Studies toward the Unique Pederin Family Member Psymberin: Full Structure Elucidation, Two Alternative Total Syntheses, and Analogs

Two synthetic approaches to psymberin have been accomplished. A highly convergent first generation synthesis led to the complete stereochemical assignment and demonstrated that psymberin and irciniastatin A are identical compounds. This synthesis featured a diastereoselective aldol coupling between the aryl fragment and a central tetrahydropyran core and a novel one-pot procedure to convert an amide, via intermediacy of a sensitive methyl imidate, to the <i>N</i>-acyl aminal reminiscent of psymberin. The highlights of the second generation synthesis include an efficient iridium-catalyzed enantioselective bisallylation of neopentyl glycol and a stepwise Sonogashira coupling/cycloisomerization/reduction sequence to construct the dihydroisocoumarin unit. The two synthetic avenues were achieved in 17–18 steps (longest linear sequence, ∼14–15 isolations) from 3 fragments prepared in 7–8 (first generation) and 3–8 (second generation) steps each. This convergent approach allowed for the preparation of sufficient amounts of psymberin (∼ 0.5 g) for follow-up biological studies. Meanwhile, our highly flexible strategy enabled the design and synthesis of multiple analogs, including a psymberin–pederin hybrid, termed psympederin, that proved crucial to a comprehensive understanding of the chemical biology of psymberin and related compounds that will be described in a subsequent manuscript

Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE

<div><p>GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an <i>Escherichia coli</i> homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE. Using molecular dynamics simulations, we evaluated the free energy profiles of the transition between inward- and outward-facing conformations for the <i>apo</i> proteins. Our results revealed the correlation between the protonation state and conformational preference in XylE, which is supported by the crystal structures. In addition, our simulations suggested a thermodynamic difference between XylE and GLUT1 that cannot be explained by the single residue variation at the protonation site. To understand the molecular basis, we applied Bayesian network models to analyze the alteration in the architecture of the hydrogen bond networks during conformational transition. The models and subsequent experimental validation suggest that multiple residue substitutions are required to produce the thermodynamic and functional distinction between XylE and GLUT1. Despite the lack of simulation studies with substrates, these computational and biochemical characterizations provide unprecedented insight into the mechanistic difference between proton symporters and uniporters.</p></div

Additional file 1: of Prolonged inhibition of class I PI3K promotes liver cancer stem cell expansion by augmenting SGK3/GSK-3β/β-catenin signalling

Table S1. Primer sequences for quantitative RT-PCR. (DOCX 24 kb

Conformation sampling and free energies of GLUT1, XylE_H and XylE_noH.

<p><b>(A)</b> The definitions of extracellular and intracellular gates. Extracellular gate (EG) comprises of two groups of interacting helices at periplasmic side, including TM 1, 2&5 and TM 7, 8&11 (highlighted in yellow). Likewise, cytoplasmic portions of TM 2, 4&5 and TM 8, 10&11 compose the intracellular gate (IG) residues. The centers of mass (COM) of Cα atoms in the two gating groups are used to depict gate distances. <b>(B)</b> List of simulation sets performed on GLUT1, XylE_H and XylE_noH systems. <b>(C)</b> The unweighted contour maps for aMD trajectories in the 2D space of Extracellular and Intracellular Gate distances. The positions of initial structures for GLUT1 (PDB ID: 4PYP) and XylE systems (PDB ID: 4JA3) are shown as red dots. Dashed circles denote the supposed regions of inward- and outward-facing conformations. <b>(D)</b> Free energy profiles along discretized BEUS images/windows. GLUT1, XylE_H and XylE_noH are colored red, blue and yellow, respectively.</p

Residues responsible for thermodynamic difference between XylE_H and GLUT1.

<p><b>(A)</b> Schematic diagram of identifying the key residues for free-energy discrepancy. The candidate residues are supposed to cause the free energy profile of one transporter to resemble the other upon mutation. Applying inference on H-bond networks, we could pinpoint mutants that reduce the energy barrier in XylE_H or introduce one in GLUT1 according to the changes in HB values. In such cases, the ΔHB of IF and OF conformations should be comparable, while ΔHB_TS should differ from ΔHB_IF and ΔHB_OF significantly. <b>(B)</b> (<b><i>Left panel</i></b>) Identification of GLUT1 mutants that imitate XylE_H by destabilizing TS (ΔΔHB_IF→TS < -0.5 and ΔΔHB_OF→TS < -0.5; highlight as blue region). (<b><i>Right panel</i></b>) Identification of XylE_H mutants that imitate GLUT1 by stabilizing TS (ΔΔHB_IF→TS > 0.5 and ΔΔHB_OF→TS > 0.5; highlight as red region). <b>(C)</b> Table of candidates predicted for the GLUT1→XylE_H conversion and vice versa. The mutants in gray letters are conserved, unaligned for SP family members, or critical in sugar coordination. <b>(D)</b> (<b><i>Left panel</i></b>) Structural view of GLUT1 residues identified in the left panel of (<b>B</b>). (<b><i>Right panel</i></b>) ΔHB illustration of GLUT1 possessing all 7 mutations that mimics T45V, T60A, D236L, S294A, T295P, S313V, and Y424M, as listed in (<b>C</b>). Backbone H-bonds of residue 295 were also modulated to fit T295P mutation. Error bars were shown as gray shadow. <b>(E)</b> Transport activities of XylE mutants. The effect of negative control was already subtracted (see Cell-based uptake assay in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005603#sec008" target="_blank">Methods</a> section for details). Except for XylE WT, all other variants were based on D27N mutation. ‘7 mutations’ labeling indicates the combination of V43T, A52T, A300S, P301T, L248D, V321T, and M428Y. <b>(F)</b> Transport cycles of uniporter GLUT1 and proton symporter XylE. The reactions investigated in this work are highlighted by blue arrows with line widths indicating reaction rates. H and S represent proton and substrate, respectively. The horizontal gray dashed lines separate OF and IF states.</p

Electrochemical Properties and Applications of Nanocrystalline, Microcrystalline, and Epitaxial Cubic Silicon Carbide Films

Microstructures of the materials (e.g., crystallinitiy, defects, and composition, etc.) determine their properties, which eventually lead to their diverse applications. In this contribution, the properties, especially the electrochemical properties, of cubic silicon carbide (3C-SiC) films have been engineered by controlling their microstructures. By manipulating the deposition conditions, nanocrystalline, microcrystalline and epitaxial (001) 3C-SiC films are obtained with varied properties. The epitaxial 3C-SiC film presents the lowest double-layer capacitance and the highest reversibility of redox probes, because of its perfect (001) orientation and high phase purity. The highest double-layer capacitance and the lowest reversibility of redox probes have been realized on the nanocrystalline 3C-SiC film. Those are ascribed to its high amount of grain boundaries, amorphous phases and large diversity in its crystal size. Based on their diverse properties, the electrochemical performances of 3C-SiC films are evaluated in two kinds of potential applications, namely an electrochemical capacitor using a nanocrystalline film and an electrochemical dopamine sensor using the epitaxial 3C-SiC film. The nanocrystalline 3C-SiC film shows not only a high double layer capacitance (43–70 μF/cm²) but also a long-term stability of its capacitance. The epitaxial 3C-SiC film shows a low detection limit toward dopamine, which is one to 2 orders of magnitude lower than its normal concentration in tissue. Therefore, 3C-SiC film is a novel but designable material for different emerging electrochemical applications such as energy storage, biomedical/chemical sensors, environmental pollutant detectors, and so on

Network variations upon disrupting Asp27-Arg133 interaction in XylE systems.

<p><b>(A)</b> Overview of local network around Asp27 inside NTD. The residues affected by forcing Asp27_SC-Arg133_SC H-bonds to 0 in either XylE_H or XylE_noH are colored yellow. <b>(B)</b> Overall HB changes in IF, TS and OF states for XylE_H and XylE_noH, with error bars shown as gray shadow. <b>(C-D)</b> Details in the variations of local networks in XylE systems. The nodes with greatly perturbed HB value (|ΔHB| > 0.05) are included. The colors in the nodes reflect their ΔHB (see the color bar on the left). Arrows and dashed lines denote the strong and weak causalities between nodes, respectively. Positions of TM helices are shown as gray shadow.</p

DataSheet_1_Prognosis and pain dissection of novel signatures in kidney renal clear cell carcinoma based on fatty acid metabolism-related genes.docx

Renal cell carcinoma (RCC) is a malignant tumor that is characterized by the accumulation of intracellular lipid droplets. The prognostic value of fatty acid metabolism-related genes (FMGs) in RCC remains unclear. Alongside this insight, we collected data from three RCC cohorts, namely, The Cancer Genome Atlas (TCGA), E-MTAB-1980, and GSE22541 cohorts, and identified a total of 309 FMGs that could be associated with RCC prognosis. First, we determined the copy number variation and expression levels of these FMGs, and identified 52 overall survival (OS)-related FMGs of the TCGA-KIRC and the E-MTAB-1980 cohort data. Next, 10 of these genes—FASN, ACOT9, MID1IP1, CYP2C9, ABCD1, CPT2, CRAT, TP53INP2, FAAH2, and PTPRG—were identified as pivotal OS-related FMGs based on least absolute shrinkage and selection operator and Cox regression analyses. The expression of some of these genes was confirmed in patients with RCC by immunohistochemical analyses. Kaplan–Meier analysis showed that the identified FMGs were effective in predicting the prognosis of RCC. Moreover, an optimal nomogram was constructed based on FMG-based risk scores and clinical factors, and its robustness was verified by time-dependent receiver operating characteristic analysis, calibration curve analysis, and decision curve analysis. We have also described the biological processes and the tumor immune microenvironment based on FMG-based risk score classification. Given the close association between fatty acid metabolism and cancer-related pain, our 10-FMG signature may also serve as a potential therapeutic target with dual effects on ccRCC prognosis and cancer pain and, therefore, warrants further investigation.</p

Template Approach to Crystalline GaN Nanosheets

Crystalline GaN nanosheets hold great challenge in growth and promising application in optoelectronic nanodevices. In this work, we reported an accessible template approach toward the rational synthesis of GaN nanosheets through the nitridation of metastable γ-Ga₂O₃ nanosheets synthesized from a hydrothermal reaction. The cubic γ-Ga₂O₃ nanosheets with smooth surface and decent crystallinity can be directly converted into hexagonal GaN nanosheets with similar morphology framework and comparable crystal quality in NH₃ at 850 °C. UV–vis spectrum measurement reveals that the GaN nanosheets show a band gap of 3.30 eV with strong visible absorption in the range of 370–500 nm. The template synthetic strategy proposed in this work will open up more opportunities for the achievement of a variety of sheetlike nanostructures that can not be obtained through conventional routines and will undoubtedly further promote the fundamental research of newly emerging sheetlike nanostructures and nanotechnology

Solid Solution, Phase Separation, and Cathodoluminescence of GaP–ZnS Nanostructures

Quaternary solid-solution nanowires made of GaP and ZnS have been synthesized through well-designed synthetic routines. The as-synthesized GaP–ZnS solid-solution nanowires exhibit decent crystallinity with the GaP phase as the host, while a large amount of twin structural defects are observed in ZnS-rich nanowires. Cathodoluminescence studies showed that GaP-rich solid-solution nanowires have a strong visible emission centered at 600 nm and the ZnS-rich solid-solution nanowires exhibited a weak emission peak in the UV range and a broad band in the range 400–600 nm. The formation mechanism, processes, and optical emissions of GaP–ZnS solid-solution nanowires were discussed in detail