 19% mean absolute error. To facilitate batch processing of several sequences, a standalone version of this tool is also provided. AVAILABILITY: Online predictions are available at http://www.netasa.org/rvp-net/. Standalone version of the program can be obtained from the corresponding author by E-mail request.

Algorithms↗
PubMed1984

Predominant synthesis of fibroin heavy and light chains on the membrane-bound polysomes prepared from the posterior silk gland of the silkworm, Bombyx mori.

Membrane-bound polysomes were prepared from the posterior silk gland of the silkworm, Bombyx mori, on the fourth to fifth day in the fifth larval instar. The polysomes, when supplemented with a soluble fraction from the posterior silk gland, exhibited the elongation reaction of the growing polypeptide-chains, but the initiation reaction of polypeptide synthesis was not demonstrated in this system. The predominant products synthesized on the membrane-bound polysomes were fibroin heavy chain (H-chain) and light chain (L-chain), while polypeptides of heterogeneous size classes were synthesized on the 105,000 X g-sedimentable polysomes. A substantial fraction of the fibroin L-chain synthesized was bound to the H-chain by disulfide bond. Most of the newly synthesized fibroin H- and L-chains on the membrane-bound polysomes were proved to be present within microsomal membrane vesicles because of their insensitivity to digestion with proteases in the absence of Triton X-100.

Animals↗
PubMed1990

Reconstitution of photophosphorylation in EDTA-treated thylakoids by added chloroplast coupling factor 1 (ATPase) and chloroplast coupling factor 1 lacking the delta subunit. Structural or functional?

Upon EDTA treatment thylakoids lose the chloroplast coupling factor 1 (CF1) part of their ATP synthase, CF0CF1, this exposes the proton channel, CF0. The previously established ability of the CF1 subunit delta to block the proton leak through CF0 prompted us to study (a) the ability of complete CF1 and, for comparison, CF1 lacking the delta subunit to block proton leakage and thereby to reconstitute structurally some photophosphorylation activity of the remaining CF0CF1 molecules and (b) their ability to form functional enzymes (functional reconstitution). In order to discriminate between activities caused by added CF1 or CF1(-delta) and remaining CF0CF1, the former were inhibited by chemical modification of subunit beta by N,N'-dicyclohexyl carbodiimide (DCCD) and the latter by tentoxin. We found that added CF1 acted both structurally and functionally while added DCCD-treated CF1 (DCCD-CF1) acted only structurally. In contrast to previous observations, CF1(-delta) and DCCD-CF1(-delta) also acted structurally although the reduction of proton leakage was smaller than with DCCD-CF1. Hence there was no functional reconstitution without subunit delta present. Previous studies indicated that only a small fraction of exposed CF0 is highly conducting and that this small fraction is distinguished by its high affinity for added CF1. The results of this study point rather to a wider distribution of CF0 conductance states and binding affinities.

Cell-Free System↗
PubMed1980

Activity of 2-acetylpyridine thiosemicarbazones against Trypanosoma rhodesiense in vitro.

Twenty-seven 2-acetylpyridine thiosemicarbazones and analogs were tested for antitrypanosomal activity against Trypanosoma rhodesiense using a semiautomated in vitro assay system. Activity was determined by relative inhibition of uptake of two radiolabeled macromolecular precursors, [methyl-3H]thymidine and L-[U-14C]leucine, as compared to untreated controls. It was observed that the nitrogen atom of the pyridyl moiety of the 2-acetylpyridine thiosemicarbazones was essential for antitrypanosomal activity. The 2-acetylpyridine thiosemicarbazones generally inhibited the uptake of L-[U-14C]leucine to a greater extent than they inhibited [methyl-3H]thymidine uptake. Twenty-four of the 27 compounds tested exhibited activity comparable to that found for the antitrypanosomal agent ethidium bromide.

Animals↗
PubMed1993

Mammalian U6 small nuclear RNA undergoes 3' end modifications within the spliceosome.

Mammalian U6 small nuclear RNA (snRNA) is heterogeneous with respect to the number of 3' terminal U residues. The major form terminates with five U residues and a 2',3' cyclic phosphate. Because of the presence in HeLa cell nuclear extracts of a terminal uridylyl transferase, a minor form of U6 snRNA is elongated, producing multiple species containing up to 12 U residues. In this study we have used glycerol gradients to demonstrate that these U6 snRNA forms are assembled into U6 ribonucleoprotein (RNP), U4/U6 snRNPs, and U4/U5/U6 tri-snRNP complexes. Furthermore, glycerol gradients combined with affinity selection of biotinylated pre-mRNAs led us to show that elongated forms of U6 snRNAs enter the spliceosome and that some of these become shortened with time to a single species having the same characteristics as the major form of U6 snRNA present in mammalian nuclear extracts. We propose that this elongation-shortening process is related to the function of U6 snRNA in mammalian pre-mRNA splicing.

Base Composition↗
PubMed1978

SOluble and insoluble immune complex-platelet interactions in rheumatoid inflammation.

The interactions of soluble and insoluble immunoglobulin G (IgG) complexes with macromolecular rheumatoid factor (RF) and platelets were examined in an in vitro system permitting observation of platelet activities which may contribute to rheumatoid inflammation. Studies of the aggregation phenomenon by the nephalometric technique and by selective sedimentation of 51Cr-labelled platelets revealed no aggregation by platelets exposed to heat aggregated IgG (HAIgG) complexes or their RF precipitates in a plasma test system. Release of serotonin was demonstrated by the increasing radioactivity of platelet supernates to 45 min by 14C-serotonin labelled platelets exposed to insoluble IgG heat aggregates. Significantly less release was shown with saline, native IgG, and soluble IgG complexes. When RF was added to soluble HAIgG complexes, the resulting precipitate caused significantly higher release than controls. No concomitant release of the lysosomal enzyme beta-glucuronidase was detected. Thus, although soluble complexes do not cause significant release of biologically active amines, conversion of soluble complexes to insoluble immune precipitates by RF is associated with this activity which is independent of platelet aggregation and/or lyosomal enzyme release in our test system. Release of biologically active amines from platelets exposed to insoluble complexes may be important in the initiation and propagation of inflammation in rheumatoid arthritis.

Antigen-Antibody Complex↗
PubMed2005

Exploiting chinks in the plant's armor: evolution and emergence of geminiviruses.

The majority of plant-infecting viruses utilize an RNA genome, suggesting that plants have imposed strict constraints on the evolution of DNA viruses. The geminiviruses represent a family of DNA viruses that has circumvented these impediments to emerge as one of the most successful viral pathogens, causing severe economic losses to agricultural production worldwide. The genetic diversity reflected in present-day geminiviruses provides important insights into the evolution and biology of these pathogens. To maximize replication of their DNA genome, these viruses acquired and evolved mechanisms to manipulate the plant cell cycle machinery for DNA replication, and to optimize the number of cells available for infection. In addition, several strategies for cell-to-cell and long-distance movement of the infectious viral DNA were evolved and refined to be compatible with the constraints imposed by the host endogenous macromolecular trafficking machinery. Mechanisms also evolved to circumvent the host antiviral defense systems. Effectively combatting diseases caused by geminiviruses represents a major challenge and opportunity for biotechnology.

Biological Evolution↗
PubMed2002

Enhancement of VDR-mediated transcription by phosphorylation: correlation with increased interaction between the VDR and DRIP205, a subunit of the VDR-interacting protein coactivator complex.

When UMR-106 osteoblastic cells, LLCPK1 kidney cells, and VDR transfected COS-7 cells were transfected with the rat 24-hydroxylase [24(OH)ase] promoter (-1,367/+74) or the mouse osteopontin (OPN) promoter (-777/+79), we found that the response to 1,25dihydroxyvitamin D(3) [1,25-(OH)(2)D(3)] could be significantly enhanced 2- to 5-fold by the protein phosphatase inhibitor, okadaic acid (OA). Enhancement of 1,25-(OH)(2)D(3)-induced transcription by OA was also observed using a synthetic reporter gene containing either the proximal 24(OH)ase vitamin D response element (VDRE) or the OPN VDRE, suggesting that the VDRE is sufficient to mediate this effect. OA also enhanced the 1,25-(OH)(2)D(3)-induced levels of 24(OH)ase and OPN mRNA in UMR osteoblastic cells. The effect of OA was not due to an up-regulation of VDR or to an increase in VDR-RXR interaction with the VDRE. To determine whether phosphorylation regulates VDR-mediated transcription by modulating interactions with protein partners, we examined the effect of phosphorylation on the protein-protein interaction between VDR and DRIP205, a subunit of the vitamin D receptor-interacting protein (DRIP) coactivator complex, using glutathione-S-transferase pull-down assays. Similar to the functional studies, OA treatment was consistently found to enhance the interaction of VDR with DRIP205 3- to 4-fold above the interaction observed in the presence of 1,25-(OH)(2)D(3) alone. In addition, studies were done with the activation function-2 defective VDR mutant, L417S, which is unable to stimulate transcription in response to 1,25-(OH)(2)D(3) or to interact with DRIP205. However, in the presence of OA, the mutant VDR was able to activate 24(OH)ase and OPN transcription and to recruit DRIP205, suggesting that OA treatment may result in a conformational change in the activation function-2 defective mutant that creates an active interaction surface with DRIP205. Taken together, these findings suggest that increased interaction between VDR and coactivators such as DRIP205 may be a major mechanism that couples extracellular signals to vitamin D action.

Animals↗
PubMed2000

Effect of angiotensin-converting enzyme inhibition on glomerular basement membrane permeability and distribution of zonula occludens-1 in MWF rats.

The mechanism(s) by which angiotensin-converting enzyme (ACE) inhibitors prevent glomerular membrane loss of permselective function is still not understood. In male MWF rats, which develop spontaneous proteinuria with age, ACE inhibitors prevent proteinuria and increase glomerular ultrafiltration coefficient. These renoprotective effects are not associated with ultrastructural changes of capillary wall components. This study was undertaken to investigate whether ACE inhibitors modulate functional properties of glomerular basement membrane (GBM) and/or of epithelial cells, both of which have been suggested to play a role in the maintenance of the glomerular filtration barrier. The hydraulic and macromolecular permeability of the GBM were determined, by an in vitro filtration system, in untreated or lisinopril-treated rats and in Wistar rats taken as controls. By indirect immunofluorescence and immunoelectron microscopy, glomerular distribution of the tight junction protein zonula occludens- (ZO-1), a component of the slit diaphragm, was also studied. Results document that spontaneous proteinuria in MWF rats develops without significant changes in the permeability of the GBM to water and albumin, or in the ultrastructure of the podocyte foot processes, but is associated with an important alteration in the distribution of ZO-1 at the glomerular level. Lisinopril, which prevented proteinuria, also prevented glomerular redistribution of the protein. Thus, renoprotective effects of ACE inhibitors are not associated with changes in intrinsic functional properties of GBM, or ultrastructural changes of the epithelial cells, but rather with preservation of glomerular ZO-1 distribution and slit diaphragm function, which are essential for maintaining the filtration barrier.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2005

Macromolecular and nanotechnological modification of camptothecin and its analogs to improve the efficacy.

Camptothecin (CPT) and its analogs are some of the most potent antitumor agents known. However, their poor water-solubility and high toxicity require changes of their physicochemical and biological characteristics. Active lactone forms have provoked interest in the utility of CPT and its analogs again. Macromolecular chemical modifications and nanotechnological formulations have been used to obtain improved systems of CPT-related compounds. In these systems, one of the most important concepts is the enhanced permeability and retention (EPR) effect. The outcomes obtained by these approaches are displayed by introducing concrete examples.

Animals↗
PubMed1999

Photochemical internalization: a novel technology for delivery of macromolecules into cytosol.

The therapeutic usefulness of macromolecules, such as in gene therapy, is often limited by an inefficient transfer of the macromolecule to the cytosol and a lack of tissue-specific targeting. The possibility of photochemically releasing macromolecules from endosomes and lysosomes into the cytosol was examined. Endocytosed macromolecules and photosensitizer were exposed to light and intracellular localization and the expression of macomolecules in the cytosol was analyzed. This novel technology, named photochemical internalization (PCI), was found to efficiently deliver type I ribosome-inactivating proteins, horseradish peroxidase, a p21ras-derived peptide, and a plasmid encoding green fluorescent protein into cytosol in a light-dependent manner. The results presented here show that PCI can induce efficient light-directed delivery of macromolecules into the cytosol, indicating that PCI may have a variety of useful applications for site-specific drug delivery, e.g., in gene therapy, vaccination, and cancer treatment.

Cytosol↗
PubMed2000

Inhalable drugs for systemic therapy.

Although oral and injectable drug formulations still dominate the market, interest in pulmonary delivery has been rising steadily. Given patients' desire for an alternative to injections, and recent advances in aerosol science and pulmonary medicine, the potential for improved disease management outcomes by using aerosols for systemic drug delivery should lead the way for a shift to inhalables.

Administration, Inhalation↗
PubMed1979

The formation of binary and ternary complexes of cytochrome P-450scc with adrenodoxin and adrenodoxin reductase.adrenodoxin complex. The implication in ACTH function.

Binary and ternary complexes of bovine adrenocortical mitochondrial cytochrome P-450scc with adrenodoxin and adrenodoxin reductase.adrenodoxin complex are formed in the presence of cholesterol and Emulgen 913. Both cholesterol and Emulgen 913 are required for the binding of cytochrome P-450scc with adrenodoxin. Since phospholipids are able to replace Emulgen 913 in this reaction, in vivo phospholipids of the mitochondrial inner membrane appear to play the function of the detergent. The dissociation constants of the cytochrome.adrenodoxin complex are 0.3 to 0.4 microM at 130 microM dimyristoylphosphatidylcholine and 0.9 microM at 120 microM Emulgen 913, whereas the dissociation constant for the ternary complex of cytochrome P-450scc with adrenodoxin reductase and adrenodoxin is 4.0 microM at 150 microM Emulgen 913. The stoichiometry of binary and ternary complexes reveals the 1:1 and 1:1:1 molar ratios, respectively, judging from chemical analyses after the fractionation of the complexes by gel filtration. Emulgen 913, Tween 20, ethylene glycol, myristoyllysophosphatidylcholine, dimyristoylphosphatidylcholine, and phosphatidylethanolamine show the enhanced activity of cholesterol side chain cleavage reaction with cytochrome P-450scc, adrenodoxin, adrenodoxin reductase, and NADPH. These results, in conjunction with earlier experiments, lead us to the proposal on the structure of the hydroxylase complex in the membrane and to the hypothesis on the regulation of the enzymatic activity by the availability of substrate cholesterol to the cytochrome. Hence, we propose a mobile P-450scc hypothesis for the response of the mitochondrion to adrenocorticotropic hormone stimuli.

Adrenal Cortex↗