Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure.

The small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5' side of a human telomeric G-quadruplex (HTG) sequence with four telomeric repeats (Q4), resulting in a nanomolar binding affinity (KD approximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI-binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures under physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5' end. Q4-ds-A is an excellent EPI binder with a KD of 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight binding of Q4 and Q4-ds-A with EPI allows us to develop a novel magnetic bead-based affinity purification system to effectively extract EPI from Rhizoma coptidis (Huang Lian) extracts.

Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations.

Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the first step in triacylglycerol synthesis. Understanding its substrate recognition mechanism may help to design drugs to regulate the production of glycerol lipids in cells. In this work, we investigate how the native substrate, glycerol-3-phosphate (G3P), and palmitoyl-coenzyme A (CoA) bind to the human GPAT isoform GPAT4 via molecular dynamics simulations (MD). As no experimentally resolved GPAT4 structure is available, the AlphaFold model is employed to construct the GPAT4-substrate complex model. Using another isoform, GPAT1, we demonstrate that once the ligand binding is properly addressed, the AlphaFold complex model can deliver similar results to the experimentally resolved structure in MD simulations. Following the validated protocol of complex construction, we perform MD simulations using the GPAT4-substrate complex. Our simulations reveal that R427 is an important residue in recognizing G3P via a stable salt bridge, but its motion can bring the ligand to different binding hotspots on GPAT4. Such high flexibility can be attributed to the flexible region that exists only on GPAT4 and not on GPAT1. Our study reveals the substrate recognition mechanism of GPAT4 and hence paves the way towards designing GPAT4 inhibitors.

Study on Seepage Characteristics of Grouting Slurry for Water-Absorbing Mudstone with Rough Fissure.

Based on the computed tomography scanning, which abbreviation is CT scanning, and fractal theory, geometric parameters of mudstone fissures are obtained. The physical model of a single fissured channel is obtained in combination with Barton standard curves and 3D printing technology, and similar materials of mudstone are developed based on the water absorption of natural mudstone to prepare single fissured water-absorbing grouting test blocks with different roughness levels for the grouting simulation testing. By analyzing the viscosity change characteristics of grouting slurry before and after grouting, the seepage characteristics of the grouting slurry in the rough fissures of the water-absorbing mudstone are revealed. The results show that when the roughness is small, the grouting slurry will have an obvious water loss effect after passing through mudstone fissures. However, with the flow of the slurry, the water loss effect of the subsequent grouting slurry will be weakened. For fissures with high roughness, the water absorption properties of the rough surfaces and the walls of the mudstone fissures work together, leading to the sedimentation and blockage of the fissure channels, thereby hindering the flow of slurry.

Structural insights into the activation and inhibition of CXC chemokine receptor 3.

The chemotaxis of CD4+ type 1 helper cells and CD8+ cytotoxic lymphocytes, guided by interferon-inducible CXC chemokine 9-11 (CXCL9-11) and CXC chemokine receptor 3 (CXCR3), plays a critical role in type 1 immunity. Here we determined the structures of human CXCR3-DNGi complexes activated by chemokine CXCL11, peptidomimetic agonist PS372424 and biaryl-type agonist VUF11222, and the structure of inactive CXCR3 bound to noncompetitive antagonist SCH546738. Structural analysis revealed that PS372424 shares a similar orthosteric binding pocket to the N terminus of CXCL11, while VUF11222 buries deeper and activates the receptor in a distinct manner. We showed an allosteric binding site between TM5 and TM6, accommodating SCH546738 in the inactive CXCR3. SCH546738 may restrain the receptor at an inactive state by preventing the repacking of TM5 and TM6. By revealing the binding patterns and the pharmacological properties of the four modulators, we present the activation mechanisms of CXCR3 and provide insights for future drug development.

Research on Soft Rock Damage Softening Model and Roadway Deformation and Failure Characteristics.

To determine a reasonable control strategy for deep buried soft rock roadways, a study on deformation and failure characteristics was carried out. The Weibull distribution damage variable was introduced to construct a damage-softening model considering the lateral deformation of the rock mass, and the functional relationship between the model parameters F0 and m and the confining pressure were discussed. The nonlinear fitting method was used to correct the model parameters. Using the model, the failure characteristics of deep buried soft rock roadways were analyzed. A comprehensive and step-by-step joint support control strategy was proposed based on the numerical simulation results. The research results showed that the damage-softening model curve established could genuinely reflect the whole process of mudstone failure. The apparent stress concentration phenomenon occurred in the surrounding rock. The surrounding rock deformation showed that roadway floors had larger plastic failure areas than sides and vaults. The plastic failure depth could reach 2.45 m. After a comprehensive and step-by-step joint support control strategy was adopted, the deformation rate of the roadway at the section was less than 0.1 mm/d. The optimized support scheme can effectively improve the stability of the roadway.

In Situ Formation of Metal Oxide Nanocrystals Embedded in Laser-Induced Graphene.

Hybrid materials incorporating the advantages of graphene and nanoparticles have been widely studied. Here we develop an improved cost-effective approach for preparation of porous graphene embedded with various types of nanoparticles. Direct laser scribing on metal-complex-containing polyimide film leads to in situ formation of nanoparticles embedded in porous graphene. These materials are highly active in electrochemical oxygen reduction reactions, converting O2 into OH(-), with a low metal loading of less than 1 at. %. In addition, the nanoparticles can vary from metal oxide to metal dichalcogenides through lateral doping, making the composite active in other electrocatalytic reactions such as hydrogen evolution.

Design and test of miniaturized glass ceramics HeNe laser with frequency and intensity simultaneously stabilized.

A miniaturized HeNe laser with intensity and frequency simultaneously stabilized is described. The laser uses a monoblock glass ceramics as its tube to construct an improved steady structure. The closed loop cavity length control system stabilizes its frequency and the discharge current regulating system stabilizes its intensity. The electronic system integrating power supply and stabilization system is designed within two small circuit boards. The laser tube and circuit boards are assembled into a small package with dimensions of 180 mm×100 mm×150 mm. The laser outputs s-polarized light at wavelength of 632.99 nm with power of 0.44 mW. Test results show that its frequency stability can reach 8.4×10(-11) (1s Allan variance over 3 h) and frequency reproducibility at 1.3×10(-8). The laser's intensity stability is 0.011% over 9 h.