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1.
Jason A. SOMARELLI Annia MESA Ambrish ROY Yang ZHANG Rene J. HERRERA 《Entomological Research》2010,40(2):104-112
Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes. 相似文献
2.
Multiple effects of tumor necrosis factor on lipoprotein lipase in vivo 总被引:13,自引:0,他引:13
H Semb J Peterson J Tavernier T Olivecrona 《The Journal of biological chemistry》1987,262(17):8390-8394
A single dose of recombinant murine tumor necrosis factor (TNF) suppressed lipoprotein lipase activity in adipose tissue of fed rats, mice, and guinea pigs for 48 h, even though TNF itself is rapidly metabolized in vivo. Immunoprecipitation of [35S]lipoprotein lipase from fat pads pulse-labeled with [35S]methionine showed a decrease in relative synthesis of the enzyme, which correlated to the decrease in activity. There was no decrease in general protein synthesis and no change in distribution of the enzyme between adipocytes and extracellular locations in the tissue. This is in contrast to fasting in which case there is redistribution of the enzyme within the tissue, decrease in general protein synthesis, but no change in relative synthesis of lipoprotein lipase. TNF did not decrease lipoprotein lipase activity in any tissue other than the adipose but increased the activity in several cases, most markedly in the liver. No [35S]methionine was incorporated into lipoprotein lipase by liver slices from normal or TNF-treated animals. Thus, the increased activity can not be ascribed to enhanced hepatic synthesis of the enzyme. There was an increase in lipoprotein lipase activity in plasma, which correlated to the increase in liver. Thus, TNF suppresses lipoprotein lipase synthesis in adipocytes, but not in other tissues, and has some as yet undefined effect on lipoprotein lipase turnover in extrahepatic tissues, which results in increased transport of active lipase through plasma to the liver. 相似文献
3.
Tumor necrosis factor induces acute phase proteins in rats 总被引:2,自引:0,他引:2
I Gresser F Delers N Tran Quangs S Marion R Engler C Maury C Soria J Soria W Fiers J Tavernier 《Journal of biological regulators and homeostatic agents》1987,1(4):173-176
Inoculation of WAG rats with recombinant mouse tumor necrosis factor results in a rapid and marked increase in several acute phase proteins in the serum (haptoglobin, alpha 1 acid glycoprotein, alpha 2 macroglobulin) and in the plasma (fibrinogen). We conclude that TNF may play an important role in the inflammatory response in vivo and possibly in the pathogenesis of inflammatory disorders. 相似文献
4.
Conserved residues of tumour necrosis factor and lymphotoxin constitute the framework of the trimeric structure 总被引:1,自引:0,他引:1
J Tavernier X van Ostade G Hauquier T Prange I Lasters M de Maeyer A Lewit-Bentley R Fourme 《FEBS letters》1989,257(2):315-318
Four distinct areas of primary sequence conservation between known tumour necrosis factor and lymphotoxin polypeptides from various species can be recognized. When these amino acid sequences are highlighted in the three-dimensional structure, all are found in the same region, constituting the framework of the trimeric structure. 相似文献
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6.
The inhibitory effects of synthetic phenolic compounds on benzo(a)pyrene-induced neoplasia of the mouse forestomach have been measured by Wattenberg et al6 The efficiency of this inhibition has been estimated for each phenol, using R, the ratio of the number of tumors per mouse in the protected group over the number of tumours per mouse in the control group. We have observed a linear correlation between the chemoprotection efficiency R and the logarithm of the rate of quenching of singlet oxygen. k. by this family of phenols, log k being itself correlated with the one-electron oxidation potential of the phenols. These correlations suggest a charge transfer mechanism for the inhibition of neoplasia induced hy benzo(a)py-rene. The correlations described provide a theoretical basis for scaling the inhibitors of mutagenicity induced by polycyclic aromatic compounds in terms of their oxidation potentials 相似文献
7.
Attached media reactors are used for enhancement of wastewater treatment processes including anaerobic condition. Selection of a suitable biofilm carrier is a compelling method to improve anaerobic digestion systems. This study investigates the performance of four fibrous biofilms installed in batch biogas reactors for treatment of cow manure. BioCords HS1, HS2, LS1, and LS2 are manufactured by Bishop Water Technologies, ON, Canada. Effluents and attached growth media were analyzed after batch experiment; methane production, methane yield, transfer efficiencies, organic and solid removal efficiencies, pH, and attached volatile suspended solid (VSS) were measured; VSS attached to biofilms mainly correlated with the specific surface area of each biofilm. Additionally, SEM (scanning electron microscopy) was used for further understanding of biofilm formation process for BioCords and the dissimilarity in their performance. The results indicated that BioCord LS2 had positive impact on achieving higher methane production and removal efficiencies compared to other support media utilized in batch reactors. It was also demonstrated from the experiment that BioCord LS2 potentially could generate higher methane production than conventional batch bioreactor. 相似文献
8.
Tom Bongiorno Jacob Kazlow Roman Mezencev Sarah Griffiths Rene Olivares-Navarrete John F. McDonald Zvi Schwartz Barbara D. Boyan Todd C. McDevitt Todd Sulchek 《Journal of biomechanics》2014
Although it has been established that cellular stiffness can change as a stem cell differentiates, the precise relationship between cell mechanics and other phenotypic properties remains unclear. Inherent cell heterogeneity and asynchronous differentiation complicate population analysis; therefore, single-cell analysis was employed to determine how changes in cell stiffness correlate with changes in molecular biomarkers during differentiation. Design of a custom gridded tissue culture dish facilitated single-cell comparisons between cell mechanics and other differentiation biomarkers by enabling sequential measurement of cell mechanics and protein biomarker expression at the single cell level. The Young’s modulus of mesenchymal stem cells was shown not only to decrease during chemically-induced osteoblast differentiation, but also to correlate more closely with the day of differentiation than did the relative expression of the traditional osteoblast differentiation markers, bone sialoprotein and osteocalcin. Therefore, cell stiffness, a measurable property of individual cells, may serve as an improved indicator of single-cell osteoblast differentiation compared to traditional biological markers. Revelation of additional osteoblast differentiation indicators, such as cell stiffness, can improve identification and collection of starting cell populations, with applications to mesenchymal stem cell therapies and stem cell-based tissue engineering. 相似文献
9.
10.
Elmar Porten Beate Seliger Verena A. Schneider Stefan W?ll Daniela Stangel Rene Ramseger Stephan Kr?ger 《The Journal of biological chemistry》2010,285(5):3114-3125
Clustering or overexpression of the transmembrane form of the extracellular matrix proteoglycan agrin in neurons results in the formation of numerous highly motile filopodia-like processes extending from axons and dendrites. Here we show that similar processes can be induced by overexpression of transmembrane-agrin in several non-neuronal cell lines. Mapping of the process-inducing activity in neurons and non-neuronal cells demonstrates that the cytoplasmic part of transmembrane agrin is dispensable and that the extracellular region is necessary for process formation. Site-directed mutagenesis reveals an essential role for the loop between β-sheets 3 and 4 within the Kazal subdomain of the seventh follistatin-like domain of TM-agrin. An aspartic acid residue within this loop is critical for process formation. The seventh follistatin-like domain could be functionally replaced by the first and sixth but not by the eighth follistatin-like domain, demonstrating a functional redundancy among some follistatin-like domains of agrin. Moreover, a critical distance of the seventh follistatin-like domain to the plasma membrane appears to be required for process formation. These results demonstrate that different regions within the agrin protein are responsible for synapse formation at the neuromuscular junction and for process formation in central nervous system neurons and suggest a role for agrin''s follistatin-like domains in the developing central nervous system. 相似文献