Crystallography Reports最新文献

Abstract

Nucleoid-associated proteins (NAPs) control the structure and functions of bacterial nucleoid. Histone-like HU proteins are most abundant NAPs in dividing bacterial cells. Previously, structural ensembles of conformations of HU proteins from pathogenic mycoplasmas Spiroplasma melliferum and Mycoplasma gallisepticum were obtained using NMR spectroscopy. A structural study of these mycoplasma proteins is performed by small-angle X-ray scattering (SAXS). The occurrence of individual conformations from the ensemble, obtained by NMR, is estimated from the scattering data on HU protein solutions. In particular, an approach based on characterization of equilibrium mixtures in terms of volume fractions of their components was applied. The general shape of the proteins and their oligomeric state are independently confirmed using ab initio bead modelling. The flexibility of DNA-binding protein domains is analyzed by the ensemble optimization method, which is based on comparison of the structural characteristics of conformations fitting the SAXS data to the distribution of these characteristics in a randomly generated set. The results obtained give a new insight on the variability of the structure of HU proteins, which is necessary for their functioning.

Abstract

The current epidemiological situation, including the existence of new SARS-CoV-2 virus with a high mutagenicity, requires fundamentally new deadlines for the development of vaccines, which may be achieved only applying modern computing technologies and simulation. Epitopes have been found in the spike protein of the SARS-CoV-2 virus using immunoinformatics methods, and their allergenicity and immunogenecity was predicted. It is shown that a vaccine against SARS-CoV-2 can be designed based on these epitopes.

Abstract

During determination of the thiocyanate dehydrogenase (TcDH) structure difficulties have occurred, related to the fact that enzyme crystals have been either twinned or strongly anisotropic. The diffraction quality of crystals can be improved by using mutant forms as objects of a study or by studying the structure of a related enzyme from another organism. Based on the analysis of the oligomeric structure of TcDH, the mutant forms of the enzyme that are promising for improving the diffraction properties have been proposed. The crystals have been obtained and the structures of the TcDH mutant forms with the substitutions T169A and K281A have been solved. The structure of the mutant form with the substitution T169A is found to be similar to the previously solved structures. In the structure of the mutant form with the substitution K281A, a change in the tetramer structure that made twinning impossible has been detected.

Abstract

The genome of African swine fever (ASF) has been analyzed, and a protein that can serve an immunogen has been identified. A water-soluble fragment of this protein is shown (by the molecular dynamics) to be stable in an aqueous saline solution. Immunomodeling has shown that this fragment causes a cellular response and, therefore, may serve a vaccine prototype.

Abstract

Influenza A virus pandemics still remain a threat to global health. One class of antiviral drugs, namely, inhibitors of the specific viral enzyme neuraminidase, is predominantly used in the fight against these pandemics. These antivirals include zanamivir (Relenza™) and oseltamivir (Tamiflu™). The viral resistance to this class of compounds steadily increases. The M2 proton channel of influenza A virus is an alternative clinically proven target for antiviral therapy. However, many circulating virus strains bear amino acid mutations in the M2 protein, causing resistance to drugs of the adamantane series, M2 blockers, such as rimantadine and amantadine. Consequently, inhibitors targeting mutants of the M2 channel are urgently needed for public biosafety and health. This review is devoted to structural-functional interactions used in practice and mediated by the action of experimental drugs on the protein target, the transmembrane domain of the influenza virus M2 proton channel. An analysis of the experimental and model structural data available in open access is presented.

Abstract

Prions form an infectious version of amyloid; they are involved in the pathogenesis of some human neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases. Yeast prions, in particular, the Sup35 protein, serve an effective model for studying the basic properties of amyloids. Strain versions of the prion form of Sup35 lie in the basis of the conformational diversity of the amyloid structures formed by it, which exhibit different biological properties. The spatial organization of the Sup35 prion has not yet been established. The structure of the strain version W of Sup35 prion protein, isolated ex vivo from yeast Saccharomyces cerevisiae, was studied by transmission electron microscopy (TEM). The parameters of the fibril were estimated, and its structure was reconstructed with a low resolution.

Abstract

The molecular mechanisms of the interaction of anticancer antibiotic doxorubicin with lipid cell membrane models have been investigated using grazing incidence X-ray diffraction (XRD) and X-ray reflectivity (XRR). The model systems were monolayers of four types of phospholipids, related to the main components of animal cell membranes. New information on the processes of damage of phospholipid monolayer lattice caused by doxorubicin is obtained. It is established that the action of doxorubicin on anionic phospholipid monolayers is determined by the electrostatic interaction: positively charged doxorubicin molecules are incorporated between negatively charged phospholipid functional groups. In the case of neutral phospholipids the key role belongs to the hydrophobic interaction: doxorubicin molecules are coordinated with phospholipid hydrocarbon tails in disordered regions.

Abstract

The calcium-carbonate-induced mineralization of multilayer shells of emulsion capsules, formed using layer-by-layer assembly of polyelectrolytes, has been investigated. Optimal conditions for forming microcapsules with a core from shea butter and an organic–inorganic shell from synthetic polyelectrolytes and calcium carbonate are found. The shell morphology and stability of capsules in an aqueous suspension upon heating are investigated, and their cytotoxicity for human fibroblast cells is estimated. It is shown that mineralization of emulsion polyelectrolyte capsules by calcium carbonate in the form of vaterite strengthens the capsule walls and increases their biocompatibility.

The room-temperature X-ray and Mössbauer data on the BiFeO₃, Bi_0.95Sr_0.05FeO_{3 – y}, and Bi_0.90Sr_0.10FeO_{3 – y} multiferroics obtained by solid-phase synthesis are presented. The samples have a rhombohedral crystal structure with the sp. gr. R3c. The lattice parameter a_h is invariable, while the parameter c_h decreases with increasing strontium content. The ⁵⁷Fe Mössbauer spectra recorded at a temperature of 295 K have been interpreted within the cycloid spatial spin-modulated structure model. It has been established that the easy-axis magnetic anisotropy is implemented in the investigated multiferroics. The anharmonicity parameter m of the spin-modulated structure has been measured. Upon replacement of trivalent Bi³⁺ ions in small amounts (x = 0–0.10) with divalent Sr²⁺ ions, the parameter m increases by a factor of more than 3: from 0.10(4) at x = 0.00 to 0.36(10) at x = 0.10.

The phonon dispersion and Raman spectrum of the PbMnBO₄ ferromagnetic crystal have been calculated within the density functional theory. Imaginary phonon branches have been observed at the points Y, Z, and Г and along the X–S direction of the Brillouin zone, which indicates structural instability and a possible phase transition with variation in external factors (temperature and pressure). The shapes of vibrations and symmetry types of the normal modes of the crystal at the center of the Brillouin zone have been determined. The calculation results are compared with the experimental and theoretical spectra from other studies. It is shown that the vibrational mode of highest intensity at 692.5 cm^–1 in the spectrum and the mode at 272.3 cm^–1, corresponding to the experimental modes at 690.5 and 224.7 cm^–1, are bending vibrations of oxygen atoms in distorted MnO₆ octahedra.