Positron Binding and Annihilation Properties of Amino Acid Systems
Ontology highlight
ABSTRACT:
SUBMITTER: Ozaki M
PROVIDER: S-EPMC8581980 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:We report a 511-keV photon flux enhancement that was observed inside a thundercloud and is a result of positron annihilation. The observation was made with the In-flight Lightning Damage Assessment System (ILDAS) on board of an A340 test aircraft. The aircraft was intentionally flying through a thunderstorm at 12-km altitude over Northern Australia in January 2016. Two gamma ray detectors showed a significant count rate increase synchronously with fast electromagnetic field variations registered by an on-board antenna. A sequence of 10 gamma ray enhancements was detected, each lasted for about 1 s. Their spectrum mainly consists of 511-keV photons and their Compton component. The local electric activity during the emission was identified as a series of static discharges of the aircraft. A full-scale Geant4 model of the aircraft was created to estimate the emission area. Monte Carlo simulation indicated that the positrons annihilated in direct vicinity or in the aircraft body.
| S-EPMC6473548 | biostudies-literature
Project description:The paper presents the results of experimental studies on the impact of impulse shot peening parameters on surface roughness (Sa, Sz, Sp, Sv), surface layer microhardness, and the mean positron lifetime (τmean). In the study, samples made of the Inconel 718 nickel alloy were subjected to impulse shot peening on an originally designed stand. The variable factors of the experiment included the impact energy, the diameter of the peening element, and the number of impacts per unit area. The impulse shot peening resulted in changes in the surface structure and an increase in surface layer microhardness. After the application of impulse shot peening, the analyzed roughness parameters increased in relation to post-milling values. An increase in microhardness was obtained, i.e., from 27 HV 0.05 to 108 HV 0.05 at the surface, while the maximum increase the microhardness occur at the depth from 0.04 mm to 0.08 mm. The changes in the physical properties of the surface layer were accompanied by an increase in the mean positron lifetime τmean. This is probably related to the increased positron annihilation in point defects. In the case of small surface deformations, the increase in microhardness was accompanied by a much lower increase in τmean, which may indicate a different course of changes in the defect structure consisting mainly in modification of the dislocation system. The dependent variables were subjected to ANOVA analysis of variance (it was one-factor analysis), and the effect of independent variables was evaluated using post-hoc tests (Tukey test).
| S-EPMC8658380 | biostudies-literature
Project description:Nano-scale investigations of bainitic structures formed at temperatures below 350?°C have shown that the bainitic ferrite lattice is super-saturated in carbon. A high density of intrinsic defects would be playing a part in the carbon-supersaturation levels detected. In this work, the role of C-vacancy complexes on carbon-supersaturation in low temperature bainite is investigated by means of Positron Annihilation Spectroscopy. Results reveal the presence of a significant amount of monovacancies in the structures that plays an important role on the formation of carbon clusters in the ferrite lattice of nano-scale bainitic structures.
| S-EPMC6965194 | biostudies-literature
Project description:We present a novel route for the preparation of amino acid-derived cyclic imide dioxime derivatives. Readily accessible amino acids were conveniently converted to their corresponding cyclic imide dioximes in simple synthetic steps. The aim of this work was to describe and compare the iron-chelating and antioxidant properties of synthesized compounds in relation to their molecular structure, and in particular, which of those features are essential for iron(II)-chelating ability. The glutarimide dioxime moiety has been established as an iron(II)-binding motif and imparts potent anti-Fenton properties to the compounds. Compound 3 was shown to strongly suppress hydroxyl radical formation by preventing iron cycling via Fe-complexation. These findings provide insights into the structural requirements for achieving anti-Fenton activity and highlight the potential use of glutarimide dioximes as antioxidants.
| S-EPMC6826749 | biostudies-literature
Project description:That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.
| S-EPMC4072533 | biostudies-literature
Project description:We employ a positron annihilation technique, the spin-polarized two-dimensional angular correlation of annihilation radiation (2D-ACAR), to measure the spin-difference spectra of ferromagnetic nickel. The experimental data are compared with the theoretical results obtained within a combination of the local spin density approximation (LSDA) and the many-body dynamical mean-field theory (DMFT). We find that the self-energy defining the electronic correlations in Ni leads to anisotropic contributions to the momentum distribution. By direct comparison of the theoretical and experimental results we determine the strength of the local electronic interaction U in ferromagnetic Ni as 2.0 ± 0.1 eV.
| S-EPMC4754699 | biostudies-other
Project description:Auger processes involving the filling of holes in the valence band are thought to make important contributions to the low-energy photoelectron and secondary electron spectrum from many solids. However, measurements of the energy spectrum and the efficiency with which electrons are emitted in this process remain elusive due to a large unrelated background resulting from primary beam-induced secondary electrons. Here, we report the direct measurement of the energy spectra of electrons emitted from single layer graphene as a result of the decay of deep holes in the valence band. These measurements were made possible by eliminating competing backgrounds by employing low-energy positrons (<1.25?eV) to create valence-band holes by annihilation. Our experimental results, supported by theoretical calculations, indicate that between 80 and 100% of the deep valence-band holes in graphene are filled via an Auger transition.
| S-EPMC5511367 | biostudies-literature
Project description:Every protein has a biosynthetic cost to the cell based on the synthesis of its constituent amino acids. In order to optimise growth and reproduction, natural selection is expected, where possible, to favour the use of proteins whose constituents are cheaper to produce, as reduced biosynthetic cost may confer a fitness advantage to the organism. Quantifying the cost of amino acid biosynthesis presents challenges, since energetic requirements may change across different cellular and environmental conditions. We developed a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models and investigated the effects of the cost of amino acid synthesis on Saccharomyces cerevisiae gene expression and protein evolution. First, we used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify which of these factors best predict transcript and protein levels. Second, we compared amino acid cost with rates of amino acid substitution across four species in the genus Saccharomyces. Regardless of which cost measure is used, amino acid biosynthetic cost is weakly associated with transcript and protein levels. In contrast, we find that biosynthetic cost and amino acid substitution rates show a negative correlation, but for only a subset of cost measures. In the economy of the yeast cell, we find that the cost of amino acid synthesis plays a limited role in shaping transcript and protein expression levels compared to that of translational optimisation. Biosynthetic cost does, however, appear to affect rates of amino acid evolution in Saccharomyces, suggesting that expensive amino acids may only be used when they have specific structural or functional roles in protein sequences. However, as there appears to be no single currency to compute the cost of amino acid synthesis across all cellular and environmental conditions, we conclude that a systems approach is necessary to unravel the full effects of amino acid biosynthetic cost in complex biological systems.
| S-EPMC2923148 | biostudies-literature
Project description:The morphology of thin film composite (TFC) membranes used in reverse osmosis (RO) and nanofiltration (NF) water treatment was explored with small-angle neutron scattering (SANS) and positron-annihilation lifetime spectroscopy (PALS). The combination of both methods allowed the characterization of the bulk porous structure from a few Å to µm in radius. PALS shows pores of 4.5 Å average radius in a surface layer of about 4 m thickness, which become 40% smaller at the free surface of the membranes. This observation may correlate with the glass state of the involved polymer. Pores of similar size appear in SANS as closely packed pores of 6 Å radius distributed with an average distance of 30 Å. The main effort of SANS was the characterization of the morphology of the porous polysulfone support layer as well as the fibers of the nonwoven fabric layer. Contrast variation using the media H2O/D2O and supercritical CO2 and CD4 identified the polymers of the support layers as well as internal heterogeneities.
| S-EPMC7142468 | biostudies-literature
Project description:Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.
| S-EPMC7831508 | biostudies-literature