229 research outputs found
Heliophyllite: A discredited mineral species identical to ecdemite
The type material for heliophyllite, preserved in the Swedish Museum of Natural History in Stockholm, was re-investigated through a combined EPMA (electron probe X-ray microanalysis), Raman, and X-ray powder diffraction (XRPD) and single-crystal study. EPMA chemical data, together with Raman and single-crystal structural studies, point to heliophyllite being identical to ecdemite. XRPD synchrotron data highlight the presence of a minor quantity of finely admixed finnemanite in the analyzed material, explaining the presence of some additional diffraction peaks, not indexable with the ecdemite unit cell, reported in the literature. The discreditation of heliophyllite has been approved by the IMA Commission on New Minerals and Mineral Names (proposal 19-H, 2019)
Simulation of Diffusion Time of Small Molecules in Protein Crystals
SummaryA simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals
The Role of Structural Biology Task Force: Validation of the Binding Mode of Repurposed Drugs Against SARS-CoV-2 Protein Targets: Focus on SARS-CoV-2 Main Protease (Mpro): A Promising Target for COVID-19 Treatment
The main protease (Mpro) of SARS-CoV-2, a cysteine protease that plays a key role in generating the active proteins essential for coronavirus replication, is a validated drug target for treating COVID-19. The structure of Mpro has been elucidated by macromolecular crystallography, but owing to its conformational flexibility, finding effective inhibitory ligands was challenging. Screening libraries of ligands as part of EXaSCale smArt pLatform Against paThogEns (ExScalate4CoV) yielded several potential drug molecules that inhibit SARS-CoV-2 replication in vitro. We solved the crystal structures of Mpro in complex with repurposed drugs like myricetin, a natural flavonoid, and MG-132, a synthetic peptide aldehyde. We found that both inhibitors covalently bind the catalytic cysteine. Notably, myricetin has an unexpected binding mode, showing an inverted orientation with respect to that of the flavonoid baicalein. Moreover, the crystallographic model validates the docking pose suggested by molecular dynamics experiments. The mechanism of MG-132 activity against SARS-CoV-2 Mpro was elucidated by comparison of apo and inhibitor-bound crystals, showing that regardless of the redox state of the environment and the crystalline symmetry, this inhibitor binds covalently to Cys145 with a well-preserved binding pose that extends along the whole substrate binding site. MG-132 also fits well into the catalytic pocket of human cathepsin L, as shown by computational docking, suggesting that it might represent a good start to developing dual-targeting drugs against COVID-1
Combined Structural and Compositional Evolution of Planetary Rings Due to Micrometeoroid Impacts and Ballistic Transport
We introduce improved numerical techniques for simulating the structural and compositional evolution of planetary rings due to micrometeoroid bombardment and subsequent ballistic transport of impact ejecta. Our current, robust code is capable of modeling structural changes and pollution transport simultaneously over long times on both local and global scales. In this paper, we describe the methodology based on the original structural code of Durisen et al. (1989, Icarus 80, 136-166) and on the pollution transport code of Cuzzi and Estrada (1998, Icarus 132, 1-35). We provide demonstrative simulations to compare with, and extend upon previous work, as well as examples of how ballistic transport can maintain the observed structure in Saturn's rings using available Cassini occultation optical depth data. In particular, we explicitly verify the claim that the inner B (and presumably A) ring edge can be maintained over long periods of time due to an ejecta distribution that is heavily biased in the prograde direction through a balance between the sharpening effects of ballistic transport and the broadening effects of viscosity. We also see that a "ramp"-like feature forms over time just inside that edge. However, it does not remain linear for the duration of the runs presented here unless a less steep ejecta velocity distribution is adopted. We also model the C ring plateaus and find that their outer edges can be maintained at their observed sharpness for long periods due to ballistic transport. We hypothesize that the addition of a significant component of a retrograde-biased ejecta distribution may help explain the linearity of the ramp and is probably essential for maintaining the sharpness of C ring plateau inner edges. This component would arise for the subset of micrometeoroid impacts which are destructive rather than merely cratering. Such a distribution will be introduced in future work
Giant Shape-Persistent Tetrahedral Porphyrin System: Light-Induced Charge Separation
Tetraphenylmethane appended with four pyridylpyridinium units works as a scaffold to self-assemble four ruthenium porphyrins in a tetrahedral shape-persistent giant architecture. The resulting supramolecular structure has been characterised in the solid state by X-ray single crystal analysis and in solution by various techniques. Multinuclear NMR spectroscopy confirms the 1 : 4 stoichiometry with the formation of a highly symmetric structure. The self-assembly process can be monitored by changes of the redox potentials, as well as by modifications in the visible absorption spectrum of the ruthenium porphyrin and by a complete quenching of both the bright fluorescence of the tetracationic scaffold and the weak phosphorescence of the ruthenium porphyrin. An ultrafast photoinduced electron transfer is responsible for this quenching process. The lifetime of the resulting charge separated state (800 ps) is about four times longer in the giant supramolecular structure compared to the model 1 : 1 complex formed by the ruthenium porphyrin and a single pyridylpyridinium unit. Electron delocalization over the tetrameric pyridinium structure is likely to be responsible for this effect
Isselite, Cu6(SO4)(OH)10(H2O)4·h2O, a new mineral species from Eastern Liguria, Italy
The new mineral isselite, Cu6(SO4)(OH)10(H2O)4·H2O, has been discovered in the Lagoscuro mine, Monte Ramazzo mining complex, Genoa, Eastern Liguria, Italy. It occurs as sprays of blue acicular crystals, up to 0.1 mm long, associated with brochantite and posnjakite. Streak is light blue and the lustre is vitreous. Isselite is brittle, with irregular fracture and good cleavage on {001} and {100}. Measured density is 3.00(2) g/cm3. Isselite is optically biaxial (-), with α = 1.599(2), β = 1.633(2) and γ = 1.647(2) (determined in white light). The measured 2V is 63.6(5)°. Dispersion is moderate, with r > v. The optical orientation is X = b, Y = c and Z = a. Isselite is pleochroic, with X = light blue, Y = blue, Z = blue; X << Z < Y. Electron microprobe analyses give (wt.%): SO3 11.45(21), MgO 0.31(7), CoO 1.07(14), NiO 9.41(90), CuO 51.29(126), ZnO 1.10(20), H2Ocalc 24.21, total 98.84. The empirical formula of isselite, based on Σ(Mg,Co,Ni,Cu,Zn) = 6 atoms per formula unit, is (Cu4.80Ni0.94Co0.11Zn0.10Mg0.06)Σ6.00(S1.06O4.19)(OH)10·5H2O. Isselite is orthorhombic, space group Pmn21, with unit-cell parameters a = 6.8070(14), b = 5.8970(12), c = 20.653(4) Å, V = 829.0(3) Å3 and Z = 2. The crystal structure of isselite was refined from single-crystal X-ray diffraction data to R1 = 0.067 on the basis of 2964 reflections with Fo > 4σ(Fo). It shows a layered structure formed by zig-zag {001} layers of Cu-centred polyhedra. Sulfate groups occur in the interlayer along with one H2O group. Isselite is chemically related to redgillite and montetrisaite
Structure and metal-binding properties of PA4063, a novel player in periplasmic zinc trafficking by Pseudomonas aeruginosa
The capability to obtain essential nutrients in hostile environments is a critical skill for pathogens. Under zinc-deficient conditions, Pseudomonas aeruginosa expresses a pool of metal homeostasis control systems that is complex compared with other Gram-negative bacteria and has only been partially characterized. Here, the structure and zinc-binding properties of the protein PA4063, the first component of the PA4063-PA4066 operon, are described. PA4063 has no homologs in other organisms and is characterized by the presence of two histidine-rich sequences. ITC titration detected two zinc-binding sites with micromolar affinity. Crystallographic characterization, performed both with and without zinc, revealed an α/β-sandwich structure that can be classified as a noncanonical ferredoxin-like fold since it differs in size and topology. The histidine-rich stretches located at the N-terminus and between β3 and β4 are disordered in the apo structure, but a few residues become structured in the presence of zinc, contributing to coordination in one of the two sites. The ability to bind two zinc ions at relatively low affinity, the absence of catalytic cavities and the presence of two histidine-rich loops are properties and structural features which suggest that PA4063 might play a role as a periplasmic zinc chaperone or as a concentration sensor useful for optimizing the response of the pathogen to zinc deficiency
Synthesis and anticancer activity of Pt(0)-olefin complexes bearing 1,3,5-triaza-7-phosphaadamantane and N-heterocyclic carbene ligands
A series of Pt(0)-η2-olefin complexes bearing 1,3,5-triaza-7-phosphaadamantane (PTA) or N-heterocyclic carbenes are prepared following different synthetic strategies depending on the nature of coordinated alkene and spectator ligands. These new platinum(0) derivatives have been tested in vitro as anticancer agents toward three different tumor (human ovarian cancer A2780 and A2780cis and K562 myelogenous leukemia) and one non-tumor (Hacat keratinocytes) cell lines, proving to be in several cases highly and selectively cytotoxic against ovarian cancer cells. Furthermore, this antiproliferative effect is associated with the activation of an apoptosis process. In particular, complexes equipped with PTA as spectator ligand give comparable IC50 values on A2780 (cisplatin sensitive) and A2780cis (cisplatin resistant) cell lines, indirectly proving that these new Pt(0) substrates act with a mechanism of action conceivably different from cisplatin. This hypothesis is also confirmed by the fact that our compounds, in contrast to cisplatin, are not able to promote erythroid-differentiation activity on the K562 myelogenous leukemia cell line
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