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8,057 result(s) for "Structure determination"
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Monetary policy and bank profitability in a low interest rate environment
We analyse the impact of standard and non-standard monetary policy on bank profitability. We use both proprietary and commercial data on individual euro area bank balance-sheets and market prices. Our results show that a monetary policy easing – a decrease in short-term interest rates and/or a flattening of the yield curve – is not associated with lower bank profits once we control for the endogeneity of the policy measures to expected macroeconomic and financial conditions. Accommodative monetary conditions asymmetrically affect the main components of bank profitability, with a positive impact on loan loss provisions and non-interest income offsetting the negative one on net interest income. A protracted period of low monetary rates has a negative effect on profits that, however, only materialises after a long time period and is counterbalanced by improved macroeconomic conditions. Monetary policy easing surprises during the low interest rate period improve bank stock prices and CDS.
Entrapped Transient Chloroform Solvates of Bilastine
The knowledge about the solid forms landscape of Bilastine (BL) has been extended. The crystal structures of two anhydrous forms have been determined, and the relative thermodynamic stability among the three known anhydrous polymorphs has been established. Moreover, three chloroform solvates with variable stoichiometry have been identified and characterized, showing that S3CHCl3-H2O and SCHCl3 can be classified as transient solvates which transform into the new chloroform solvate SCHCl3-H2O when removed from the mother liquor. The determination of their crystal structures from combined single crystal/synchrotron X-ray powder diffraction data has allowed the complete characterization of these solvates, being two of them heterosolvates (S3CHCl3-H2O and SCHCl3-H2O) and SCHCl3 a monosolvate. Moreover, the temperature dependent stability and interrelation pathways among the chloroform solvates and the anhydrous forms of BL have been studied.
Bioactive Compounds from the Mushroom-Forming Fungus Chlorophyllum molybdites
A novel compound (1) along with two known compounds (2 and 3) were isolated from the culture broth of Chlorophyllum molybdites, and three known compounds (4–6) were isolated from its fruiting bodies. The planar structure of 1 was determined by the interpretation of spectroscopic data. By comparing the specific rotation of the compound with that of the analog compound, the absolute configuration of 1 was determined to be R. This is the first time that compounds 2–4 were isolated from a mushroom-forming fungus. Compound 2 showed significant inhibition activity against Axl and immune checkpoints (PD-L1, PD-L2). In the bioassay to examine growth inhibitory activity against the phytopathogenic bacteria Peptobacterium carotovorum, Clavibacter michiganensis and Burkholderia glumae, compounds 2 and 3 inhibited the growth of P. carotovorum and C. michiganensis. In the bioassay to examine plant growth regulatory activity, compounds 1–4 showed a significant regulatory activity on lettuce growth.
Trioctahedral Fe-rich micas; relationships between magnetic behavior and crystal chemistry
Six Fe-bearing mica samples with different Fe ordering, Fe2+/(Fe2++Fe3+) ratio, octahedral, and tetrahedral composition were studied. Four micas belong to the phlogopite-annite join (space group C2/m), two are Mg-rich annite and two are Fe-rich phlogopite, one is a tetra-ferriphlogopite (space group C2/m) and one is Li-rich siderophyllite (space group C2). Thus these samples had a different environment around the Fe cations and layer symmetry. These micas were characterized by chemical analyses, single-crystal X-ray diffraction, X-ray absorption spectroscopy, and magnetic measurements. In samples with Fe mostly in octahedral coordination, dominant magnetic interactions among Fe atoms are ferromagnetic, which reach a maximum at higher Fe2+/(Fe2++Fe3+) ratios. Samples with higher Fe2+/(Fe2++Fe3+) ratio are also characterized by higher values of the Curie-Weiss θ constant. Where Fe2+/(Fe2++Fe3+) ratios decrease, θ values also decrease. The Fe3+-rich phlogopite shows predominant Fe3+ in tetrahedral coordination and shows anti-ferromagnetic interactions with a negative value of the Curie-Weiss θ constant (i.e., θ=-25 K). Fe ordering in octahedral trans- and in one of the two cis-sites accounts for a greater θ value in Li-rich siderophyllite when compared to other samples showing similar octahedral Fe content. Our data suggest that Fe3+ cations and other non-ferromagnetic cations hinder long range magnetic ordering. This observation may produce for the different role of octahedral Fe magnetic interactions that can in principle develop along long Fe-rich octahedral chains, when compared to tetrahedral-octahedral interactions that are confined within the layer by the non-ferromagnetic cations of the interlayer. Spin glass behavior is indicated by the dependency of the temperature to produce maxima in the susceptibility curve. These maxima are related to the frequency of the applied AC magnetic field.
Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy
Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides. Significance Circular dichroism (CD) spectroscopy is widely used for protein secondary structure analysis. However, quantitative estimation for β-sheet–containing proteins is problematic due to the huge morphological and spectral diversity of β-structures. We show that parallel/antiparallel orientation and twisting of β-sheets account for the observed spectral diversity. Taking into account the twist of β-structures, our method accurately estimates the secondary structure for a broad range of protein folds, particularly for β-sheet–rich proteins and amyloid fibrils. Moreover, the method can predict the protein fold down to the topology level following the CATH classification. We provide a general tool for a quick and reliable structure analysis using conventional or synchrotron radiation CD spectroscopy, which is especially useful when X-ray or NMR techniques fail.
Multifunctional graphene supports for electron cryomicroscopy
With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In practice, the primary barrier to structure determination is the preparation of a frozen specimen suitable for high-resolution imaging. To address this, we present a multifunctional specimen support for cryoEM, comprising large-crystal monolayer graphene suspended across the surface of an ultrastable gold specimen support. Using a low-energy plasma surface modification system, we tune the surface of this support to the specimen by patterning a range of covalent functionalizations across the graphene layer on a single grid. This support design reduces specimen movement during imaging, improves image quality, and allows high-resolution structure determination with a minimum of material and data.
Improved AlphaFold modeling with implicit experimental information
Machine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps. This paper presents an iterative procedure where AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions.
Expression system for structural and functional studies of human glycosylation enzymes
Vertebrate glycoproteins and glycolipids are synthesized in complex biosynthetic pathways localized predominantly within membrane compartments of the secretory pathway. The enzymes that catalyze these reactions are exquisitely specific, yet few have been extensively characterized because of challenges associated with their recombinant expression as functional products. We used a modular approach to create an expression vector library encoding all known human glycosyltransferases, glycoside hydrolases, and sulfotransferases, as well as other glycan-modifying enzymes. We then expressed the enzymes as secreted catalytic domain fusion proteins in mammalian and insect cell hosts, purified and characterized a subset of the enzymes, and determined the structure of one enzyme, the sialyltransferase ST6GalNAcII. Many enzymes were produced at high yields and at similar levels in both hosts, but individual protein expression levels varied widely. This expression vector library will be a transformative resource for recombinant enzyme production, broadly enabling structure-function studies and expanding applications of these enzymes in glycochemistry and glycobiology.
Structural basis for the modulation of voltage-gated sodium channels by animal toxins
In “excitable” cells, like neurons and muscle cells, a difference in electrical potential is used to transmit signals across the cell membrane. This difference is regulated by opening or closing ion channels in the cell membrane. For example, mutations in human voltage-gated sodium (Na v ) channels are associated with disorders such as chronic pain, epilepsy, and cardiac arrhythmia. Pan et al. report the high-resolution structure of a human Na v channel, and Shen et al. report the structures of an insect Na v channel bound to the toxins that cause pufferfish and shellfish poisoning in humans. Together, the structures give insight into the molecular basis of sodium ion permeation and provide a path toward structure-based drug discovery. Science , this issue p. eaau2486 , p. eaau2596 Structures provide insight into how voltage-gated sodium channels function and how they can be inhibited. Animal toxins that modulate the activity of voltage-gated sodium (Na v ) channels are broadly divided into two categories—pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are responsible for puffer fish and shellfish poisoning in humans, respectively. Here, we present structures of the insect Na v channel Na v PaS bound to a gating modifier toxin Dc1a at 2.8 angstrom-resolution and in the presence of TTX or STX at 2.6-Å and 3.2-Å resolution, respectively. Dc1a inserts into the cleft between VSD II and the pore of Na v PaS, making key contacts with both domains. The structures with bound TTX or STX reveal the molecular details for the specific blockade of Na + access to the selectivity filter from the extracellular side by these guanidinium toxins. The structures shed light on structure-based development of Na v channel drugs.
Structural Insights into Catalytic Versatility of the Flavin-dependent Hydroxylase (HpaB) from Escherichia coli
4-Hydroxyphenylacetate 3-hydroxylase (EcHpaB) from Escherichia coli is capable of efficient orthohydroxylation of a wide range of phenolic compounds and demonstrates great potential for broad chemoenzymatic applications. To understand the structural and mechanistic basis of its catalytic versatility, we elucidated the crystal structure of EcHpaB by X-ray crystallography, which revealed a unique loop structure covering the active site. We further performed mutagenesis studies of this loop to probe its role in substrate specificity and catalytic activity. Our results not only showed the loop has great plasticity and strong tolerance towards extensive mutagenesis, but also suggested a flexible loop that enables the entrance and stable binding of substrates into the active site is the key factor to the enzyme catalytic versatility. These findings lay the groundwork for editing the loop sequence and structure for generation of EcHpaB mutants with improved performance for broader laboratory and industrial use.