Structural information on nanometer-sized gold particles has been limited, due in part to the problem of preparing homogeneous material. Here we report the crystallization and x-ray structure ...determination of a p-mercaptobenzoic acid (p-MBA)-protected gold nanoparticle, which comprises 102 gold atoms and 44 p-MBAs. The central gold atoms are packed in a Marks decahedron, surrounded by additional layers of gold atoms in unanticipated geometries. The p-MBAs interact not only with the gold but also with one another, forming a rigid surface layer. The particles are chiral, with the two enantiomers alternating in the crystal lattice. The discrete nature of the particle may be explained by the closing of a 58-electron shell.
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Synthesis, characterization, and functionalization of self-assembled, ligand-stabilized gold nanoparticles are long-standing issues in the chemistry of nanomaterials. Factors driving the ...thermodynamic stability of well documented discrete sizes are largely unknown. Herein, we provide a unified view of principles that underlie the stability of particles protected by thiolate (SR) or phosphine and halide (PR₃, X) ligands. The picture has emerged from analysis of large-scale density functional theory calculations of structurally characterized compounds, namely Au₁₀₂(SR)₄₄, Au₃₉(PR₃)₁₄X₆⁻, Au₁₁(PR₃)₇X₃, and Au₁₃(PR₃)₁₀X₂³⁺, where X is either a halogen or a thiolate. Attributable to a compact, symmetric core and complete steric protection, each compound has a filled spherical electronic shell and a major energy gap to unoccupied states. Consequently, the exceptional stability is best described by a "noble-gas superatom" analogy. The explanatory power of this concept is shown by its application to many monomeric and oligomeric compounds of precisely known composition and structure, and its predictive power is indicated through suggestions offered for a series of anomalously stable cluster compositions which are still awaiting a precise structure determination.
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Abstract
We present Very Large Array (VLA) and Atacama Large Millimeter/submillimeter Array (ALMA) observations of the close (0.″3 = 90 au separation) protobinary system SVS 13. We detect two small ...circumstellar disks (radii ∼12 and ∼9 au in dust, and ∼30 au in gas) with masses of ∼0.004–0.009
M
☉
for VLA 4A (the western component) and ∼0.009–0.030
M
☉
for VLA 4B (the eastern component). A circumbinary disk with prominent spiral arms extending ∼500 au and a mass of ∼0.052
M
☉
appears to be in the earliest stages of formation. The dust emission is more compact and with a very high optical depth toward VLA 4B, while toward VLA 4A the dust column density is lower, allowing the detection of stronger molecular transitions. We infer rotational temperatures of ∼140 K, on scales of ∼30 au, across the whole source, and a rich chemistry. Molecular transitions typical of hot corinos are detected toward both protostars, being stronger toward VLA 4A, with several ethylene glycol transitions detected only toward this source. There are clear velocity gradients, which we interpret in terms of infall plus rotation of the circumbinary disk, and pure rotation of the circumstellar disk of VLA 4A. We measured orbital proper motions and determined a total stellar mass of 1
M
☉
. From the molecular kinematics, we infer the geometry and orientation of the system, and stellar masses of ∼0.26
M
☉
for VLA 4A and ∼0.60
M
☉
for VLA 4B.
G protein-coupled receptors (GPCRs) participate in ubiquitous transmembrane signal transduction processes by activating heterotrimeric G proteins. In the current “canonical” model of GPCR signaling, ...arrestins terminate receptor signaling by impairing receptor–G-protein coupling and promoting receptor internalization. However, parathyroid hormone receptor type 1 (PTHR), an essential GPCR involved in bone and mineral metabolism, does not follow this conventional desensitization paradigm. β-Arrestins prolong G protein (G S)-mediated cAMP generation triggered by PTH, a process that correlates with the persistence of arrestin–PTHR complexes on endosomes and which is thought to be associated with prolonged physiological calcemic and phosphate responses. This presents an inescapable paradox for the current model of arrestin-mediated receptor–G-protein decoupling. Here we show that PTHR forms a ternary complex that includes arrestin and the Gβγ dimer in response to PTH stimulation, which in turn causes an accelerated rate of G S activation and increases the steady-state levels of activated G S, leading to prolonged generation of cAMP. This work provides the mechanistic basis for an alternative model of GPCR signaling in which arrestins contribute to sustaining the effect of an agonist hormone on the receptor.
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The HIV-1 accessory protein Vpr is required for efficient viral infection of macrophages and promotion of viral replication in T cells. Vpr's biological activities are closely linked to the ...interaction with human DCAF1, a cellular substrate receptor of the Cullin4-RING E3 ubiquitin ligase (CRL4) of the host ubiquitin-proteasome-mediated protein degradation pathway. The molecular details of how Vpr usurps the protein degradation pathway have not been delineated. Here we present the crystal structure of the DDB1-DCAF1-HIV-1-Vpr-uracil-DNA glycosylase (UNG2) complex. The structure reveals how Vpr engages with DCAF1, creating a binding interface for UNG2 recruitment in a manner distinct from the recruitment of SAMHD1 by Vpx proteins. Vpr and Vpx use similar N-terminal and helical regions to bind the substrate receptor, whereas different regions target the specific cellular substrates. Furthermore, Vpr uses molecular mimicry of DNA by a variable loop for specific recruitment of the UNG2 substrate.
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ABSTRACT
In this work we analyse the structural and photometric properties of 21 barred simulated galaxies from the Auriga Project. These consist of Milky Way-mass magnetohydrodynamical simulations ...in a Λ cold dark matter (ΛCDM) cosmological context. In order to compare with observations, we generate synthetic SDSS-like broad-band images from the numerical data at z = 0 with different inclinations (from face-on to edge-on). Ellipse fits are used to determine the bar lengths, and 2D bulge/disc/bar decompositions with galfit are also performed, modelling the bar component with the modified Ferrer profile. We find a wide range of bar sizes and luminosities in the sample, and their structural parameters are in good agreement with the observations. All bulges present low Sérsic indexes, and are classified as pseudobulges. In regard to the discs, the same breaks in the surface brightness profiles observed in real galaxies are found, and the radii at which these take place are in agreement with the observations. Also, from edge-on unsharp-masked images at z = 0, boxy or peanut-shaped (B/P) structures are clearly identified in the inner part of four bars, and also two more bars are found in buckling phase. The sizes of the B/P match fairly well with those obtained from observations. We thus conclude that the observed photometric and structural properties of galaxies with bars, which are the main drivers of secular evolution, can be developed in present state-of-the-art ΛCDM cosmological simulations.
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•High microbial diversity within the porcine slaughterhouse and pork products.•Bacteria and stress genes were more prevalent in the first slaughterhouse zones.•SOS are the most ...prevalent genes, possibly associated with genomic changes.•Porcine-type-C oncovirus was mainly found at the end and pork products.•HLE disinfection strategy may avoid gene spread and microbial contaminants.
The use of shotgun metagenomic sequencing to understand ecological-level spread of microbes and their genes has provided new insights for the prevention, surveillance and control of microbial contaminants in the slaughterhouse environment. Here, microbial samples were collected from products and surrounding areas though a porcine slaughter process; shotgun metagenomic DNA-sequencing of these samples revealed a high community diversity within the porcine slaughterhouse and pork products, in zones originating from animal arrival through to the sale zones. Bacteria were more prevalent in the first zones, such as arrival- and anesthesia-zones, and DNA viruses were prevalent in the scorching-and-whip zone, animal products and sale zone. Data revealed the dominance of Firmicutes and Proteobacteria phyla followed by Actinobacteria, with a clear shift in the relative abundance of lactic acid bacteria (mainly Lactobacillus sp.) from early slaughtering steps to Proteobacteria and then to viruses suggesting site-specific community compositions occur in the slaughterhouse. Porcine-type-C oncovirus was the main virus found in slaughterhouse, which causes malignant diseases in animals and humans. As such, to guarantee food safety in a slaughterhouse, a better decipher of ecology and adaptation strategies of microbes becomes crucial. Analysis of functional genes further revealed high abundance of diverse genes associated with stress, especially in early zones (animal and environmental surfaces of arrival zone with 57,710 and 40,806 genes, respectively); SOS responsive genes represented the most prevalent, possibly associated with genomic changes responsible of biofilm formation, stringent response, heat shock, antimicrobial production and antibiotic response. The presence of several antibiotic resistance genes suggests horizontal gene transfer, thus increasing the likelihood for resistance selection in human pathogens. These findings are of great concern, with the suggestion to focus control measures and establish good disinfection strategies to avoid gene spread and microbial contaminants (bacteria and viruses) from the animal surface into the food chain and environment, which was achieved by applying HLE disinfectant after washing with detergent.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures ...of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that “open/closed” conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation.
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•Co-crystal structure of Pol II in complex with a nucleic acid scaffold (NAS)•Pol II interacts with upstream and downstream DNA duplexes•Pol II coordinates strand annealing and the nascent transcript at the upstream fork•Trigger loop/non-template strand interactions may contribute to NAS translocation
Barnes et al. reveal the architecture of Pol II bound to a nucleic acid scaffold (NAS), comprising both upstream and downstream DNA duplexes and transcriptional forks. The co-crystal structure uncovers the large range of interactions between Pol II and the NAS and possible mechanistic links between NAS binding and translocation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Previous x-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A structure of an RNA ...polymerase II-general transcription factor TFIIB complex at 4.5 angstrom resolution revealed the amino-terminal region of TFIIB, including a loop termed the "B finger," reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the carboxyl-terminal region. A new crystal structure of the same complex at 3.8 angstrom resolution obtained under different solution conditions is complementary with the previous one, revealing the carboxyl-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B finger. In the new structure, the linker between the amino- and carboxyl-terminal regions can also be seen, snaking down from above the cleft toward the active center. The two structures, taken together with others previously obtained, dispel long-standing mysteries of the transcription initiation process.
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Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold ...cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.
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