- Prof. Joon-Hwa Lee (Department of Chemistry, Gyeongsang National University, Jinju, Gyeongnam, Korea)
NMR study of the sequence discrimination in the DNA-protein interaction
- Prof. Sung You Hong (Department of Chemistry, UNIST)
Synthesis of (Het)Aromatic Compounds via Annulation and Catalytic Cycloaddition Reactions
- Guipeun Kang (University of Texas Southwestern Medical Center )
Comparative structural analysis of sensory receptors that drive octopus and squid predatory behavior
- Prof. Juyong Lee (College of Pharmacy, Seoul National University)
Chemical linguistics: atomic environments as new chemical alphabets and their applications for retrosynthesis prediction
- Prof. Dr. Torsten Schwede (University of Basel & Swiss Institute of Bioinformatics)
Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds
Chemical decomposition pathway of residual lithium carbonate of Li-ion battery cathodes
Decomposition of Li2CO3, which aggravates battery performance and safety by causing gas formation and side reactions, is a key obstacle that requires mitigation based on a comprehensive understanding of its decomposition pathway. However, it is challenging to compromise the decomposition pathway of Li2CO3, owing to the complication of various reactions at the cathode-electrolyte interface. Herein, we investigated the correlation between the amount of CO2 evolution and the population of ethylene carbonate that does not coordinate salt ions (free EC) by modifying electrolyte concentration. CO2 evolution, which serves as direct evidence of Li2CO3 decomposition, occurs at a greater extent in free EC-enriched environment. Linear sweep voltammetry confirmed higher levels of anodic dehydrogenation, releasing protons according to free EC population. Moreover, 1H nuclear magnetic resonance spectroscopy confirmed the formation of vinylene carbonate, with two protons removed from ethylene carbonate. Thus, we concluded that free EC near the surface of electrode facilitates chemical decomposition of Li2CO3 into CO2. The results demonstrate that modifying the free EC population can suppress the decomposition and further enhance the stability of the cathode. It is therefore concluded that cathode electrolyte interface stability can be modulated by designing the electrolyte to ensure the performance of the Li-ion battery.
Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel
Connexin 36 (Cx36) is responsible for signal transmission in electrical synapses by forming interneuronal gap junctions. Despite the critical role of Cx36 in normal brain function, the molecular architecture of the Cx36 gap junction channel (GJC) is unknown. Here, we determine cryo-electron microscopy structures of Cx36 GJC at 2.2–3.6 Å resolutions, revealing a dynamic equilibrium between its closed and open states. In the closed state, channel pores are obstructed by lipids, while N-terminal helices (NTHs) are excluded from the pore. In the open state with pore-lining NTHs, the pore is more acidic than those in Cx26 and Cx46/50 GJCs, explaining its strong cation selectivity. The conformational change during channel opening also includes the α-to-π-helix transition of the first transmembrane helix, which weakens the protomer-protomer interaction. Our structural analyses provide high resolution information on the conformational flexibility of Cx36 GJC and suggest a potential role of lipids in the channel gating.
A multifunctional peroxidase-based reaction for imaging, sensing and networking of spatial biology
Peroxidase is a heme-containing enzyme that reduces hydrogen peroxide to water by extracting electron(s) from aromatic compounds via a sequential turnover reaction. This reaction can generate various aromatic radicals in the form of short-lived “spray” molecules. These can be either covalently attached to proximal proteins or polymerized via radical–radical coupling. Recent studies have shown that these peroxidase-generated radicals can be utilized as effective tools for spatial research in biological systems, including imaging studies aimed at the spatial localization of proteins using electron microscopy, spatial proteome mapping, and spatial sensing of metabolites (e.g., heme and hydrogen peroxide). This review may facilitate the wider utilization of these peroxidase-based methods for spatial discovery in cellular biology.
How the sunflower gets its rings
The circadian clock may help to control the development patterns which allow the florets on a sunflower head to go through their final stages of maturation at precisely the right time.
Underlying Role of Hydrophobic Environments in Tuning Metal Elements for Efficient Enzyme Catalysis
The catalytic functions of metalloenzymes are often strongly correlated with metal elements in the active sites. However, dioxygen-activating nonheme quercetin dioxygenases (QueD) are found with various first-row transition-metal ions when metal swapping inactivates their innate catalytic activity. To unveil the molecular basis of this seemingly promiscuous yet metal-specific enzyme, we transformed manganese-dependent QueD into a nickel-dependent enzyme by sequence- and structure-based directed evolution. Although the net effect of acquired mutations was primarily to rearrange hydrophobic residues in the active site pocket, biochemical, kinetic, X-ray crystallographic, spectroscopic, and computational studies suggest that these modifications in the secondary coordination spheres can adjust the electronic structure of the enzyme–substrate complex to counteract the effects induced by the metal substitution. These results explicitly demonstrate that such noncovalent interactions encrypt metal specificity in a finely modulated manner, revealing the underestimated chemical power of the hydrophobic sequence network in enzyme catalysis.
Photocatalytic C–O Coupling Enzymes That Operate via Intramolecular Electron Transfer
Efficient and environmentally friendly conversion of light energy for direct utilization in chemical production has been a long-standing goal in enzyme design. Herein, we synthesized artificial photocatalytic enzymes by introducing an Ir photocatalyst and a Ni(bpy) complex to an optimal protein scaffold in close proximity. Consequently, the enzyme generated C–O coupling products with up to 96% yields by harvesting visible light and performing intramolecular electron transfer between the two catalysts. We systematically modulated the catalytic activities of the artificial photocatalytic cross-coupling enzymes by tuning the electrochemical properties of the catalytic components, their positions, and distances within a protein. As a result, we discovered the best-performing mutant that showed broad substrate scopes under optimized conditions. This work explicitly demonstrated that we could integrate and control both the inorganic and biochemical components of photocatalytic biocatalysis to achieve high yield and selectivity in valuable chemical transformations.
Electronic Effect on Phenoxide Migration at a Nickel(II) Center Supported by a Tridentate Bis
A phosphide nickel(II) phenoxide pincer complex (2) reacts with CO(g) to give a pseudo-tetrahedral nickel(0) monocarbonyl complex (3) possessing a phosphinite moiety. This metal–ligand cooperative (MLC) transformation occurs with a (PPP)Ni scaffold (PPP– = P[2-PiPr2–C6H4]2–), which can accommodate both square planar and tetrahedral geometries. The 2-electron reduction of a nickel(II) species induced by CO coordination involves group transfer to generate a P–O bond. For better mechanistic understanding, a series of nickel(II) phenolate complexes (2a–2e, XC6H4O– (X = OMe, Me, H, and CF3) and pentafluorophenolate) were prepared. Kinetic experimental data reveal that a phenolate species with an electron-withdrawing group reacts faster than those with electron-donating groups. The reaction kinetic experiments were conducted in pseudo-first order conditions at room temperature monitored by UV–vis spectroscopy. A pentafluorophenolate nickel(II) complex (2e) reveals instantaneous reactions even at −40 °C to give a nickel(0) monocarbonyl species (3e) and the reverse reaction is also possible. According to kinetic experiments, the rate determining step (RDS) would be the formation of a 5-coordinate intermediate 4 with a negative entropy value (ΔS‡ < 0), and a positive ρ value based on the Hammett plot indicates that the electron-deficient phenolate leads to a faster CO association. Furthermore, scramble experiments suggest that phenolate de-coordinates from the intermediate 4, which gives a (PPP)Ni–CO species 6. The cationic nickel monocarbonyl intermediate can possess a P––Ni(II), P•–Ni(I), or even a P+–Ni(0) character. Such an inner-sphere electron transfer is suggested when a π-acidic ligand such as CO coordinates to a metal ion. Another possible reaction is homolysis of a Ni–O bond to give P––Ni(I) or P•–Ni(0), when a phenoxyl radical is liberated. Considering the P–O bond formation, closed-shell nucleophilic and open-shell radical pathways are suggested. A phenolate pathway reveals a lower energy state for 2e relative to other complexes (2c and 2d), while its radical pathway undergoes via a higher energy state. Therefore, the formation of a P–O bond may occur with the binding of a closed-shell phenolate to the electron-deficient P center.
Self-cleaving protein linkers with modulated pH-responsiveness: A new platform for selective control of protein drug function
In this study, we propose a self-cleaving protein that responds to acidic pH, pH inteinN150, as a pH-responsive linker for the selective delivery of protein-based drugs. Being stable at neutral and degradable at weakly acidic pH, pH inteinN150 can be obtained by mutating key amino acids of pH intein, thus stimulating self-cleavage. Unlike chemical linkers, which require additional conjugation steps, protein linkers can be incorporated into protein pharmaceuticals during protein expression. As proof-of-concepts, intracellular penetration of proteins can be selectively turned on or off by cleaving pH inteinN150 near the cell-penetrating peptide sequence at weakly acidic pH. Furthermore, the apoptosis-inducing activity of human tumor necrosis factor-related apoptosis-inducing ligand (hTRAIL) can be selectively activated by cleaving pH inteinN150 adjacent to the albumin binding domain (ABD) at weakly acidic pH. Thus, we expect that this new protein linker can be used for actively controlling various protein-based drugs responding to delicate pH variations around inflammatory or cancerous tissues. These findings have been revealed in an in vivo tumor xenograft mouse model showing elongated systemic circulation and selective induction of tumor toxicity by ABD-pH inteinN150-hTRAIL.
Synergistic effect of Pt-loaded Cosingle bondNsingle bondC electrocatalysts for hydrogen evolution reaction in alkaline conditions
Designing efficient electrocatalysts for the hydrogen evolution reaction (HER) is important for a renewable and sustainable hydrogen economy. Alkaline HER remains particularly challenging because it involves water dissociation in addition to hydrogen recombination. Herein, we developed a simple precursor solution-based electrocatalyst in which Pt nanoparticles (NPs) are positioned independently of the Co-dispersed nitrogen-doped carbon (Co-N-C). The Pt/Co-N-C catalyst exhibited enhanced HER activity in an alkaline electrolyte compared to Pt/C and Co-N-C, achieving a decreased overpotential (33 mV at 10 mA cm−2) and lower Tafel slope (36.8 mV dec−1). Comparison of HER activities under acidic and alkaline electrolyte conditions revealed that the synergistic enhancement of Pt/Co-N-C was only obtained under the alkaline condition. Evaluation of the adsorption/desorption of H or OH through cyclic voltammetry analysis suggested that Co-N-C support can play a role to facilitate water-dissociation under alkaline conditions and leads to a larger charge ratio of Hupd/OHad on Pt, thus improving the HER activity at the Pt NP active sites.
Two-qubit atomic gates: spatio-temporal control of Rydberg interaction
By controlling the temporal and spatial features of light, we propose a novel protocol to prepare two-qubit entangling gates on atoms trapped at close distance, which could potentially speed up the operation of the gate from the sub-micro to the nanosecond scale. The protocol is robust to variations in the pulse areas and the position of the atoms, by virtue of the coherent properties of a dark state, which is used to drive the population through Rydberg states. From the time-domain perspective, the protocol generalizes the one proposed by Jaksch and coworkers [Jaksch et al., Phys. Rev. Lett., 2000, 85, 2208], with three pulses that operate symmetrically in time, but with different pulse areas. From the spatial-domain perspective, it uses structured light. We analyze the map of the gate fidelity, which forms rotated and distorted lattices in the solution space. Finally, we study the effect of an additional qubit to the gate performance and propose generalizations that operate with multi-pulse sequences.