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The subject matter of this paper is assessment of the suitability of a dynamic cone penetrometer for determination of the state of soil. The principle of operation of the dynamic cone penetrometer, similar to commonly used DPL penetrometers, is described in the paper. Next the results of investigation conducted in Poland using a new dynamic cone penetrometer are presented. A series of measurements were performed in real field conditions. An attempt was made to correlate the results obtained with the dynamic and static cone penetrometers (CPT) respectively. These correlations were then subjected to validation to obtain a preliminary evaluation of the suitability of the dynamic cone penetrometer for determining the state of soil.

Within the INMOP 3 research project, an attempt was made to solve a number of problems associated with the methodology of modelling travel in urban areas and the application of intermodal models. One of these is the ability to describe the behaviour of transport system users, when it comes to making decisions regarding the selection of means of transport and searching for relationships between travel describing factors and the decisions made in regard of means of transport choice.

The subject of this paper is analysis of the influence of horizontal forces estimated on the basis of Eurocode on the stability of an exemplary railway embankment located in the horizontal curve. The work begins with an overview of the methods for determining the earthworks stability. The methods are presented along with a reference to the recommendations contained in Eurocode 7. On the basis of the Eurocode, the loads acting on the analyzed embankment are presented together. In addition to the standard vertical interactions (from the rolling stock, the weight of the track structure and ground), the calculations also take into account horizontal forces caused by: wind forces on rolling stock, centrifugal forces and nosing force of the rolling stock as well as thermal stresses in the rails. Next, there are 15 load combinations calculated according to the Eurocode guidelines. At the end of the work the values of safety factors of the embankment obtained by shear strength reduction method are presented. The obtained results show a significant influence of horizontal forces calculated on the basis of the Eurocode on the stability of the railway embankment analyzed in the work.

The dynamic probing methods are commonly used for the subsoil identification. For example, the relative density/density index (ID) of cohesionless soils can be determined by using appropriate correlation relationships. The results obtained by various probing methods (DPL, DPH, DPM) may vary from one to another. Thus, the field tests were conducted in order to determine how important these discrepancies are. Each of the above mentioned methods were performed 10 times at one location. The effect of the influence of the penetrometer type on the relative density estimation results was determined. Based on the analysis, it can be concluded that the results obtained by the medium and heavy penetrometers are very close to each other. On the other hand, the discrepancies between the results obtained with the light penetrometer and the other two penetrometers are greater, both in terms of mean difference and scatter.

The insect gut, which plays a role in ion and water balance, has been shown to leak solutes in the cold. Cold stress can also activate insect immune systems, but it is unknown whether the leak of the gut microbiome is a possible immune trigger in the cold. We developed a novel feeding protocol to load the gut of locusts (Locusta migratoria) with fluorescent bacteria before exposing them to -2°C for up to 48 h. No bacteria were recovered from the hemolymph of cold-exposed locusts, regardless of exposure duration. To examine this further, we used an ex vivo gut sac preparation to re-test cold-induced fluorescent FITC-dextran leak across the gut and found no increased rate of leak. These results question not only the validity of FITC-dextran as a marker of paracellular barrier permeability in the gut, but also to what extent the insect gut becomes leaky in the cold., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2023. Published by The Company of Biologists Ltd.)

Covalent triazine-based frameworks have attracted much interest recently due to their high surface area and excellent thermal and electrochemical stabilities. This study shows that covalently immobilizing triazine-based structures on spherical carbon nanostructures results in the organization of micro- and mesopores in a three-dimensional manner. We selected the nitrile-functionalized pyrrolo[3,2-b]pyrrole unit to form triazine rings to construct a covalent organic framework. Combining spherical carbon nanostructures with the triazine framework produced a material with unique physicochemical properties, exhibiting the highest specific capacitance value of 638 F g -1 in aqueous acidic solutions. This phenomenon is attributed to many factors. The material exhibits a large surface area, a high content of micropores, a high content of graphitic N, and N-sites with basicity and semi-crystalline character. Thanks to the high structural organization and reproducibility, and remarkably high specific capacitance, these systems are promising materials for use in electrochemistry. For the first time, hybrid systems containing triazine-based frameworks and carbon nano-onions were used as electrodes for supercapacitors., (© 2023. The Author(s).)

Most naturally occurring nucleotides and nucleosides are N -glycosyl derivatives of β-d-ribose. These N -ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N -ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.

Metabolic gene clusters (MGCs) are groups of genes involved in a common biosynthetic pathway. They are frequently formed in dynamic chromosomal regions, which may lead to intraspecies variation and cause phenotypic diversity. We examined copy number variations (CNVs) in four Arabidopsis thaliana MGCs in over one thousand accessions with experimental and bioinformatic approaches. Tirucalladienol and marneral gene clusters showed little variation, and the latter was fixed in the population. Thalianol and especially arabidiol/baruol gene clusters displayed substantial diversity. The compact version of the thalianol gene cluster was predominant and more conserved than the noncontiguous version. In the arabidiol/baruol cluster, we found a large genomic insertion containing divergent duplicates of the CYP705A2 and BARS1 genes. The BARS1 paralog, which we named BARS 2, encoded a novel oxidosqualene synthase. The expression of the entire arabidiol/baruol gene cluster was altered in the accessions with the duplication. Moreover, they presented different root growth dynamics and were associated with warmer climates compared to the reference-like accessions. In the entire genome, paired genes encoding terpene synthases and cytochrome P450 oxidases were more variable than their nonpaired counterparts. Our study highlights the role of dynamically evolving MGCs in plant adaptation and phenotypic diversity., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Marszalek-Zenczak, Satyr, Wojciechowski, Zenczak, Sobieszczanska, Brzezinski, Iefimenko, Figlerowicz and Zmienko.)

Four new compounds, 5-hydroxy-2',6'-dimethoxyflavone ( 4 ), 5-hydroxy-2',3',6'-trimethoxyflavone ( 5 ), 5-dihydroxy-6-methoxyflavone ( 6 ), and 5,6'-dihydroxy-2',3'-dimethoxyflavone ( 7 ), and three known compounds, 1,3-diphenylpropane-1,3-dione ( 1 ), 5-hydroxyflavone ( 2 ), and 5-hydroxy-2'-methoxyflavone ( 3 ), were isolated from the aerial parts of Hottonia palustris . Their chemical structures were determined through the use of spectral, spectroscopic and crystallographic methods. The quantitative analysis of the compounds ( 1-7 ) and the zapotin ( ZAP ) in methanol ( HP1 ), petroleum ( HP6 ), and two chloroform extracts ( HP7 and HP8 ) were also determined using HPLC-PDA. The biological activity of these compounds and extracts on the oral squamous carcinoma cell (SCC-25) line was investigated by considering their cytotoxic effects using the MTT assay. Subsequently, the most active compounds and extracts were assessed for their effect on DNA biosynthesis. It was found that all tested samples during 48 h treatment of SCC-25 cells induced the DNA biosynthesis-inhibitory activity: compound 1 (IC 50 , 29.10 ± 1.45 µM), compound 7 (IC 50 , 40.60 ± 1.65 µM) and extracts ZAP (IC 50 , 20.33 ± 1.01 µM), HP6 (IC 50 , 14.90 ± 0.74 µg), HP7 (IC 50 , 16.70 ± 0.83 µg), and HP1 (IC 50 , 30.30 ± 1.15 µg). The data suggest that the novel polymethoxyflavones isolated from Hottonia palustris evoke potent DNA biosynthesis inhibitory activity that may be considered in further studies on experimental pharmacotherapy of oral squamous cell carcinoma.

Derivatives based on pyridine-2-6- and furan-2,5-dicarboxamide scaffolds reveal numerous chemical properties and biological activities. This fact makes them an exciting research topic in supramolecular and coordination chemistry and in discovering new pharmacologically-active compounds. This work aimed to obtain a series of symmetrical pyridine-2-6- and furan-2,5-dicarboxamides through a condensation reaction of the appropriate acyl chlorides and aromatic amides. Successful syntheses were confirmed with NMR spectroscopy. We solved their crystal structures for seven compounds; two pyridine and five furan derivatives. Based on our crystallographic studies, we were able to indicate supramolecular features of the crystals under investigation. Additionally, Hirshfeld surface analysis allowed us to calculate a distribution of intermolecular contacts in the dicarboxamide crystals.

Sutures are fibrous joints that occur between bone elements in vertebrate skulls, where they play a variety of roles including facilitating skull growth and function. In addition, a variety of studies examining sutures from diverse perspectives in many taxa have enabled the determination of anatomical homologs. Surprisingly, one important aspect of sutures-histology-remains unknown in the key model organism of the chicken. To fill this gap in our knowledge, we generated histological sections of six different cranial sutures across a range of developmental stages in embryonic chicken. Despite having a skull that is largely co-ossified or fused as an adult, we found that the types, components, and ontogeny of sutures in chicken skulls are very similar to sutures in other vertebrates. We did, however, find a new transient stage in the ontogeny of sutures between endochondral bone elements, in which one element has ossified and one was still cartilaginous. Moreover, to better understand the morphogenetic events at the onset of suture formation, we compared the developmental histology of six sutures with that of the space between the two ossification centers of the frontal-a location expected to be void of suture structures. We found that the mesenchymal cells in sutures condense and form a middle vascular layer. This was not found to be the case in the space between the two ossifications of the frontal, where instead only osteoid occurs., (© 2021 Anatomical Society.)

Curcumin (CUR) is a natural compound that exhibits anti-inflammatory, anti-bacterial, and other biological properties. However, its application as an effective drug is problematic due to its poor oral bioavailability, solubility in water, and poor absorption from the gastrointestinal tract. The aim of this work is to synthesize monocarbonyl analogs of CUR based on the 9-methyl-9-azabicyclo[3.2.1]nonan-3-one (pseudopelletierine, granatanone) scaffold to improve its bioavailability. Granatane is a homologue of tropane, whose structure is present in numerous naturally occurring alkaloids, e.g., l-cocaine and l-scopolamine. In this study, ten new pseudopelletierine-derived monocarbonyl analogs of CUR were successfully synthesized and characterized by spectral methods and X-ray crystallography. Additionally, in vitro test of the cytotoxicity and anti-inflammatory properties of the synthesized compounds were performed.

There is a growing appreciation that insect distribution and abundance are associated with the limits of thermal tolerance, but the physiology underlying thermal tolerance remains poorly understood. Many insects, like the migratory locust ( Locusta migratoria ), suffer a loss of ion and water balance leading to hyperkalaemia (high extracellular [K + ]) in the cold that indirectly causes cell death. Cells can die in several ways under stress, and how they die is of critical importance to identifying and understanding the nature of thermal adaptation. Whether apoptotic or necrotic cell death pathways are responsible for low-temperature injury is unclear. Here, we use a caspase-3 specific assay to indirectly quantify apoptotic cell death in three locust tissues (muscle, nerves and midgut) following prolonged chilling and recovery from an injury-inducing cold exposure. Furthermore, we obtain matching measurements of injury, extracellular [K + ] and muscle caspase-3 activity in individual locusts to gain further insight into the mechanistic nature of chilling injury. We found a significant increase in muscle caspase-3 activity, but no such increase was observed in either nervous or gut tissue from the same animals, suggesting that chill injury primarily relates to muscle cell death. Levels of chilling injury measured at the whole animal level, however, were strongly correlated with the degree of haemolymph hyperkalaemia, and not apoptosis. These results support the notion that cold-induced ion balance disruption triggers cell death but also that apoptosis is not the main form of cell damage driving low-temperature injury.

S -adenosyl-l-homocysteine hydrolase (SAHase) is a major regulator of cellular methylation reactions that occur in eukaryotic and prokaryotic organisms. SAHase activity is also a significant source of l-homocysteine and adenosine, two compounds involved in numerous vital, as well as pathological processes. Therefore, apart from cellular methylation, the enzyme may also influence other processes important for the physiology of particular organisms. Herein, presented is the structural characterization and comparison of SAHases of eukaryotic and prokaryotic origin, with an emphasis on the two principal domains of SAHase subunit based on the Rossmann motif. The first domain is involved in the binding of a substrate, e.g., S -adenosyl-l-homocysteine or adenosine and the second domain binds the NAD + cofactor. Despite their structural similarity, the molecular interactions between an adenosine-based ligand molecule and macromolecular environment are different in each domain. As a consequence, significant differences in the conformation of d-ribofuranose rings of nucleoside and nucleotide ligands, especially those attached to adenosine moiety, are observed. On the other hand, the chemical nature of adenine ring recognition, as well as an orientation of the adenine ring around the N -glycosidic bond are of high similarity for the ligands bound in the substrate- and cofactor-binding domains.

Chalcones, including dibenzoylmethane, are an important subgroup of natural polyphenolic compounds that exhibit a wide spectrum of pharmacological and industrial applications. Dibenzoylmethane was isolated from Hottonia palustris L. (Primulaceae). The compound was crystallized in two polymorphic forms: in monoclinic space group P2 1 /c and orthorhombic space group Pbca. Crystal structures of the polymorphs were solved and refined against diffraction data measured at 100 and 293 K. In both crystal structures, the chalcone occurs in its keto-enol tautomeric form with the hydroxyl H atom mutually bound by two oxygen atoms rather than covalently attached to a particular oxygen atom. To explain this phenomenon in more detail, density functional theory and quantum theory of atoms in molecules based quantum chemistry calculations were applied. Additionally, high-resolution experimental data of very high quality measured for the monoclinic and orthorhombic crystals at 100 K allowed the engagement of the quantum crystallography method, based on Hirshfeld atom refinement, to determine the position of each individual H atom. It is suggested that the presence of the particular tautomeric form of dibenzoylmethane with a centred H atom position results from the π-stacking interaction between the phenyl ring and the malondialdehyde quasi-ring causes delocalization of the electron density in the latter.

Chill-susceptible insects, like the migratory locust, often die when exposed to low temperatures from an accumulation of tissue damage that is unrelated to freezing (chilling injury). Chilling injury is often associated with a loss of ion balance across the gut epithelia. It has recently been suggested that this imbalance is at least partly caused by a cold-induced disruption of epithelial barrier function. Here, we aimed to test this hypothesis in the migratory locust ( Locusta ). First, chill tolerance was quantified by exposing locusts to -2°C and recording chill coma recovery time and survival 24 h post-cold exposure. Longer exposure times significantly increased recovery time and caused injury and death. Ion-selective microelectrodes were also used to test for a loss of ion balance in the cold. We found a significant increase of haemolymph K migratoria ). First, chill tolerance was quantified by exposing locusts to -2°C and recording chill coma recovery time and survival 24 h post-cold exposure. Longer exposure times significantly increased recovery time and caused injury and death. Ion-selective microelectrodes were also used to test for a loss of ion balance in the cold. We found a significant increase of haemolymph K + and decrease of haemolymph Na + concentration over time. Next, barrier failure along the gut was tested by monitoring the movement of an epithelial barrier marker (FITC-dextran) across the gut epithelia during exposure to -2°C. We found a significant increase in haemolymph FITC-dextran concentration over time in the cold when assayed in the mucosal to serosal direction. However, when tested in the serosal to mucosal direction, we saw minimal marker movement across the gut epithelia. This suggests that while cold-induced barrier disruption is present, it is apparently unidirectional. It is important to note that these data reveal only the phenomenon itself. The location of this leak as well as the underlying mechanisms remain unclear and require further investigation., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

Metallophthalocyanine (MPc) and carbon nano-onion (CNO) derivatives were synthesized and characterized by using ultraviolet-visible spectroscopy, infrared and Raman spectroscopy, scanning electron microscopy with energy-dispersive X-ray spectroscopy and X-ray powder diffraction. The unmodified CNOs and MPc-CNO derivatives were used as photocatalysts for rhodamine B (RhB) degradation under visible-light irradiation. The photocatalytic studies revealed that the MPc-CNO nanostructural materials simultaneously exhibited a high absorption capacity and an excellent visible-light-driven photocatalytic activity towards RhB. These nanostructures possess great potential for use as active photocatalysts for organic pollutant degradation., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Many insects enter coma upon exposure to anoxia, a feature routinely exploited by experimentalists to handle them. But the genetic and physiological bases of anoxic coma induction and recovery are only partially understood, as are the long-term consequences for the animal's performance. We examined three populations of Drosophila melanogaster (designated B) that have been inadvertently under selection for rapid recovery from CO 2 exposure for nearly 40 years (around 1000 generations) resulting from routine maintenance practices. We contrasted CO 2 and N 2 (presumed a less reactive gas) knockdown and recovery times of these B flies with six populations of common ancestry (A and C populations) that were not exposed to CO 2 over the same period. We found that B populations showed faster and more consistent locomotor recovery than A or C populations after CO 2 knockdown, a result also observed with N 2 knockdown. A and C populations showed much higher variance in recovery time after CO 2 exposure than after N 2 exposure, suggesting gas-specific effects on pathways associated with locomotor recovery. Although these selection treatments result in considerable variation in life history attributes and body size, with the characteristic intermediacy of B populations, their superiority in resistance to gas exposure and locomotor recovery suggests that this is a direct consequence of prior repeated exposure to anoxia, broadly, and CO 2 , specifically. Hence we describe a powerful new evolutionary model for the genetic and physiological investigation of anoxic coma in insects., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa (PaSAHase) coordinates one K + ion and one Zn 2+ ion in the substrate binding area. The cations affect the enzymatic activity and substrate binding but the molecular mechanisms of their action are unknown. Enzymatic and isothermal titration calorimetry studies demonstrated that the K + ions stimulate the highest activity and strongest ligand binding in comparison to other alkali cations, while the Zn 2+ ions inhibit the enzyme activity. PaSAHase was crystallized in the presence of adenine nucleosides and K + or Rb + ions. The crystal structures show that the alkali ion is coordinated in close proximity of the purine ring and a 23 Na NMR study showed that the monovalent cation coordination site is formed upon ligand binding. The cation, bound in the area of a molecular hinge, orders and accurately positions the amide group of Q65 residue to allow its interaction with the ligand. Moreover, binding of potassium is required to enable unique dynamic properties of the enzyme that ensure its maximum catalytic activity. The Zn 2+ ion is bound in the area of a molecular gate that regulates access to the active site. Zn 2+ coordination switches the gate to a shut state and arrests the enzyme in its closed, inactive conformation.

Histidine-containing phosphotransfer proteins (HPts) take part in hormone signal transduction in higher plants. The overall pathway of this process is reminiscent of the two-component system initially identified in prokaryotes. HPts function in histidine-aspartate phosphorelays in which they mediate the signal from sensory kinases (usually membrane proteins) to RRs in the nucleus. Here, we report the crystal structure of an HPt protein from Medicago truncatula (MtHPt1) determined at 1.45 Å resolution and refined to an R-factor of 16.7% using low-temperature synchrotron-radiation X-ray diffraction data. There is one MtHPt1 molecule in the asymmetric unit of the crystal lattice with P2(1)2(1)2(1) symmetry. The protein fold consists of six α helices, four of which form a C-terminal helix bundle. The coiled-coil structure of the bundle is stabilized by a network of S-aromatic interactions involving highly conserved sulfur-containing residues. The structure reveals a solvent-exposed side chain of His79, which is the phosphorylation site, as demonstrated by autoradiography combined with site-directed mutation. It is surrounded by highly conserved residues present in all plant HPts. These residues form a putative docking interface for either the receiver domain of the sensory kinase, or for the RR. The biological activity of MtHPt1 was tested by autoradiography. It demonstrated phosphorylation by the intracellular kinase domain of the cytokinin receptor MtCRE1. Complex formation between MtHPt1 and the intracellular fragment of MtCRE1 was confirmed by thermophoresis, with a dissociation constant K(d) of 14 μM., (© 2013 FEBS.)

There are two tetra-ethyl-ammonium cations and two toluene-4-sulfate anions in the asymmetric unit of the title salt, C8H20N(+)·C7H7O3S(-). One of the anions is disordered over two positions, with refined occupancies of 0.447 (3) and 0.553 (3). In the crystal, the cations and anions are linked by C-H⋯O hydrogen bonds, forming ribbons along [10-1]. The ribbons are linked via C-H⋯O hydrogen bonds, forming a two-dimensional network lying parallel to (10-1).

The title compounds, C21H22BrNO2, are isomeric 8-benzyl-2-[(4-bromophenyl)(hydroxy)methyl]-8-azabicyclo[3.2.1]octan-3-ones. Compound (I), the (±)-exo,syn-(1RS,2SR,5SR,9SR) isomer, crystallizes in the hexagonal space group R-3, while compounds (II) [the (+)-exo,anti-(1R,2S,5S,9R) isomer] and (III) [the (±)-exo,anti-(1RS,2SR,5SR,9RS) isomer] crystallize in the orthorhombic space groups P212121 and Pna21, respectively. The absolute configuration was determined for enantiomerically pure (II). For the noncentrosymmetric crystal of (III), its absolute structure was established. In the crystal structures of (I) and (II), an intramolecular hydrogen bond is formed between the hydroxy group and the heterocyclic N atom. In the crystal structure of racemic (III), hydrogen-bonded chains of molecules are formed via intermolecular O-H...O interactions. Additionally, face-to-edge π-π interactions are present in the crystal structures of (I) and (II). In all three structures, the piperidinone rings adopt chair conformations and the N-benzyl substituents occupy the equatorial positions.

The asymmetric unit of the title compound, [Ru(C12H8N2)3](ClO4)2, contains one octahedrally coordinated Ru(II) cation of the ruthenium-phenanthroline complex and three differently occupied perchlorate anions: two, denoted A and B, are located on the twofold axis while another, denoted C, is positioned in the proximity of the twofold screw axis. Perchlorate anions B and C are severely disordered. The occupancies of the two major conformers of anion B refined to 0.302 (6) and 0.198 (6). Perchlorate ion C was modeled in two alternate conformations which refined to occupancies of 0.552 (10) and 0.448 (10).

The asymmetric unit of the title compound, [Ru(C(15)H(11)N(3))(2)](ClO(4))(2)·0.5H(2)O, contains one ruthenium-terpiridine complex cation, two perchlorate anions and one half-mol-ecule of water. Face-to-face and face-to-edge π-stacking inter-actions between terpyridine units [centroid-centroid distances = 3.793 (2) and 3.801 (2)  Å] stabilize the crystal lattice The partially occupied water mol-ecule inter-acts with two perchlorate ions via O-H⋯O hydrogen bonds. In the crystal lattice, the complex cations, perchlorate ion-water pairs and the second perchlorate anions are arranged into columns along b direction.

In the crystal structure of the racemic title compound, C(22)H(25)NO(2), solved and refined against sychrotron diffraction data, the hy-droxy group and the carbonyl O atom participate in the formation of O-H⋯O hydrogen bonds between pairs of enanti-omers related by a crystallographic centre of symmetry.

The crystal of the title compound, C(21)H(23)NO(2), was chosen from a conglomerate formed by a racemic mixture. An intra-molecular hydrogen bond is formed between hy-droxy group and heterocyclic N atom of the aza-bicyclo-[3.2.1]octan-3-one system. The crystal structure is stabilized by C-H⋯O inter-actions between aliphatic C-H groups and the carbonyl O atom. For the title chiral crystal, the highly redundant and accurate diffraction data set collected with low energy copper radiation gave a Flack parameter of 0.12 (18) for anomalous scattering effects originating from O atoms.

The crystal structure of the title compound, C(14)H(17)NO(2), solved and refined against synchrotron diffraction data, contains one formula unit in an asymmetric unit. In the crystal, mol-ecules form right-handed helices located at the 2(1) screw axis parallel to the a-axis direction, generated by O-H⋯N hydrogen bonding between the hy-droxy group and carbonitrile group of an adjacent mol-ecule.

The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

The crystal structure of the title compound, C(28)H(38)O(11), solved and refined against synchrotron diffraction data, contains two formula units in the asymmetric unit. In both mol-ecules, the dihydro-pyran ring along with its methyl substituents is disordered and adopts two alternative half-chair conformations. The occupancy of the major conformers of the two mol-ecules refined to 0.858 (5) and 0.523 (5).

The crystal structure of the title water-soluble analogue of vitamin E, trolox amide, C(14)H(19)NO(3), solved and refined against synchrotron diffraction data, contains two mol-ecules in the asymmetric unit. In both molecules, the heterocyclic ring is in a half-chair conformation. The crystal packing features a herring-bone pattern generated by N-H⋯O hydrogen bonds between the hy-droxy and amide groups. O-H⋯O hydrogen bonds also occur.

The crystal structure of the title compound, C(90)H(100)N(6)O(24)S(2)·C(4)H(8)O(2)·0.25C(6)H(14), solved and refined against synchrotron diffraction data, contains two formula units in the asymmetric unit with the all-trans n-hexane mol-ecule having half-occupancy and one of the ethyl acetate mol-ecules disordered over two positions. The two symmetry-independent disulfide mol-ecules are assembled by approximate face-to-face and face-to-edge inter-actions between their 4-nitro-benzo-yloxy groups into an inter-twined dimer having a double-helix-type structure. The centrally placed disulfide bridges in the two symmetry-independent mol-ecules exhibit different helicity as shown by the C-S-S-C torsion angles of 71.0 (1) and -92.5 (1)°.

By degrading S-adenosyl-L-homocysteine, which is a byproduct of S-adenosyl-L-methionine-dependent methylation reactions, S-adenosyl-L-homocysteine hydrolase (SAHase) acts as a regulator of cellular methylation processes. S-Adenosyl-L-homocysteine hydrolase from the leguminose plant yellow lupin (Lupinus luteus), LlSAHase, which is composed of 485 amino acids and has a molecular weight of 55 kDa, has been cloned, expressed in Escherichia coli and purified. Crystals of LlSAHase in complex with adenosine were obtained by the hanging-drop vapour-diffusion method using 20%(w/v) PEG 4000 and 10%(v/v) 2-propanol as precipitants in 0.1 M Tris-HCl buffer pH 8.0. The crystals were tetragonal, space group P4(3)2(1)2, with unit-cell parameters a = 122.4, c = 126.5 A and contained two protein molecules in the asymmetric unit, corresponding to the functional dimeric form of the enzyme. Atomic resolution (1.17 A) X-ray diffraction data have been collected using synchrotron radiation.

The fucosyltransferase NodZ is involved in the biosynthesis of the nodulation factor in nitrogen-fixing symbiotic bacteria. It catalyzes alpha1,6 transfer of l-fucose from GDP-fucose to the reducing residue of the synthesized Nod oligosaccharide. We present the structure of the NodZ protein from Bradyrhizobium expressed in Escherichia coli and crystallized in the presence of phosphate ions in two crystal forms. The enzyme is arranged into two domains of nearly equal size. Although NodZ falls in one broad class (GT-B) with other two-domain glycosyltransferases, the topology of its domains deviates from the canonical Rossmann fold, with particularly high distortions in the N-terminal domain. Mutational data combined with structural and sequence alignments indicate residues of potential importance in GDP-fucose binding or in the catalytic mechanism. They are all clustered in three conserved sequence motifs located in the C-terminal domain.

The crystal structure of Escherichia coli isoaspartyl aminopeptidase/asparaginase (EcAIII), an enzyme belonging to the N-terminal nucleophile (Ntn)-hydrolases family, has been determined at 1.9-A resolution for a complex obtained by cocrystallization with l-aspartate, which is a product of both enzymatic reactions catalyzed by EcAIII. The enzyme is a dimer of heterodimers, (alphabeta)(2). The (alphabeta) heterodimer, which arises by autoproteolytic cleavage of the immature protein, exhibits an alphabetabetaalpha-sandwich fold, typical for Ntn-hydrolases. The asymmetric unit contains one copy of the EcAIII.Asp complex, with clearly visible l-aspartate ligands, one bound in each of the two active sites of the enzyme. The l-aspartate ligand is located near Thr(179), the N-terminal residue of subunit beta liberated in the autoproteolytic event. Structural comparisons with the free form of EcAIII reveal that there are no major rearrangements of the active site upon aspartate binding. Although the ligand binding mode is similar to that observed in an l-aspartate complex of the related enzyme human aspartylglucosaminidase, the architecture of the EcAIII active site sheds light on the question of substrate specificity and explains why EcAIII is not able to hydrolyze glycosylated asparagine substrates.

We describe the expression, purification, and biochemical characterization of two homologous enzymes, with amidohydrolase activities, of plant (Lupinus luteus potassium-independent asparaginase, LlA) and bacterial (Escherichia coli, ybiK/spt/iaaA gene product, EcAIII) origin. Both enzymes were expressed in E. coli cells, with (LlA) or without (EcAIII) a His-tag sequence. The proteins were purified, yielding 6 or 30 mg.L(-1) of culture, respectively. The enzymes are heat-stable up to 60 degrees C and show both isoaspartyl dipeptidase and l-asparaginase activities. Kinetic parameters for both enzymatic reactions have been determined, showing that the isoaspartyl peptidase activity is the dominating one. Despite sequence similarity to aspartylglucosaminidases, no aspartylglucosaminidase activity could be detected. Phylogenetic analysis demonstrated the relationship of these proteins to other asparaginases and aspartylglucosaminidases and suggested their classification as N-terminal nucleophile hydrolases. This is consistent with the observed autocatalytic breakdown of the immature proteins into two subunits, with liberation of an N-terminal threonine as a potential catalytic residue.