The features of the spatial structure of the gramicidine A-cesium complex

AbstractEarlier obtained two-dimensional 1H-NMR spectroscopy data were used to analyze the spatial structure and conformational mobility of the double right ↑↓ ππLD7.2 helix of the complex formed by gramicidine A and Cs+ ions in an organic solvent (a chloroform-methanol mixture). Analysis of the experimental data permitted the determination of a set of conformations for each of the high-mobility residue side chains in the solution. The energy refinement of the most probable conformation of the double right ↑↓ ππLD7.2 helix was made and conformational rearrangements of the tryptophan residue side chain were studied in detail

Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization

Background: Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units. Methods: We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues—“information unit”. The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences. Results: The developed mathematical apparatus gives stable results on the structural unit description even with a significant variation in the parameters. The optimal length of the information unit is five, and the number of allowed substitutions is one. Examples of the application of the method for the design of protein molecules, intermolecular interactions analysis, and the study of the mechanisms of functioning of protein molecular machines are given. Conclusions: ANIS method makes it possible not only to analyze native proteins but also to design artificial polypeptide chains with a given spatial organization and, possibly, function

Effect of High-Pressure Torsion on Phase Formation and Mechanical Properties of a High-Entropy TiZrHfMoCrCo Alloy

This research was funded by the Russian Ministry of Science and Higher Education (contract no. 075-15-2021-945; grant no. 13.2251.21.0013). We acknowledge DESY (Hamburg, Germany), a member of the Helmholtz Association HGF, for the provision of experimental facilities. Parts of this research were carried out at the PETRA III P65 beamline.This investigation delved into the alterations in the mechanical properties of a TiZrHfMoCrCo high-entropy alloy due to phase transformations induced by high-pressure torsion (HPT). The alloy’s genesis involved levitation melting within an argon atmosphere, presenting two distinct states for analysis: the initial, post-manufacturing state and the state subsequent to HPT treatment. The original alloy featured a composition comprising a singular A2 phase with a bcc lattice and two Laves phases, C15 and C14. The HPT process triggered significant phase modifications: a retention of one C15 Laves phase and decomposition of the bcc phase into two distinct phases exhibiting different bcc lattice parameters. The HPT-induced effect prominently manifests as strong grain refinement. However, scanning electron microscopy (SEM) observations unveiled persistent inhomogeneities at a micron scale both before and after HPT treatment. Thus, grain refinement occurs separately within each of the bcc and Laves phases, visible in the light, dark, and gray areas in SEM images, while mixing does not occur on the scale of several microns. The examination of Ti, Cr, Co, Zr, Mo, and Hf via X-ray absorption spectroscopy (EXAFS) at specific K-edges and L3-edge revealed that the HPT treatment conserves the local atomic environment of metal atoms, albeit with a slight elevation in static disorder. Assessments through microhardness and three-point bending tests demonstrated the material’s inherent hardness and brittleness. The microhardness, standing at a substantial value of 600 HV, displayed negligible augmentation post-HPT. However, the microhardness of individual phases exhibited a notable alteration, nearly doubling in magnitude. © 2023 by the authors. --//-- This is an open-access article: Gornakova, A.S.; Kabirova, D.B.; Korneva, A.; Straumal, B.; Imayev, M.F.; Kuzmin, A.; Czaja, P.; Afonikova, N.S.; Orlov, V.I.; Nekrasov, A.N.; et al. Effect of High-Pressure Torsion on Phase Formation and Mechanical Properties of a High-Entropy TiZrHfMoCrCo Alloy. Materials 2023, 16, 7558. https://doi.org/10.3390/ma16247558 published under the CC BY 4.0 licence.Russian Ministry of Science and Higher Education (contract no. 075-15-2021-945; grant no. 13.2251.21.0013); The Institute of Solid State Physics, University of Latvia at the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART2

Entropy Analysis of Protein Sequences Reveals a Hierarchical Organization

Background: Analyzing the local sequence content in proteins, earlier we found that amino acid residue frequencies differ on various distances between amino acid positions in the sequence, assuming the existence of structural units. Methods: We used informational entropy of protein sequences to find that the structural unit of proteins is a block of adjacent amino acid residues—“information unit”. The ANIS (ANalysis of Informational Structure) method uses these information units for revealing hierarchically organized Elements of the Information Structure (ELIS) in amino acid sequences. Results: The developed mathematical apparatus gives stable results on the structural unit description even with a significant variation in the parameters. The optimal length of the information unit is five, and the number of allowed substitutions is one. Examples of the application of the method for the design of protein molecules, intermolecular interactions analysis, and the study of the mechanisms of functioning of protein molecular machines are given. Conclusions: ANIS method makes it possible not only to analyze native proteins but also to design artificial polypeptide chains with a given spatial organization and, possibly, function

Topology of WC/Co Interfaces in Cemented Carbides

WC–Co cemented carbides build one of the important classes of metal matrix composites. We show in this paper that the use of machine vision methods makes it possible to obtain sufficiently informative statistical data on the topology of the interfaces between tungsten carbide grains (WC) and a cobalt matrix (Co). For the first time, the outlines of the regions of the cobalt binder were chosen as a tool for describing the structure of cemented carbides. Numerical processing of micrographs of cross sections of three WC–Co alloys, which differ in the average grain size, was carried out. The distribution density of the angles in the contours of cobalt “lakes” is bimodal. The peaks close to 110° (so-called outcoming angles) correspond to the contacts between the cobalt binder and the WC/WC grain boundaries. The peaks close to 240° (or incoming angles) correspond to the WC “capes” contacting the cobalt “lakes” and are determined by the angles between facets of WC crystallites. The distribution density of the linear dimensions of the regions of the cobalt binder, approximated with ellipses, were also obtained. The distribution density exponentially decreases with the lengths of the semi-axes of the ellipsoid, approximating the area of the cobalt binder. The possible connection between the obtained data on the shape of cobalt areas and the crack trajectories in cemented carbides is discussed

Amino Acid Substitutions in the Non-Ordered Ω-Loop 70–85 Affect Electron Transfer Function and Secondary Structure of Mitochondrial Cytochrome c

The secondary structure of horse cytochrome c with mutations in the P76GTKMIFA83 site of the Ω-loop, exhibiting reduced efficiency of electron transfer, were studied. CD spectroscopy studies showed that the ordering of mutant structure increases by 3–6% compared to that of the WT molecules due to the higher content of β-structural elements. The IR spectroscopy data are consistent with the CD results and demonstrate that some α-helical elements change into β-structures, and the amount of the non-structured elements is decreased. The analysis of the 1H-NMR spectra demonstrated that cytochrome c mutants have a well-determined secondary structure with some specific features related to changes in the heme microenvironment. The observed changes in the structure of cytochrome c mutants are likely to be responsible for the decrease in the conformational mobility of the P76GTKMIFA83 sequence carrying mutations and for the decline in succinate:cytochrome c-reductase and cytochrome c-oxidase activities in the mitoplast system in the presence of these cytochromes c. We suggest that the decreased efficiency of the electron transfer of the studied cytochromes c may arise due to: (1) the change in the protein conformation in sites responsible for the interaction of cytochrome c with complexes III and IV and (2) the change in the heme conformation that deteriorates its optimal orientation towards donor and acceptor in complexes III and IV therefore slows down electron transfer. The results obtained are consistent with the previously proposed model of mitochondrial cytochrome c functioning associated with the deterministic mobility of protein globule parts