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
Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems. 相似文献
Previous studies on spinal cord injury (SCI) have confirmed that percutaneous photobiomodulation (PBM) therapy can ameliorate immunoinflammatory responses at sites of injury, accelerate nerve regeneration, suppress glial scar formation and promote the subsequent recovery of locomotor function. The current study was performed to evaluate a large‐animal model employing implanted optical fibers to accurately irradiate targeted spinal segments. The method's feasibility and irradiation parameters that do not cause phototoxic reaction were determined, and the methodology of irradiating the spinal cord with near‐infrared light was investigated in detail. A diffusing optical fiber was implanted above the T9 spinal cord of Bama miniature pigs and used to transfer near‐infrared light (810 nm) onto the spinal cord surface. After daily irradiation with 200, 300, 500 or 1000 mW for 14 days, both sides of the irradiated area of the spinal cord were assessed for temperature changes. The condition of the spinal cord and the position of optical fiber were investigated by magnetic resonance imaging (MRI), and different parameters indicating temperature increases or phototoxicity were measured on the normal spinal cord surface due to light irradiation (ie, heat shock responses, inflammatory reactions and neuronal apoptosis), and the animals' lower‐limb neurological function and gait were assessed during the irradiation process. The implanted device was stable inside the freely moving animals, and light energy could be directly projected onto the spinal cord surface. The screening of different irradiation parameters preliminary showed that direct irradiation onto the spinal cord surface at 200 and 300 mW did not significantly increase the temperature, stress responses, inflammatory reactions and neural apoptosis, whereas irradiation at 500 mW slightly increased these parameters, and irradiation at 1000 mW induced a significant temperature increase, heat shock, inflammation and apoptosis responses. HE staining of spinal cord tissue sections did not reveal any significant structural changes of the tissues compared to the control group, and the neurological function and gait of all irradiated animals were normal. In this study, we established an in‐vivo optical fiber implantation method, which might be safe and stable and could be used to directly project light energy onto the spinal cord surface. This study might provide a new perspective for clinical applications of PBM in acute SCI. 相似文献
Largemouth bass (Micropterus salmoides, a carnivorous fish native to North America) prefers to utilize amino acids as energy sources rather than glucose and fatty acids. However, little is known about the nutritional regulation of substrate oxidation in the fish. Therefore, this study was conducted to determine whether the oxidation of glutamate, glutamine, glucose and palmitate in its tissues might be influenced by dietary protein intake. Juvenile largemouth bass (initial weight 18.3 ± 0.1 g) were fed three isocaloric diets containing 40%, 45% and 50% protein for 8 weeks. The growth performance, energy retention, and lipid retention of juvenile fish increased with increasing dietary protein levels. The rate of oxidation of glutamate by the intestine was much greater than that of glutamine, explaining why increasing the dietary protein content from 40% to 50% had no effect on the serum concentration of glutamate but increased that of glutamine in the fish. The liver of fish fed the 50% protein diet had a higher (P < 0.05) rate of glutamine oxidation than that in the 40% and 45% protein groups. In contrast, augmenting dietary protein content from 40% to 45% increased (P < 0.05) both glutamine and glutamate oxidation in the proximal intestine of the fish and renal glutamine oxidation, without changes in intestinal or renal AA oxidation between the 45% and 50% protein groups. Furthermore, the rates of glucose oxidation in the liver, kidney, and intestine of largemouth bass were decreased in response to an increase in dietary protein content from 40% to 45% and a concomitant decrease in dietary starch content from 22.3% to 15.78%, but did not differ between the 45% and 50% protein groups. The rates of oxidation of glucose in skeletal muscle and those of palmitate in all tissues (except for the kidney) were not affected by the diets. Collectively, these results indicate that the largemouth bass can regulate substrate metabolism in a tissue-specific manner to favor protein and lipid gains as dietary protein content increases from 40% to 50% and have a lower ability to oxidize fatty acids and glucose than amino acids regardless of the dietary protein intake.
