Search Results (7)

CrystalShift is an open-source computational tool tailored for the analysis, transformation, and conversion of crystallographic data, with a particular emphasis on organic crystal structures. It offers a comprehensive suite of features valuable for the computational study of solids: format conversion, crystallographic basis transformation, atomic coordinate editing, and molecular layer analysis. These options are especially valuable for studying the mechanical properties of molecular crystals with potential applications in organic materials science. Written in the C programming language, CrystalShift offers computational efficiency and compatibility with widely used crystallographic formats such as CIF, POSCAR, and XYZ. It provides a command-line interface, enabling seamless integration into research workflows while addressing specific challenges in crystallography, such as handling non-standard file formats and robust error correction. CrystalShift may be applied for both in-depth study of particular crystal structure origins and the high-throughput conversion of crystallographic datasets prior to DFT calculations with periodic boundary conditions using VASP code. Full article

Benzodiazepines are frequently encountered in crime scenes, often mixed with adulterants and diluents, complicating their analysis. This study investigates the interactions between two benzodiazepines, lorazepam (LOR) and alprazolam (ALP), with common adulterants/diluents (paracetamol, caffeine, glucose, and lactose) using infrared (IR) spectroscopy and quantum chemical methods. The crystallographic structures of LOR and ALP were optimized using several functionals (B3LYP, B3LYP-D3BJ, B3PW91, CAM-B3LYP, M05-2X, and M06-2X) combined with the 6-311++G(d,p) basis set. M05-2X was the most accurate when comparing experimental and theoretical bond lengths and angles. Vibrational and ¹³C NMR spectra were calculated to validate the functional’s applicability. The differences between LOR’s experimental and theoretical IR spectra were attributed to intramolecular interactions between LOR monomers, examined through density functional theory (DFT) optimization and quantum theory of atoms in molecules (QTAIM) analysis. Molecular dynamics simulations modeled benzodiazepine–adulterant/diluent systems, predicting the most stable structures, which were further analyzed using QTAIM. The strongest interactions and their effects on IR spectra were identified. Comparisons between experimental and theoretical spectra confirmed spectral changes due to interactions. This study demonstrates the potential of quantum chemical methods in analyzing complex mixtures, elucidating spectral changes, and assessing the structural stability of benzodiazepines in forensic samples. Full article

Titanium alloys are characterized by insufficient ductility. One of the parameters affecting their ductility is their crystal structure and texture. The present study characterizes the changes in the crystallographic texture of the Ti-3Al-8V-6Cr-4Zr-4Mo alloy in solution-treated and aged conditions on the basis of texture intensity indices and pole figures. Analysis of crystal structure changes was performed before and after tensile testing. The investigated alloy in the solution-treated condition showed a single-phase β-solution structure with a body-centered cubic (BCC) crystal structure. The process of β phase aging affected the result of the tensile test, affecting the parameters of the texture of the β phase. The analysis of the texture intensity indices for each set of planes (hkl) related to the intensity for the plane (110) indicated that the highest texture intensity occurs for β titanium alloy aged at 550 °C both before and after tensile test. After plastic deformation, the largest difference with respect to the benchmark value was observed for the (220) and (310) planes. The least amount of texture intensity occurred after aging at 450 °C. The most varied values of diffraction peak intensity in relation to the benchmark were obtained for the alloy aged at 450 °C for the (310), and (200) and (211) planes, indicating the dominance of the (211) orientation, where an elongation of 10.4% was achieved. For the highest elongation of 14.2%, achieved for the sample solution-treated at 550 °C, the diffraction peak intensities were intermediate with the dominance of peaks from the planes (200) and (310). Full article

Sarcoendoplasmic reticulum calcium ATPase (SERCA), a member of the P-type ATPase family of ion and lipid pumps, is responsible for the active transport of Ca²⁺ from the cytoplasm into the sarcoplasmic reticulum lumen of muscle cells, into the endoplasmic reticulum (ER) of non-muscle cells. X-ray crystallography has proven to be an invaluable tool in understanding the structural changes of SERCA, and more than 70 SERCA crystal structures representing major biochemical states (defined by bound ligand) have been deposited in the Protein Data Bank. Consequently, SERCA is one of the best characterized components of the calcium transport machinery in the cell. Emerging approaches in the field, including spectroscopy and molecular simulation, now help integrate and interpret this rich structural information to understand the conformational transitions of SERCA that occur during activation, inhibition, and regulation. In this review, we provide an overview of the crystal structures of SERCA, focusing on identifying metrics that facilitate structure-based categorization of major steps along the catalytic cycle. We examine the integration of crystallographic data with different biophysical approaches and computational methods to link biochemical and structural states of SERCA that are populated in the cell. Finally, we discuss the challenges and new opportunities in the field, including structural elucidation of functionally important and novel regulatory complexes of SERCA, understanding the structural basis of functional divergence among homologous SERCA regulators, and bridging the gap between basic and translational research directed toward therapeutic modulation of SERCA. Full article

Biosynthesis of branched-chain amino acids (BCAAs), including isoleucine, leucine and valine, is required for survival and virulence of a bacterial pathogen such as Streptococcus pneumoniae. IlvC, a ketol-acid reductoisomerase (E.C. 1.1.1.86) with NADP(H) and Mg²⁺ as cofactors from the pathogenic Streptococcus pneumoniae (SpIlvC), catalyzes the second step in the BCAA biosynthetic pathway. To elucidate the structural basis for the IlvC-mediated reaction, we determined the crystal structure of SpIlvC at 1.69 Å resolution. The crystal structure of SpIlvC contains an asymmetric dimer in which one subunit is in apo-form and the other in NADP(H) and Mg²⁺-bound form. Crystallographic analysis combined with an activity assay and small-angle X-ray scattering suggested that SpIlvC retains dimeric arrangement in solution and that D83 in the NADP(H) binding site and E195 in the Mg²⁺ binding site are the most critical in the catalytic activity of SpIlvC. Crystal structures of SpIlvC mutants (R49E, D83G, D191G and E195S) revealed local conformational changes only in the NADP(H) binding site. Taken together, our results establish the molecular mechanism for understanding functions of SpIlvC in pneumococcal growth and virulence. Full article

The products made by the forming of polycrystalline metals and alloys, which are in high demand in modern industries, have pronounced inhomogeneous distribution of grain orientations. The presence of specific orientation modes in such materials, i.e., crystallographic texture, is responsible for anisotropy of their physical and mechanical properties, e.g., elasticity. A type of anisotropy is usually unknown a priori, and possible ways of its determination is of considerable interest both from theoretical and practical viewpoints. In this work, emphasis is placed on the identification of elasticity classes of polycrystalline materials. By the newly introduced concept of “elasticity class” the union of congruent tensor subspaces of a special form is understood. In particular, it makes it possible to consider the so-called symmetry classification, which is widely spread in solid mechanics. The problem of identification of linear elasticity class for anisotropic material with elastic moduli given in an arbitrary orthonormal basis is formulated. To solve this problem, a general procedure based on constructing the hierarchy of approximations of elasticity tensor in different classes is formulated. This approach is then applied to analyze changes in the elastic symmetry of a representative volume element of polycrystalline copper during numerical experiments on severe plastic deformation. The microstructure evolution is described using a two-level crystal elasto-visco-plasticity model. The well-defined structures, which are indicative of the existence of essentially inhomogeneous distribution of crystallite orientations, were obtained in each experiment. However, the texture obtained in the quasi-axial upsetting experiment demonstrates the absence of significant macroscopic elastic anisotropy. Using the identification framework, it has been shown that the elasticity tensor corresponding to the resultant microstructure proves to be almost isotropic. Full article

The OB-fold is a diverse structure superfamily based on a β-barrel motif that is often supplemented with additional non-conserved secondary structures. Previous deletion mutagenesis and NMR hydrogen exchange studies of three OB-fold proteins showed that the structural stabilities of sites within the conserved β-barrels were larger than sites in non-conserved segments. In this work we examined a database of 80 representative domain structures currently classified as OB-folds, to establish the basis of this effect. Residue-specific values were obtained for the number of Cα-Cα distance contacts, sequence hydrophobicities, crystallographic B-factors, and theoretical B-factors calculated from a Gaussian Network Model. All four parameters point to a larger average flexibility for the non-conserved structures compared to the conserved β-barrels. The theoretical B-factors and contact densities show the highest sensitivity.Our results suggest a model of protein structure evolution in which novel structural features develop at the periphery of conserved motifs. Core residues are more resistant to structural changes during evolution since their substitution would disrupt a larger number of interactions. Similar factors are likely to account for the differences in stability to unfolding between conserved and non-conserved structures. Full article