Radiation- and Photo-Induced Oxidation Pathways of Methionine in Model Peptide Backbone under Anoxic Conditions

Within the reactive oxygen species (ROS) generated by cellular metabolisms, hydroxyl radicals (HO^•) play an important role, being the most aggressive towards biomolecules. The reactions of HO^• with methionine residues (Met) in peptides and proteins have been intensively studied, but some fundamental aspects remain unsolved. In the present study we examined the biomimetic model made of Ac-Met-OMe, as the simplest model peptide backbone, and of HO^• generated by ionizing radiation in aqueous solutions under anoxic conditions. We performed the identification and quantification of transient species by pulse radiolysis and of final products by LC-MS and high-resolution MS/MS after γ-radiolysis. By parallel photochemical experiments, using 3-carboxybenzophenone (CB) triplet with the model peptide, we compared the outcomes in terms of short-lived intermediates and stable product identification. The result is a detailed mechanistic scheme of Met oxidation by HO^•, and by CB triplets allowed for assigning transient species to the pathways of products formation.     

α钛富氧层增厚动力学模型

为了实现在工业化生产中对α钛富氧层厚度预测和控制,通过实验研究α钛富氧层在高温空气环境中的形成及增厚过程,讨论热处理温度和时间的影响作用,建立高温(750~850℃)空气环境下关于温度、时间的富氧层增厚动力学模型。结果表明:当恒温热处理温度为750~850℃时,α钛富氧层厚度x与保温时间t0.5呈正比例关系,且升高热处理温度可显著提高富氧层增厚速度。在此温度范围内,氧原子的扩散激活能约为203473 J/mol,计算曲线与实验数据吻合性较好。结合文献中已有的扩散系数方程和实验测得的富氧层厚度数据,推导得到5个富氧层增厚动力学方程,其中3个方程的计算曲线与实验数据吻合性较好,可为实际生产中预估富氧层厚度提供理论支持。     

钨中空位及其团簇的能量学和动力学性质参数

在总结前人钨中空位及其团簇的能量学和动力学行为的研究成果基础上，采用第一性原理方法系统计算了钨中空位及其团簇的结合能和扩散能垒。研究发现，交换关联泛函PW91和PBE较PBEsol、AM05和LDA更适合用于计算钨空位的能量学性质。基于第一性原理计算结果对文献中单空位形成能、双空位作用性质等争议性问题进行了讨论，并对钨经验势进行了评估。研究结果表明，钨中孤立单空位间总是相互排斥，而空位团簇（V_n>3）对单空位具有很强的吸引作用，其结合能随着所含空位个数增多呈现波动性增大的趋势。空位团簇稳定结构可通过最小化Wigner-Seitz表面积来确定，其结合能与V_n与V_n-1之间的Wigner-Seitz面积之差呈正比。     

Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs

Rift Valley fever virus (RVFV) is a mosquito-transmitted virus from the Bunyaviridae family that causes high rates of mortality and morbidity in humans and ruminant animals. Previous studies indicated that DEAD-box helicase 17 (DDX17) restricts RVFV replication by recognizing two primary non-coding RNAs in the S-segment of the genome: the intergenic region (IGR) and 5′ non-coding region (NCR). However, we lack molecular insights into the direct binding of DDX17 with RVFV non-coding RNAs and information on the unwinding of both non-coding RNAs by DDX17. Therefore, we performed an extensive biophysical analysis of the DDX17 helicase domain (DDX17_135–555) and RVFV non-coding RNAs, IGR and 5’ NCR. The homogeneity studies using analytical ultracentrifugation indicated that DDX17_135–555, IGR, and 5’ NCR are pure. Next, we performed small-angle X-ray scattering (SAXS) experiments, which suggested that DDX17 and both RNAs are homogenous as well. SAXS analysis also demonstrated that DDX17 is globular to an extent, whereas the RNAs adopt an extended conformation in solution. Subsequently, microscale thermophoresis (MST) experiments were performed to investigate the direct binding of DDX17 to the non-coding RNAs. The MST experiments demonstrated that DDX17 binds with the IGR and 5’ NCR with a dissociation constant of 5.77 ± 0.15 µM and 9.85 ± 0.11 µM, respectively. As DDX17_135–555 is an RNA helicase, we next determined if it could unwind IGR and NCR. We developed a helicase assay using MST and fluorescently-labeled oligos, which suggested DDX17_135–555 can unwind both RNAs. Overall, our study provides direct evidence of DDX17_135–555 interacting with and unwinding RVFV non-coding regions.     

Identification of the Primary Factors Determining the Specificity of Human VKORC1 Recognition by Thioredoxin-Fold Proteins

Redox (reduction–oxidation) reactions control many important biological processes in all organisms, both prokaryotes and eukaryotes. This reaction is usually accomplished by canonical disulphide-based pathways involving a donor enzyme that reduces the oxidised cysteine residues of a target protein, resulting in the cleavage of its disulphide bonds. Focusing on human vitamin K epoxide reductase (hVKORC1) as a target and on four redoxins (protein disulphide isomerase (PDI), endoplasmic reticulum oxidoreductase (ERp18), thioredoxin-related transmembrane protein 1 (Tmx1) and thioredoxin-related transmembrane protein 4 (Tmx4)) as the most probable reducers of VKORC1, a comparative in-silico analysis that concentrates on the similarity and divergence of redoxins in their sequence, secondary and tertiary structure, dynamics, intraprotein interactions and composition of the surface exposed to the target is provided. Similarly, hVKORC1 is analysed in its native state, where two pairs of cysteine residues are covalently linked, forming two disulphide bridges, as a target for Trx-fold proteins. Such analysis is used to derive the putative recognition/binding sites on each isolated protein, and PDI is suggested as the most probable hVKORC1 partner. By probing the alternative orientation of PDI with respect to hVKORC1, the functionally related noncovalent complex formed by hVKORC1 and PDI was found, which is proposed to be a first precursor to probe thiol–disulphide exchange reactions between PDI and hVKORC1.     

Fluorescence Correlation Spectroscopy Analysis of Effect of Molecular Crowding on Self-Assembly of β-Annulus Peptide into Artificial Viral Capsid

Recent progress in the de novo design of self-assembling peptides has enabled the construction of peptide-based viral capsids. Previously, we demonstrated that 24-mer β-annulus peptides from tomato bushy stunt virus spontaneously self-assemble into an artificial viral capsid. Here we propose to use the artificial viral capsid through the self-assembly of β-annulus peptide as a simple model to analyze the effect of molecular crowding environment on the formation process of viral capsid. Artificial viral capsids formed by co-assembly of fluorescent-labelled and unmodified β-annulus peptides in dilute aqueous solutions and under molecular crowding conditions were analyzed using fluorescence correlation spectroscopy (FCS). The apparent particle size and the dissociation constant (K_d) of the assemblies decreased with increasing concentration of the molecular crowding agent, i.e., polyethylene glycol (PEG). This is the first successful in situ analysis of self-assembling process of artificial viral capsid under molecular crowding conditions.     

Silica-based ceramics toward electromagnetic microwave absorption

Silica-based ceramics have been explored extensively as a class of versatile materials for various applications in architecture, catalysis, energy, machinery, and biomedical engineering. Nevertheless, comprehensive information on silica-based ceramic and electromagnetic microwave (EMW) absorption is scarce, although excellent progress has been made in this field. Here, recent progress in the investigation of silica-based ceramics toward EMW absorption is reviewed. We first introduced the basis of ceramics (characteristics, classification, synthetic methods, potential applications). Subsequently, the silica-based ceramics, including Si-based oxides and alloys, SiOC/SiC/Si₃N₄/SiCN-based composite, Ti₃SiC₂ and composite for EMW absorption were systematically summarized. Notably, the fabrication strategies, absorption properties, and mechanisms of silica-based ceramics are described in detail, with a focus on structure and component design. Lastly, the prospects and ongoing challenges of this field in the future are presented. This review is expected to learn from the past and achieve progress toward the future of silica-based ceramic for EMW absorption.