Structural study of the X-ray-induced enzymatic reaction of octahaem cytochromecnitrite reductase

2015 ◽  
Vol 71 (5) ◽  
pp. 1087-1094 ◽  
Author(s):  
A. A. Trofimov ◽  
K. M. Polyakov ◽  
V. A. Lazarenko ◽  
A. N. Popov ◽  
T. V. Tikhonova ◽  
...  

Octahaem cytochromecnitrite reductase from the bacteriumThioalkalivibrio nitratireducenscatalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochromecnitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

2014 ◽  
Vol 70 (a1) ◽  
pp. C187-C187
Author(s):  
Alison Edwards

"The renaissance in Laue studies - at neutron sources - provides us with access to single crystal neutron diffraction data for synthetic compounds without requiring synthesis of prohibitively large amounts of compound or improbably large crystals. Such neutron diffraction studies provide vital data where proof of the presence or absence of hydrogen in particular locations is required and which cannot validly be proved by X-ray studies. Since the commissioning of KOALA at OPAL in 2009[1] we have obtained numerous data sets which demonstrate the vital importance of measuring data even where the extent of the diffraction pattern is at relatively low resolution - especially when compared to that obtainable for the same compound with X-rays. In the Laue experiment performed with a fixed radius detector, data reduction is only feasible for crystals in the ""goldilocks"" zone – where the unit cell is relatively large for the detector, a correspondingly low resolution diffraction pattern in which adjacent spots are less affected by overlap will yield more data against which a structure can be refined than a pattern of higher resolution – one where neighbouring spots overlap rendering both unusable (in our current methodology). Analogous application of powder neutron diffraction in such determinations is also considered. Single crystal neutron diffraction studies of several important compounds (up to 5KDa see figure below)[2] in which precise determination of hydride content by neutron diffraction was pivotal to the final formulation will be presented. The neutron data sets typically possess 20% or fewer unique data at substantially "lower resolution" than the corresponding X-ray data sets. Careful refinement clearly reveals chemical detail which is typically unexplored in related X-ray diffraction studies reporting high profile chemistry despite the synthetic route being one which hydride ought to be considered/excluded in product formulation."


2001 ◽  
Vol 57 (8) ◽  
pp. 1110-1118 ◽  
Author(s):  
Mark J. Ellis ◽  
Fraser E. Dodd ◽  
Richard W. Strange ◽  
Miguel Prudêncio ◽  
Gary Sawers ◽  
...  

2019 ◽  
Vol 75 (9) ◽  
pp. 804-816 ◽  
Author(s):  
Konstantin M. Polyakov ◽  
Sergei Gavryushov ◽  
Tatiana V. Fedorova ◽  
Olga A. Glazunova ◽  
Alexander N. Popov

Laccases are enzymes that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of molecular oxygen to water. Here, a subatomic resolution X-ray crystallographic study of the mechanism of inhibition of the laccase from the basidiomycete fungus Steccherinum murashkinskyi by chloride and fluoride ions is presented. Three series of X-ray diffraction data sets were collected with increasing doses of absorbed X-ray radiation from a native S. murashkinskyi laccase crystal and from crystals of complexes of the laccase with chloride and fluoride ions. The data for the native laccase crystal confirmed the previously deduced enzymatic mechanism of molecular oxygen reduction. The structures of the complexes allowed the localization of chloride and fluoride ions in the channel near the T2 copper ion. These ions replace the oxygen ligand of the T2 copper ion in this channel and can play the role of this ligand in the enzymatic reaction. As follows from analysis of the structures from the increasing dose series, the inhibition of laccases by chloride and fluoride anions can be explained by the fact that the binding of these negatively charged ions at the position of the oxygen ligand of the T2 copper ion impedes the reduction of the T2 copper ion.


1998 ◽  
Vol 54 (6) ◽  
pp. 1450-1452 ◽  
Author(s):  
Ajay Saxena ◽  
Anna Gries ◽  
Robert Schwarzenbacher ◽  
Gerhard M. Kostner ◽  
Peter Laggner ◽  
...  

Apolipoprotein-H (Apo-H, Mw ≃ 50 kDa) is a carbohydrate-rich human-plasma protein which exists in blood serum in the free form as well as distributed between several classes of lipoproteins. Single crystals of apo-H have been obtained and crystallographic data sets have been collected. The crystals belong to the orthorhombic space group C2221, with cell dimensions a = 158.47, b = 169.25, c = 113.28 Å (at 100 K). The data indicate that the crystallographic asymmetric unit contains one tetramer of the protein.


IUCrJ ◽  
2015 ◽  
Vol 2 (1) ◽  
pp. 29-34 ◽  
Author(s):  
Kartik Ayyer ◽  
Hugh T. Philipp ◽  
Mark W. Tate ◽  
Jennifer L. Wierman ◽  
Veit Elser ◽  
...  

X-ray serial microcrystallography involves the collection and merging of frames of diffraction data from randomly oriented protein microcrystals. The number of diffracted X-rays in each frame is limited by radiation damage, and this number decreases with crystal size. The data in the frame are said to be sparse if too few X-rays are collected to determine the orientation of the microcrystal. It is commonly assumed that sparse crystal diffraction frames cannot be merged, thereby setting a lower limit to the size of microcrystals that may be merged with a given source fluence. TheEMCalgorithm [Loh & Elser (2009),Phys. Rev. E,80, 026705] has previously been applied to reconstruct structures from sparse noncrystalline data of objects with unknown orientations [Philippet al.(2012),Opt. Express,20, 13129–13137; Ayyeret al.(2014),Opt. Express,22, 2403–2413]. Here, it is shown that sparse data which cannot be oriented on a per-frame basis can be used effectively as crystallographic data. As a proof-of-principle, reconstruction of the three-dimensional diffraction intensity using sparse data frames from a 1.35 kDa molecule crystal is demonstrated. The results suggest that serial microcrystallography is, in principle, not limited by the fluence of the X-ray source, and collection of complete data sets should be feasible at, for instance, storage-ring X-ray sources.


2007 ◽  
Vol 555 ◽  
pp. 141-146 ◽  
Author(s):  
Srboljub J. Stanković ◽  
M. Petrović ◽  
M. Kovačević ◽  
A. Vasić ◽  
P. Osmokrović ◽  
...  

CdZnTe detectors have been employed in diagnostic X-ray spectroscopy. This paper presents the Monte Carlo calculation of X-ray deposited energy in a CdZnTe detector for different energies of photon beam. In incident photon direction, the distribution of absorbed dose as deposited energy in detector is determined. Based on the dependence of the detector response on the thickness and different Zn fractions, some conclusions about changes of the material characteristics could be drawn. Results of numerical simulation suggest that the CdZnTe detector could be suitable for X-ray low energy.


2018 ◽  
Vol 63 (2) ◽  
pp. 62-64 ◽  
Author(s):  
А. Белоусов ◽  
A. Belousov ◽  
Г. Крусанов ◽  
G. Krusanov ◽  
А. Черняев ◽  
...  

Purpose: Determining the absorbed dose produced by photons, it is often assumed that it is equal to the radiation kerma. This assumption is valid only in the presence of an electronic equilibrium, which in turn is never ensured in practice. It leads to some uncertainty in determining the absorbed dose in the irradiated sample during radiobiological experiments. Therefore, it is necessary to estimate the uncertainty in determining the relative biological effectiveness of X-rays associated with uncertainty in the determination of the absorbed dose. Material and methods: The monochromatic X-ray photon emission is simulated through a standard 25 cm2 plastic flask containing 5 ml of the model culture medium (biological tissue with elemental composition C5H40O18N). The calculation of the absorbed dose in a culture medium is carried out in two ways: 1) the standard method, according to which the ratio of the absorbed dose in the medium and the ionization chamber is equal to the ratio of kerma in the medium and air; 2) determination of the absorbed dose in the medium and in the sensitive volume of the ionization chamber by computer simulation and calculating the ratio of these doses. For each primary photon energies, 108 histories are modeled, which makes it possible to achieve a statistical uncertainty not worse than 0.1 %. The energy step was 1 keV. The spectral distribution of X-ray energy is modeled separately for each set of anode materials, thickness and materials of the primary and secondary filters. The specification of the X-ray beams modeled in this work corresponds to the standards ISO 4037 and IEC 61267. Within the linear-quadratic model, the uncertainty of determining the RBEmax values is directly proportional to the uncertainty in the determination of the dose absorbed by the sample under study. Results: At energy of more than 60 keV, the ratios for water and biological tissue practically do not differ. At lower energies, up to about 20 keV, the ratio of the coefficients of air and water is slightly less than that of air and biological tissue. The maximum difference is ~ 1 % than usual and the equality of absorbed doses in the ionization chamber and sample is justified. At photon energy of 60 keV for the geometry in question, the uncertainty in determining the dose is about 50 %. For non-monochromatic radiation, the magnitude of the uncertainty is determined by the spectral composition of the radiation, since the curves vary greatly in the energy range 10–100 keV. It is shown that, depending on the spectral composition of X-ray radiation, uncertainty in the determination of the absorbed dose can reach 40–60 %. Such large uncertainty is due to the lack of electronic equilibrium in the radiation geometry used in practice. The spread of RBE values determined from the data of radiobiological experiments carried out by different authors can be determined both by differences in the experimental conditions and by uncertainty in the determination of the absorbed dose. Using Fricke dosimeters instead of ionization chambers in the same geometry allows you to reduce the uncertainty approximately 2 times, up to 10–30 %. Conclusion: The computer simulation of radiobiological experiments to determine the relative biological effectiveness of X-ray radiation is performed. The geometry of the experiments corresponds to the conditions for the use of standard bottles placed in the side holders. It is shown that the ratio of absorbed doses and kerma in the layers of biological tissue and air differ among themselves with an uncertainty up to 60 %. Depending on the quality of the beam, the true absorbed dose may differ from the one calculated on the assumption of kerma and dose equivalence by 50 %. Uncertainty in determining the RBE in these experiments is of the same order. The results are presented for X-ray beams with negligible fraction of photons with energies less than 10 keV. For beams of a different quality, the uncertainty in determination can significantly increase. For the correct evaluation of RBE, it is necessary to develop a uniform standard for carrying out radiobiological experiments. This standard should regulate both the geometry of the experiments and the conduct of dosimetric measurements.


2021 ◽  
Vol 503 (2) ◽  
pp. 2791-2803
Author(s):  
Swapnil Shankar ◽  
Rishi Khatri

ABSTRACT We present a new method to determine the probability distribution of the 3D shapes of galaxy clusters from the 2D images using stereology. In contrast to the conventional approach of combining different data sets (such as X-rays, Sunyaev–Zeldovich effect, and lensing) to fit a 3D model of a galaxy cluster for each cluster, our method requires only a single data set, such as X-ray observations or Sunyaev–Zeldovich effect observations, consisting of sufficiently large number of clusters. Instead of reconstructing the 3D shape of an individual object, we recover the probability distribution function (PDF) of the 3D shapes of the observed galaxy clusters. The shape PDF is the relevant statistical quantity, which can be compared with the theory and used to test the cosmological models. We apply this method to publicly available Chandra X-ray data of 89 well-resolved galaxy clusters. Assuming ellipsoidal shapes, we find that our sample of galaxy clusters is a mixture of prolate and oblate shapes, with a preference for oblateness with the most probable ratio of principle axes 1.4 : 1.3 : 1. The ellipsoidal assumption is not essential to our approach and our method is directly applicable to non-ellipsoidal shapes. Our method is insensitive to the radial density and temperature profiles of the cluster. Our method is sensitive to the changes in shape of the X-ray emitting gas from inner to outer regions and we find evidence for variation in the 3D shape of the X-ray emitting gas with distance from the centre.


Author(s):  
Sanhita Basu ◽  
Sushmita Mitra ◽  
Nilanjan Saha

AbstractWith the ever increasing demand for screening millions of prospective “novel coronavirus” or COVID-19 cases, and due to the emergence of high false negatives in the commonly used PCR tests, the necessity for probing an alternative simple screening mechanism of COVID-19 using radiological images (like chest X-Rays) assumes importance. In this scenario, machine learning (ML) and deep learning (DL) offer fast, automated, effective strategies to detect abnormalities and extract key features of the altered lung parenchyma, which may be related to specific signatures of the COVID-19 virus. However, the available COVID-19 datasets are inadequate to train deep neural networks. Therefore, we propose a new concept called domain extension transfer learning (DETL). We employ DETL, with pre-trained deep convolutional neural network, on a related large chest X-Ray dataset that is tuned for classifying between four classes viz. normal, other_disease, pneumonia and Covid — 19. A 5-fold cross validation is performed to estimate the feasibility of using chest X-Rays to diagnose COVID-19. The initial results show promise, with the possibility of replication on bigger and more diverse data sets. The overall accuracy was measured as 95.3% ± 0.02. In order to get an idea about the COVID-19 detection transparency, we employed the concept of Gradient Class Activation Map (Grad-CAM) for detecting the regions where the model paid more attention during the classification. This was found to strongly correlate with clinical findings, as validated by experts.


2020 ◽  
Vol 642 ◽  
pp. A112
Author(s):  
A. Kepa ◽  
R. Falewicz ◽  
M. Siarkowski ◽  
M. Pietras

Context. Soft X-ray spectra (3.33 Å–6.15 Å) from the RESIK instrument on CORONAS-F constitute a unique database for the study of the physical conditions of solar flare plasmas, enabling the calculation of differential emission measures. The two RESIK channels for the shortest wavelengths overlap with the lower end of the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) spectral energy range, which is located around 3 keV, making it possible to compare both data sets. Aims. We aim to compare observations from RESIK and RHESSI spectrometers and cross-correlate these instruments. Observations are compared with synthetic spectra calculated based on the results of one-dimensional hydrodynamical (1D-HD) modelling. The analysis was performed for the flare on 20 September 2002 (SOL2002-09-20T09:28). Methods. We estimated the geometry of the flaring loop, necessary for 1D-HD modelling, based on images from RHESSI and the Extreme-Ultraviolet Imaging Telescope aboard the Solar and Heliospheric Observatory. The distribution of non-thermal electrons (NTEs) was determined from RHESSI spectra. The 1D-HD model assumes that non-thermal electrons with a power-law spectrum were injected at the apex of the flaring loop. The NTEs then heat and evaporate the chromosphere, filling the loop with hot and dense plasma radiating in soft X-rays. The total energy of electrons was constrained by comparing observed and calculated fluxes from Geostationary Operational Environmental Satellite 1–8 Å data. We determined the temperature and density at every point of the flaring loop throughout the evolution of the flare, calculating the resulting X-ray spectra. Results. The synthetic spectra calculated based on the results of hydrodynamic modelling for the 20 September 2002 flare are consistent within a factor of two with the observed RESIK spectra during most of the duration of the flare. This discrepancy factor is probably related to the uncertainty on the cross-calibration between RESIK and RHESSI instruments.


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