Synthesis and Evaluation of 1,3-Disubstituted Imidazolidine-2,4,5-triones as Inhibitors of Pyruvate Carboxylase.

Substituted imidazolidinetriones (IZTs) have been identified as potent inhibitors of pyruvate carboxylase (PC) through an in silico screening approach. Alkyl 2-(2,4,5-trioxo-3-substituted imidazolidin-1-yl)acetates (6i-6r) are the most potent of the series, with IC50 values between 3 and 12 µM, and several IZTs demonstrate high passive permeability across an artificial membrane. IZTs are mixed-type inhibitors with respect to pyruvate and noncompetitive with respect to ATP. This class of inhibitors appears to be selective for PC. Inhibitors in the IZT series do not inhibit the metalloenzymes human carbonic anhydrase II and matrix metalloprotease-12, and they do not inhibit the related biotin-dependent enzyme, guanidine carboxylase. Altogether, IZTs offer promise as PC inhibitors with potential downstream applications in cellular and in vivo systems.

Synthesis and Evaluation of 5-(Heteroarylmethylene)hydantoins as Glycogen Synthase Kinase-3ß Inhibitors.

Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase which plays a center role in the phosphorylation of a wide variety of proteins, generally leading to their inactivation. As such, GSK-3 is viewed as a therapeutic target. An ever-increasing number of small organic molecule inhibitors of GSK-3 have been reported. Phenylmethylene hydantoins are known to exhibit a wide range of inhibitory activities including for GSK-3ß. A family of fourteen 2-heterocycle substituted methylene hydantoins (14, 17-29) were prepared and evaluated for the inhibition of GSK-3ß at 25 µM. The IC50 values of five of these compounds was determined; the two best inhibitors are 5-[(4'-chloro-2-pyridinyl)methylene]hydantoin (IC50 = 2.14 ± 0.18 µM) and 5-[(6'-bromo-2-pyridinyl)methylene]hydantoin (IC50 = 3.39 ± 0.16 µM). The computational docking of the compounds with GSK-3ß (pdb 1q41) revealed poses with hydrogen bonding to the backbone at Val135. The 5-[(heteroaryl)methylene]hydantoins did not strongly inhibit other metalloenzymes, demonstrating poor inhibitory activity against matrix metalloproteinase-12 at 25 µM and against human carbonic anhydrase at 200 µM, and were not inhibitors for Staphylococcus aureus pyruvate carboxylase at concentrations >1000 µM.

Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase.

Allosteric regulation of the essential anaplerotic enzyme, pyruvate carboxylase (PC), is vital for metabolic homeostasis. PC catalyzes the bicarbonate- and ATP-dependent carboxylation of pyruvate to form oxaloacetate. Dysregulation of PC activity can impact glucose and redox metabolism, which contributes to the pathogenicity of many diseases. To maintain homeostasis, PC is allosterically activated by acetyl-CoA and allosterically inhibited by l-aspartate. In this study, we further characterize the molecular basis of allosteric regulation in Staphylococcus aureus PC (SaPC) using slowly/nonhydrolyzable dethia analogues of acetyl-CoA and site-directed mutagenesis of residues at the biotin carboxylase homodimer interface. The dethia analogues fully activate SaPC but demonstrate significantly reduced binding affinities relative to acetyl-CoA. Residues Arg21, Lys46, and Glu418 of SaPC are located at the biotin carboxylase dimer interface and play a critical role in both allosteric activation and inhibition. A structure of R21A SaPC in complex with acetyl-CoA reveals an intact molecule of acetyl-CoA bound at the allosteric site, offering new molecular insights into the acetyl-CoA binding site. This study demonstrates that the biotin carboxylase domain dimer interface is a critical allosteric site in PC, serving as a convergence point for allosteric activation by acetyl-CoA and inhibition by l-aspartate.

Temperature Dependent Nanochemistry and Growth Kinetics Using Liquid Cell Transmission Electron Microscopy.

Liquid cell transmission electron microscopy has become a powerful and increasingly accessible technique for in situ studies of nanoscale processes in liquid and solution phase. Exploring reaction mechanisms in electrochemical or crystal growth processes requires precise control over experimental conditions, with temperature being one of the most critical factors. Here we carry out a series of crystal growth experiments and simulations at different temperatures in the well-studied system of Ag nanocrystal growth driven by the changes in redox environment caused by the electron beam. Liquid cell experiments show strong changes in both morphology and growth rate with temperature. We develop a kinetic model to predict the temperature-dependent solution composition, and we discuss how the combined effect of temperature-dependent chemistry, diffusion, and the balance between nucleation and growth rates affect the morphology. We discuss how this work may provide guidance in interpreting liquid cell TEM and potentially larger-scale synthesis experiments for systems controlled by temperature.

The WAVE complex drives the morphogenesis of the photoreceptor outer segment cilium.

The photoreceptor outer segment is a modified cilium filled with hundreds of flattened "disc" membranes responsible for efficient light capture. To maintain photoreceptor health and functionality, outer segments are continuously renewed through the addition of new discs at their base. This process is driven by branched actin polymerization nucleated by the Arp2/3 complex. To induce actin polymerization, Arp2/3 requires a nucleation promoting factor. Here, we show that the nucleation promoting factor driving disc morphogenesis is the pentameric WAVE complex and identify all protein subunits of this complex. We further demonstrate that the knockout of one of them, WASF3, abolishes actin polymerization at the site of disc morphogenesis leading to formation of disorganized membrane lamellae emanating from the photoreceptor cilium instead of an outer segment. These data establish that, despite the intrinsic ability of photoreceptor ciliary membranes to form lamellar structures, WAVE-dependent actin polymerization is essential for organizing these membranes into a proper outer segment.

Cloned antibodies from patients with HIT provide new clues to HIT pathogenesis.

Heparin-induced thrombocytopenia (HIT) is a serious adverse drug reaction characterized by antibodies that recognize platelet factor 4/heparin complexes (PF4/H) and activate platelets to create a prothrombotic state. Although a high percentage of heparin-treated patients produce antibodies to PF4/H, only a subset also makes antibodies that are platelet activating (PA). A close correlation between PA antibodies and the likelihood of experiencing HIT has been demonstrated in clinical studies, but how PA (presumptively pathogenic) and nonactivating (NA) (presumptively benign) antibodies differ from each other at the molecular level is unknown. To address this issue, we cloned 7 PA and 47 NA PF4/H-binding antibodies from 6 patients with HIT and characterized their structural and functional properties. Findings showed that PA clones differed significantly from NA clones in possessing 1 of 2 heavy chain complementarity-determining region 3 (HCDR3) motifs, RX1-2R/KX1-2R/H (RKH) and YYYYY (Y5), in an unusually long complementarity-determining region 3 (≥20 residues). Mutagenic studies showed that modification of either motif in PA clones reduced or abolished their PA activity and that appropriate amino acid substitutions in HCDR3 of NA clones can cause them to become PA. Repertoire sequencing showed that the frequency of peripheral blood IgG+ B cells possessing RKH or Y5 was significantly higher in patients with HIT than in patients without HIT given heparin, indicating expansion of B cells possessing RKH or Y5 in HIT. These findings imply that antibodies possessing RKH or Y5 are relevant to HIT pathogenesis and suggest new approaches to diagnosis and treatment of this condition.

Observations of Atmospheric Tides in the Middle and Upper Atmosphere of Mars From MAVEN and MRO.

Variability in the Martian upper atmosphere is strongly linked to the lower atmosphere and much of it can be attributed to vertical wave propagation. Atmospheric tides in particular are a well-known phenomenon in the Martian atmosphere that play a key role in the transport of energy as they propagate to higher altitudes. Previous theoretical predictions and observations suggest that tides producing wavenumber-2 and wavenumber-3 patterns are strongest in a fixed local time at high altitudes, however, the energy they carry and the region of deposition are not well characterized. Given the availability of atmospheric observations from several spacecraft at the same time, in this paper, the nature and behavior of tides are studied concurrently at several altitudes. Here, six intervals are identified focused at fixed low latitudes utilizing simultaneous observations of the middle and upper atmosphere from in situ and remote sensing instruments on different spacecraft. In the middle atmosphere, strong wavenumber-2 signatures are identified in the intervals north of the equator whereas, in the south, wavenumber-3 signatures are strongest. Wave signatures observed in the upper atmosphere seem to be dominated by a mix of wavenumbers-2 and -3. Seasonal variation is observed in the northern intervals, with very little interannual variability in all intervals considered. Estimates of energy based on dominant wavenumber amplitude suggest that most of the energy dissipates below ∼90 km. Furthermore, model sampled output captures the dominant wavenumbers observed in the middle atmosphere as well as the energy dissipation characteristics.

Dethiosulfovibrio faecalis sp. nov., a novel proteolytic, non-sulphur-reducing bacterium isolated from a marine aquaculture solid waste bioreactor.

A new Dethiosulfovibrio strain, designated F2BT, was isolated from an anaerobic digester for treating solid waste from a marine recirculating aquaculture system. The motile, Gram-negative, non-spore-forming curved rods were 2-7 µm long and 1 µm in diameter. Growth occurred at temperatures ranging from 20 to 40 °C with a maximum rate of growth at 30 °C. The pH range for growth was pH 6.0-8.0, with a maximum rate of growth at pH 7.5. This isolate was halotolerant growing in NaCl concentrations ranging from 0 to 1.6 M with a maximum rate of growth at 0.4 M. Similarly to the five described Dethiosulfovibrio species, this obligate anaerobe isolate was fermentative, capable of utilizing peptides, amino acids and some organic acids for growth, but unlike described strains in the genus did not reduce thiosulphate or elemental sulphur to hydrogen sulphide during fermentation of organic substrates. The G+C content of 55 mol% is similar to the described Dethiosulfovibrio species. The average nucleotide identity analysis between whole genome sequences showed less than 93.15% sequence similarity between strain F2BT and the five other described Dethiosulfovibrio species. Differences in the physiological and phylogenetic characteristics between the new strain and other Dethiosulfovibrio specied indicate that F2BT represents a novel species of this genus and the epithet Dethiosulfovibrio faecalis sp. nov. is proposed. The type strain is F2BT (=DSM 112078T=KCTC25378T).

Solving the Conundrum: Widespread Proteins Annotated for Urea Metabolism in Bacteria Are Carboxyguanidine Deiminases Mediating Nitrogen Assimilation from Guanidine.

Free guanidine is increasingly recognized as a relevant molecule in biological systems. Recently, it was reported that urea carboxylase acts preferentially on guanidine, and consequently, it was considered to participate directly in guanidine biodegradation. Urea carboxylase combines with allophanate hydrolase to comprise the activity of urea amidolyase, an enzyme predominantly found in bacteria and fungi that catalyzes the carboxylation and subsequent hydrolysis of urea to ammonia and carbon dioxide. Here, we demonstrate that urea carboxylase and allophanate hydrolase from Pseudomonas syringae are insufficient to catalyze the decomposition of guanidine. Rather, guanidine is decomposed to ammonia through the combined activities of urea carboxylase, allophanate hydrolase, and two additional proteins of the DUF1989 protein family, expansively annotated as urea carboxylase-associated family proteins. These proteins comprise the subunits of a heterodimeric carboxyguanidine deiminase (CgdAB), which hydrolyzes carboxyguanidine to N-carboxyurea (allophanate). The genes encoding CgdAB colocalize with genes encoding urea carboxylase and allophanate hydrolase. However, 25% of urea carboxylase genes, including all fungal urea amidolyases, do not colocalize with cgdAB. This subset of urea carboxylases correlates with a notable Asp to Asn mutation in the carboxyltransferase active site. Consistent with this observation, we demonstrate that fungal urea amidolyase retains a strong substrate preference for urea. The combined activities of urea carboxylase, carboxyguanidine deiminase and allophanate hydrolase represent a newly recognized pathway for the biodegradation of guanidine. These findings reinforce the relevance of guanidine as a biological metabolite and reveal a broadly distributed group of enzymes that act on guanidine in bacteria.

Photoreceptor disc membranes are formed through an Arp2/3-dependent lamellipodium-like mechanism.

The light-sensitive outer segment of the vertebrate photoreceptor is a highly modified primary cilium filled with disc-shaped membranes that provide a vast surface for efficient photon capture. The formation of each disc is initiated by a ciliary membrane evagination driven by an unknown molecular mechanism reportedly requiring actin polymerization. Since a distinct F-actin network resides precisely at the site of disc morphogenesis, we employed a unique proteomic approach to identify components of this network potentially driving disc morphogenesis. The only identified actin nucleator was the Arp2/3 complex, which induces the polymerization of branched actin networks. To investigate the potential involvement of Arp2/3 in the formation of new discs, we generated a conditional knockout mouse lacking its essential ArpC3 subunit in rod photoreceptors. This knockout resulted in the complete loss of the F-actin network specifically at the site of disc morphogenesis, with the time course of ArpC3 depletion correlating with the time course of F-actin loss. Without the actin network at this site, the initiation of new disc formation is completely halted, forcing all newly synthesized membrane material to be delivered to the several nascent discs whose morphogenesis had already been in progress. As a result, these discs undergo uncontrolled expansion instead of normal enclosure, which leads to formation of unusual, large membrane whorls. These data suggest a model of photoreceptor disc morphogenesis in which Arp2/3 initiates disc formation in a "lamellipodium-like" mechanism.

Spatially dependent dose rate in liquid cell transmission electron microscopy.

The use of liquid cell electron microscopy as a quantitative probe of nanomaterial structures and reactions requires an accurate understanding of how the sample is altered by the imaging electron beam. In particular, changes in the chemical environment due to beam-induced radiolysis can strongly affect processes such as solution-phase nanocrystal synthesis or electrochemical deposition. It is generally assumed that beam effects are uniform throughout the irradiated liquid. Here we show that for a liquid cell filled with water, the inevitable presence of interfaces between water and the surrounding surfaces causes a spatial variation in the energy absorbed by the water near the walls. The mechanism for this effect is that the walls act as a source of secondary and backscattered electrons which diffuse and deposit energy in the water nearby. This increased dose rate then changes the local concentrations of radiolysis species. We quantify and compare the effects for different materials used in practical liquid cells. We show that the dose rate can increase by several times within tens of nanometers of a water/Au interface, locally increasing the concentrations of species such as the hydrated electron. We discuss the implications for materials processes that are typically triggered at the solid-liquid interface.

Control of Growth Front Evolution by Bi Additives during ZnAu Electrodeposition.

The performance of many electrochemical energy storage systems can be compromised by the formation of metal dendrites during charging. Additives in the electrolyte represent a useful strategy to mitigate dendrite formation, but understanding the mechanisms involved requires knowledge of the nanoscale effects of additives during electrochemical deposition. Here we quantify the effects of an inorganic additive on the morphology of an evolving electrochemical growth front, using liquid cell electron microscopy to provide the necessary spatial and temporal resolution. We examine deposition of ZnAu on Au in the presence of Bi additive, and show that low concentrations of Bi delay but do not prevent the formation of growth front instabilities. We describe a model in which Bi segregates at the growth front and promotes the surface diffusion and relaxation of Zn, allowing better coverage of the initial Au electrode surface. A more precise knowledge of the mechanism of inorganic additive effects may help in designing electrolyte chemistry for battery and other applications where morphology control is essential.

Nanoscale evolution of interface morphology during electrodeposition.

Control of interfacial morphology in electrochemical processes is essential for applications ranging from nanomanufacturing to batteries. Here, we quantify the evolution of an electrochemical growth front, using liquid cell electron microscopy to access unexplored length and time scales. During galvanostatic deposition of copper from an acidic electrolyte, we find that the growth front initially evolves consistent with kinetic roughening theory. Subsequently, it roughens more rapidly, consistent with diffusion-limited growth physics. However, the onset of roughening is strongly delayed compared to expectations, suggesting the importance of lateral diffusion of ions. Based on these growth regimes, we discuss morphological control and demonstrate the effects of two strategies, pulse plating and the use of electrolyte additives.

Control of Electron Beam-Induced Au Nanocrystal Growth Kinetics through Solution Chemistry.

Measurements of solution-phase crystal growth provide mechanistic information that is helpful in designing and synthesizing nanostructures. Here, we examine the model system of individual Au nanocrystal formation within a defined liquid geometry during electron beam irradiation of gold chloride solution, where radiolytically formed hydrated electrons reduce Au ions to solid Au. By selecting conditions that favor the growth of well-faceted Au nanoprisms, we measure growth rates of individual crystals. The volume of each crystal increases linearly with irradiation time at a rate unaffected by its shape or proximity to neighboring crystals, implying a growth process that is controlled by the arrival of atoms from solution. Furthermore, growth requires a threshold dose rate, suggesting competition between reduction and oxidation processes in the solution. Above this threshold, the growth rate follows a power law with dose rate. To explain the observed dose rate dependence, we demonstrate that a reaction-diffusion model is required that explicitly accounts for the species H(+) and Cl(-). The model highlights the necessity of considering all species present when interpreting kinetic data obtained from beam-induced processes, and suggest conditions under which growth rates can be controlled with higher precision.

Bubble and pattern formation in liquid induced by an electron beam.

Liquid cell electron microscopy has emerged as a powerful technique for in situ studies of nanoscale processes in liquids. An accurate understanding of the interactions between the electron beam and the liquid medium is essential to account for, suppress, and exploit beam effects. We quantify the interactions of high energy electrons with water, finding that radiolysis plays an important role, while heating is typically insignificant. For typical imaging conditions, we find that radiolysis products such as hydrogen and hydrated electrons achieve equilibrium concentrations within seconds. At sufficiently high dose-rate, the gaseous products form bubbles. We image bubble nucleation, growth, and migration. We develop a simplified reaction-diffusion model for the temporally and spatially varying concentrations of radiolysis species and predict the conditions for bubble formation by H2. We discuss the conditions under which hydrated electrons cause precipitation of cations from solution and show that the electron beam can be used to "write" structures directly, such as nanowires and other complex patterns, without the need for a mask.

No sodium in the vapour plumes of Enceladus.

The discovery of water vapour and ice particles erupting from Saturn's moon Enceladus fuelled speculation that an internal ocean was the source. Alternatively, the source might be ice warmed, melted or crushed by tectonic motions. Sodium chloride (that is, salt) is expected to be present in a long-lived ocean in contact with a rocky core. Here we report a ground-based spectroscopic search for atomic sodium near Enceladus that places an upper limit on the mixing ratio in the vapour plumes orders of magnitude below the expected ocean salinity. The low sodium content of escaping vapour, together with the small fraction of salt-bearing particles, argues against a situation in which a near-surface geyser is fuelled by a salty ocean through cracks in the crust. The lack of observable sodium in the vapour is consistent with a wide variety of alternative eruption sources, including a deep ocean, a freshwater reservoir, or ice. The existing data may be insufficient to distinguish between these hypotheses.