Search results for: x-ray crystallography

Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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Authors: N. Tugrul, N. Baran Acarali, A. S. Kipcak, E. Moroydor Derun, S. Piskin

Abstract:

Turkey has 72 % of total world boron reserves on the basis of B2O3.Borates that is a refined form of boron minerals have a wide range of applications. Zinc borates can be used as multifunctional synergistic additives. The most important properties are low solubility in water and high dehydration temperature. Zinc borates dehydrate above 290°C and anhydrous zinc borate has thermal resistance about 400°C. Zinc borates can be synthesized using several methods such as hydrothermal and solid-state processes. In this study, the solid-state method was applied between 500 and 800°C using the starting materials of ZnO and H3BO3 with 1:4 mole ratio. The reaction time was determined as 4 hours after some preliminary experiments. After the synthesis, the crystal structure and the morphology of the products were examined by XRay Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FT-IR) and Raman Spectrometer. As a result the form of ZnB4O7 was synthesized with the highest crystal score at 800°C.

Keywords: Raman, solid-state method, zinc borate, XRD.

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Authors: Kamyar Shameli, Mansor Bin Ahmad, Wan Md Zin Wan Yunus, Nor Azowa Ibrahim, Maryam Jokar, Majid Darroudi

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Silver/polylactide nanocomposites (Ag/PLA-NCs) were synthesized via chemical reduction method in diphase solvent. Silver nitrate and sodium borohydride were used as a silver precursor and reducing agent in the polylactide (PLA). The properties of Ag/PLA-NCs were studied as a function of the weight percentages of silver nanoparticles (8, 16 and 32 wt% of Ag-NPs) relative to the weight of PLA. The Ag/PLA-NCs were characterized by Xray diffraction (XRD), transmission electron microscopy (TEM), electro-optical microscopy (EOM), UV-visible spectroscopy (UV-vis) and Fourier transform infrared spectroscopy (FT-IR). XRD patterns confirmed that Ag-NPs crystallographic planes were face centered cubic (fcc) type. TEM images showed that mean diameters of Ag-NPs were 3.30, 3.80 and 4.80 nm. Electro-optical microscopy revealed excellent dispersion and interaction between Ag-NPs and PLA films. The generation of silver nanoparticles was confirmed from the UVvisible spectra. FT-IR spectra showed that there were no significant differences between PLA and Ag/PLA-NCs films. The synthesized Ag/PLA-NCs were stable in organic solution over a long period of time without sign of precipitation.

Keywords: Nanocomposites, Polylactide, Silver Nanoparticles, Sodium Borohydride, Transmission Electron Microscopy.

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Authors: A. Karnis, L. Gautron

Abstract:

Considering toxicity of heavy metals and their accumulation in domestic wastes, immobilization of lead and cadmium is envisaged inside glass-ceramics. We particularly focused this work on calcium-rich phases embedded in a glassy matrix. Glass-ceramics were synthesized from glasses doped with 12 wt% and 16 wt% of PbO or CdO. They were observed and analyzed by Electron MicroProbe Analysis (EMPA) and Analytical Scanning Electron Microscopy (ASEM). Structural characterization of the samples was performed by powder XRay Diffraction. Diopside crystals of CaMgSi2O6 composition are shown to incorporate significant amounts of cadmium (up to 9 wt% of CdO). Two new crystalline phases are observed with very high Cd or Pb contents: about 40 wt% CdO for the cadmiumrich phase and near 60 wt% PbO for the lead-rich phase. We present complete chemical and structural characterization of these phases. They represent a promising way for the immobilization of toxic elements like Cd or Pb since glass ceramics are known to propose a “double barrier" protection (metal-rich crystals embedded in a glass matrix) against metal release in the environment.

Keywords: Cadmium, Calcium-rich phases, Diopside, Domesticwastes, Fly ashes, Glass-ceramics, Lead, Municipal Solid WasteIncineration.

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Authors: A. Srion, W. Thepsuwan, N. Monmaturapoj

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Two Lithium Disilicate (LD) glass ceramics based on SiO2-Li2O-K2O-Al2O3 system were prepared through a glass melting method. The glass rods were then fabricated into dental crowns via a hot pressing at 900˚C and 850˚C in order to study the effect of the pressing temperatures on the phase formation and microstructure of the glasses. Different samples of as cast glass and heat treated samples (600˚C and 700˚C) were used to press for investigating the effect of an initial microstructure on the hot pressing technique. Xray diffraction (XRD) and scanning electron microscopy (SEM) were performed to determine the phase formation and microstructure of the samples, respectively. XRD results show that the main crystalline structure was Li2Si2O5 by having Li3PO4, Li0.6Al0.6Si2O6, Li2SiO3, Ca5 (PO4)3F and SiO2 as minor phases. Glass compositions with different heat treatment temperatures exhibited a difference phase formations but have less effect during pressing. SEM micrographs showed the microstructure of Li2Si2O5 as lath-like shape in all glasses. With increasing the initial heat treatment temperature, the longer the lath-like crystals of lithium disilicate were increased especially when using glass heat treatment at 700˚C followed by pressing at 900˚C. This could be suggested that LD1 heat treatment at 700˚C which pressing at 900˚C presented the best formation by the hot pressing and compiled microstructure.

Keywords: Lithium disilicate, Hot pressing, Dental crown, Microstructure.

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Authors: Farid Jamali Sheini, Dilip S. Joag, Mahendra A. More

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A simple approach is demonstrated for growing large scale, nearly vertically aligned ZnO nanowire arrays by thermal oxidation method. To reveal effect of temperature on growth and physical properties of the ZnO nanowires, gold coated zinc substrates were annealed at 300 °C and 400 °C for 4 hours duration in air. Xray diffraction patterns of annealed samples indicated a set of well defined diffraction peaks, indexed to the wurtzite hexagonal phase of ZnO. The scanning electron microscopy studies show formation of ZnO nanowires having length of several microns and average of diameter less than 500 nm. It is found that the areal density of wires is relatively higher, when the annealing is carried out at higher temperature i.e. at 400°C. From the field emission studies, the values of the turn-on and threshold field, required to draw emission current density of 10 μA/cm2 and 100 μA/cm2 are observed to be 1.2 V/μm and 1.7 V/μm for the samples annealed at 300 °C and 2.9 V/μm and 3.7 V/μm for that annealed at 400 °C, respectively. The field emission current stability, investigated over duration of more than 2 hours at the preset value of 1 μA, is found to be fairly good in both cases. The simplicity of the synthesis route coupled with the promising field emission properties offer unprecedented advantage for the use of ZnO field emitters for high current density applications.

Keywords: ZnO, Nanowires, Thermal oxidation, FieldEmission.

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Authors: Eraricar Salleh, Ida Idayu Muhamad, Nozieanna Khairuddin

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Antimicrobial (AM) starch-based films were developed by incorporating chitosan and lauric acid as antimicrobial agent into starch-based film. Chitosan has wide range of applications as a biomaterial, but barriers still exist to its broader use due to its physical and chemical limitations. In this work, a series of starch/chitosan (SC) blend films containing 8% of lauric acid was prepared by casting method. The structure of the film was characterized by Fourier transform infrared spectroscopy (FTIR), Xray diffraction (XRD), and scanning electron microscopy (SEM). The results indicated that there were strong interactions were present between the hydroxyl groups of starch and the amino groups of chitosan resulting in a good miscibility between starch and chitosan in the blend films. Physical properties and optical properties of the AM starch-based film were evaluated. The AM starch-based films incorporated with chitosan and lauric acid showed an improvement in water vapour transmission rate (WVTR) and addition of starch content provided more transparent films while the yellowness of the film attributed to the higher chitosan content. The improvement in water barrier properties was mainly attributed to the hydrophobicity of lauric acid and optimum chitosan or starch content. AM starch based film also showed excellent oxygen barrier. Obtaining films with good oxygen permeability would be an indication of the potential use of these antimicrobial packaging as a natural packaging and an alternative packaging to the synthetic polymer to protect food from oxidation reactions

Keywords: Antimicrobial starch-based films, chitosan, lauric acid, starch.

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Authors: Rania Mustafa

Abstract:

This audit was conducted at Manchester University NHS Foundation Trust, Wythenshawe Hospital Radiology and Accident and Emergency [A&E] Department to assess the appropriateness of clinical information in X-ray requests, specifically in cases of acute ankle injuries. As per the Ottawa Ankle Rules and the recommendations of National Institute for Health and Care Excellence [NICE] and the Royal College of Radiology, we aimed to evaluate the appropriateness of referrals and the thoroughness of clinical information provided by Emergency Department [ED] clinicians for ankle radiography. Our goal was to achieve 100% compliance with these guidelines. The audit involved a comprehensive analysis spanning the period from August 2022 to January 2023, encompassing patient records, radiographic orders, and clinical assessments. Data collection included patient demographics, presenting complaints, clinical assessments, adherence to Ottawa Ankle Rules criteria, and subsequent radiography orders. Here we conducted two audit cycles, involving 38 patients in the first cycle and 86 patients in the second cycle. The data were furtherly filtered to include all patients who were referred from the ED for an ankle Xray with a history of acute trauma and age of more than 18 years. The key finding was that in August 2022, 60% of cases met the Ottawa Ankle Rules criteria accurately, indicating a need for improvement in adherence. However, by January 2023, there was a notable improvement, with 95% of cases accurately meeting the criteria. This significant change reflects an increased alignment with best practices for ankle radiography referrals.

Keywords: Ankle, injuries, Ottawa Ankle Rule, X-rays.

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.

Keywords: Seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation.

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Authors: Haleh Rezaei Zanjirabadi, Fatemeh Saberi, Bahman Rahimzadeh, Fariborz Masoudi, Mohammad Rahgosha

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In this study, apatite minerals from the iron-phosphate deposit of Yazd have been investigated within the microcontinent zone of Iran in the Zagros structural zone. The geological units in the Esfordi area belong to the pre-Cambrian to lower-Cambrian age, consisting of a succession of carbonate rocks (dolomite), shale, tuff, sandstone, and volcanic rocks. In addition to the mentioned sedimentary and volcanic rocks, the granitoid mass of Bahabad, which is the largest intrusive mass in the region, has intruded into the eastern part of this series and has caused its metamorphism and alteration. After collecting the available data, various samples of Esfordi’s apatite were prepared, and their mineralogy and crystallography were investigated using laboratory methods such as petrographic microscopy, Raman spectroscopy, EDS (Energy Dispersive Spectroscopy), and Scanning Electron Microscopy (SEM). In non-destructive Raman spectroscopy, the molecular structure of apatite minerals was revealed in four distinct spectral ranges. Initially, the spectra of phosphate and aluminum bonds with O2HO, OH, were observed, followed by the identification of Cl, OH, Al, Na, Ca and hydroxyl units depending on the type of apatite mineral family. In SEM analysis, based on various shapes and different phases of apatites, their constituent major elements were identified through EDS, indicating that the samples from the Esfordi mining area exhibit a dense and coherent texture with smooth surfaces. Based on the elemental analysis results by EDS, the apatites in the Esfordi area are classified into the calcic apatite group.

Keywords: Petrology, apatite, Esfordi, EDS, SEM, Scanning Electron Microscopy, Raman spectroscopy.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

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Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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