scholarly journals RNA protects a nucleoprotein complex against radiation damage

2016 ◽  
Vol 72 (5) ◽  
pp. 648-657 ◽  
Author(s):  
Charles S. Bury ◽  
John E. McGeehan ◽  
Alfred A. Antson ◽  
Ian Carmichael ◽  
Markus Gerstel ◽  
...  

Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3–25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein–DNA complex. Specific damage manifestations were determined within the largetrpRNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density.

Author(s):  
Robert C. Rau ◽  
John Moteff

Transmission electron microscopy has been used to study the thermal annealing of radiation induced defect clusters in polycrystalline tungsten. Specimens were taken from cylindrical tensile bars which had been irradiated to a fast (E > 1 MeV) neutron fluence of 4.2 × 1019 n/cm2 at 70°C, annealed for one hour at various temperatures in argon, and tensile tested at 240°C in helium. Foils from both the unstressed button heads and the reduced areas near the fracture were examined.Figure 1 shows typical microstructures in button head foils. In the unannealed condition, Fig. 1(a), a dispersion of fine dot clusters was present. Annealing at 435°C, Fig. 1(b), produced an apparent slight decrease in cluster concentration, but annealing at 740°C, Fig. 1(C), resulted in a noticeable densification of the clusters. Finally, annealing at 900°C and 1040°C, Figs. 1(d) and (e), caused a definite decrease in cluster concentration and led to the formation of resolvable dislocation loops.


Author(s):  
Shawn Williams ◽  
Xiaodong Zhang ◽  
Susan Lamm ◽  
Jack Van’t Hof

The Scanning Transmission X-ray Microscope (STXM) is well suited for investigating metaphase chromosome structure. The absorption cross-section of soft x-rays having energies between the carbon and oxygen K edges (284 - 531 eV) is 6 - 9.5 times greater for organic specimens than for water, which permits one to examine unstained, wet biological specimens with resolution superior to that attainable using visible light. The attenuation length of the x-rays is suitable for imaging micron thick specimens without sectioning. This large difference in cross-section yields good specimen contrast, so that fewer soft x-rays than electrons are required to image wet biological specimens at a given resolution. But most imaging techniques delivering better resolution than visible light produce radiation damage. Soft x-rays are known to be very effective in damaging biological specimens. The STXM is constructed to minimize specimen dose, but it is important to measure the actual damage induced as a function of dose in order to determine the dose range within which radiation damage does not compromise image quality.


2021 ◽  
Vol 22 (9) ◽  
pp. 4566
Author(s):  
Shin-ichi Hirano ◽  
Yusuke Ichikawa ◽  
Bunpei Sato ◽  
Haru Yamamoto ◽  
Yoshiyasu Takefuji ◽  
...  

Although ionizing radiation (radiation) is commonly used for medical diagnosis and cancer treatment, radiation-induced damages cannot be avoided. Such damages can be classified into direct and indirect damages, caused by the direct absorption of radiation energy into DNA and by free radicals, such as hydroxyl radicals (•OH), generated in the process of water radiolysis. More specifically, radiation damage concerns not only direct damages to DNA, but also secondary damages to non-DNA targets, because low-dose radiation damage is mainly caused by these indirect effects. Molecular hydrogen (H2) has the potential to be a radioprotective agent because it can selectively scavenge •OH, a reactive oxygen species with strong oxidizing power. Animal experiments and clinical trials have reported that H2 exhibits a highly safe radioprotective effect. This paper reviews previously reported radioprotective effects of H2 and discusses the mechanisms of H2, not only as an antioxidant, but also in intracellular responses including anti-inflammation, anti-apoptosis, and the regulation of gene expression. In doing so, we demonstrate the prospects of H2 as a novel and clinically applicable radioprotective agent.


Cells ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 42
Author(s):  
Xiaoyu Pu ◽  
Siyang Ma ◽  
Yan Gao ◽  
Tiankai Xu ◽  
Pengyu Chang ◽  
...  

Radiation-induced damage is a common occurrence in cancer patients who undergo radiotherapy. In this setting, radiation-induced damage can be refractory because the regeneration responses of injured tissues or organs are not well stimulated. Mesenchymal stem cells have become ideal candidates for managing radiation-induced damage. Moreover, accumulating evidence suggests that exosomes derived from mesenchymal stem cells have a similar effect on repairing tissue damage mainly because these exosomes carry various bioactive substances, such as miRNAs, proteins and lipids, which can affect immunomodulation, angiogenesis, and cell survival and proliferation. Although the mechanisms by which mesenchymal stem cell-derived exosomes repair radiation damage have not been fully elucidated, we intend to translate their biological features into a radiation damage model and aim to provide new insight into the management of radiation damage.


2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jordy Homing Lam ◽  
Yu Li ◽  
Lizhe Zhu ◽  
Ramzan Umarov ◽  
Hanlun Jiang ◽  
...  

Abstract Protein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes such as binding preference of RNA backbone constituents and different bases can be predicted from local physicochemical characteristics of protein structure surface. On a diverse set of challenging RNA-binding proteins, including Fem-3-binding-factor 2, Argonaute 2 and Ribonuclease III, NucleicNet can accurately recover interaction modes discovered by structural biology experiments. Furthermore, we show that, without seeing any in vitro or in vivo assay data, NucleicNet can still achieve consistency with experiments, including RNAcompete, Immunoprecipitation Assay, and siRNA Knockdown Benchmark. NucleicNet can thus serve to provide quantitative fitness of RNA sequences for given binding pockets or to predict potential binding pockets and binding RNAs for previously unknown RNA binding proteins.


1994 ◽  
Vol 77 (5) ◽  
pp. 1202-1217 ◽  
Author(s):  
Georg A Schreiber ◽  
Grit Schulzki ◽  
Almuth Spiegelberg ◽  
Norbert Helle ◽  
Klaus W Bögl

Abstract A method suitable for routine application was used in an interlaboratory study to detect irradiation treatment of chicken carcass, pork, and beef. By using gas chromatographic analysis, 17 participating laboratories determined the quantity of 4 different radiation-induced volatile hydrocarbons (tetradecene, pentadecane, hexadecadiene, and neptadecene) in the fat fraction of coded specimens approximately 3 and 6 months after irradiation. The specimens of each type of meat were supplied by 2 different producers. The dose range tested (0.6-7.5 kGy) included levels commercially used to reduce the number of contaminating microorganisms (1-5 kGy). The method employed permitted a correct identification of irradiated or nonirradiated in 98.3% of the 864 specimens.


Luminescence ◽  
2004 ◽  
Vol 19 (5) ◽  
pp. 278-282 ◽  
Author(s):  
Debin Zhu ◽  
Da Xing ◽  
Yadong Wei ◽  
Xian Li ◽  
Bo Gao

2019 ◽  
Vol 26 (4) ◽  
pp. 931-944 ◽  
Author(s):  
Helena Taberman ◽  
Charles S. Bury ◽  
Mark J. van der Woerd ◽  
Edward H. Snell ◽  
Elspeth F. Garman

Xylose isomerase (XI) is an industrially important metalloprotein studied for decades. Its reaction mechanism has been postulated to involve movement of the catalytic metal cofactor to several different conformations. Here, a dose-dependent approach was used to investigate the radiation damage effects on XI and their potential influence on the reaction mechanism interpreted from the X-ray derived structures. Radiation damage is still one of the major challenges for X-ray diffraction experiments and causes both global and site-specific damage. In this study, consecutive high-resolution data sets from a single XI crystal from the same wedge were collected at 100 K and the progression of radiation damage was tracked over increasing dose (0.13–3.88 MGy). The catalytic metal and its surrounding amino acid environment experience a build-up of free radicals, and the results show radiation-damage-induced structural perturbations ranging from an absolute metal positional shift to specific residue motions in the active site. The apparent metal movement is an artefact of global damage and the resulting unit-cell expansion, but residue motion appears to be driven by the dose. Understanding and identifying radiation-induced damage is an important factor in accurately interpreting the biological conclusions being drawn.


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