Full protein flexibility is essential for proper hot-spot mapping

A traditional technique for structure-based drug design (SBDD) is mapping of protein surfaces with probe molecules to identify "hot spots" where key functional groups can best complement the receptor. Common methods, such as minimization of probes or calculation of grids, use a fixed protein structure in the gas phase, ignoring both protein flexibility and proper competition between the probes and water. As a result, the potential surface is quite rugged, and many spurious local minima are identified. In this work, we compared rigid and fully flexible proteins in mixed-solvent molecular dynamics, which allows for flexibility and full solvent effects. We were surprised to find that the large number of local minima are still found when a protein's conformational sampling is restricted; the dynamic averaging of probes and competition with water do not smooth the potential surface as one might expect. Only when a protein is allowed to be fully flexible in the simulation are the proper minima located and the spurious ones eliminated. Our results indicate that inclusion of full protein flexibility is critical to accurate hot-spot mapping for SBDD.     

Supercritical Water is not Hydrogen Bonded

Thinking about water is inextricably linked to hydrogen bonds, which are highly directional in character and determine the unique structure of water, in particular its tetrahedral H-bond network. Here, we assess if this common connotation also holds for supercritical water. We employ extensive ab initio molecular dynamics simulations to systematically monitor the evolution of the H-bond network mode of water from room temperature, where it is the hallmark of its fluctuating three-dimensional network structure, to supercritical conditions. Our simulations reveal that the oscillation period required for H-bond vibrations to occur exceeds the lifetime of H-bonds in supercritical water by far. Instead, the corresponding low-frequency intermolecular vibrations of water pairs as seen in supercritical water are found to be well represented by isotropic van-der-Waals interactions only. Based on these findings, we conclude that water in its supercritical phase is not a H-bonded fluid.     

Replacing targeted compassion with multidimensional compassion: an essential paradigm shift to achieve sustainability

We are in the midst of a national, arguably global, debate about hunting and other means of controlling populations of deer and other animals that have greatly exceeded the carrying capacity of local and regional habitat. At one extreme are those who feel that, since humans have eliminated the large, natural predators, we are obligated to keep game species in balance with their environment. At the other extreme are those who value the lives of individual wild creatures and seek to prevent their destruction. Keeping in balance with nature is the essence of sustainability. This would permit the largest number of humans to occupy the planet over a long period of time. Properly managed sustainability should concomitantly make the planet more habitable for other species. The position taken in this discussion is that targeted compassion is inappropriate for sustainable use of the planet because it will not leave a habitable world for future generations.     

An RNA G-quadruplex is essential for cap-independent translation initiation in human VEGF IRES

RNA G-quadruplexes located within the 5'-UTR of mRNA are almost always known to be associated with repression of cap-dependent translation. However, in this report we present functional as well as structural evidence that sequence redundancy in a G-rich segment within the 5'-UTR of human VEGF mRNA supports a 'switchable' RNA G-quadruplex structure that is essential for IRES-mediated translation initiation. Additionally, utilization of a specific combination of G-tracts within this segment allows for the conformational switch that implies a tunable regulatory role of the quadruplex structure in translation initiation. A sequence engineered from a functionally handicapped mutant moderately rescued the activity, further indicating the importance of G-quadruplex structure for VEGF IRES-A function. This to our knowledge is the first report of a conformationally flexible RNA G-quadruplex which is essential for IRES-mediated translation initiation.     

Chelation with metal is not essential for antitumor photodynamic activity of sulfonated phthalocyanines

It is generally assumed that a central metal is essential for the efficiency of phthalocyanines in photodynamic therapy (PDT) of cancer. Contrary to the set opinion, the results of the present study indicate that the metal-free sulfonated phthalocyanines (H2PcSn, where n is the number of sulfonate groups per molecule) possess a considerable photoactivity. The relative phototoxicities of H2PcS1.5, H2PcS2.4, H2PcS3.1 and H2PcS3.8 on HEp2 human epidermoid carcinoma cells were 3.3, 20, 3.3 and 1, respectively, thus demonstrating dependence of the activity on the sulfonation degree, known for metallo-PcSn. A significant delay in tumor growth and a decrease in tumor regrowth rate were observed in mice after PDT with H2PcS2.4. The antitumor effect declined in the order H2PcS2.4 > H2PcS3.1 > H2PcS1.5 and vanished for H2PcS3.8. We demonstrate here that the high photodynamic activity of H2PcS2.4 can be explained by its physicochemical properties in living cells and tissues. Thus, H2PcSn (n is about 2) can be considered as a new alternative in PDT of light-accessible neoplasms and further clinic-oriented studies are warranted.     

Intensifying Hydrogen Spillover for Boosting Electrocatalytic Hydrogen Evolution Reaction

Hydrogen spillover has attracted increasing interests in the field of electrocatalytic hydrogen evolution reaction (HER) in recent years because of their distinct reaction mechanism and beneficial terms for simultaneously weakening the strong hydrogen adsorption on metal and strengthening the weak hydrogen adsorption on support. By taking advantageous merits of efficient hydrogen transfer, hydrogen spillover-based binary catalysts have been widely investigated, which paves a new way for boosting the development of hydrogen production by water electrolysis. In this paper, we summarize the recent progress of this interesting field by focusing on the advanced strategies for intensifying the hydrogen spillover towards HER. In addition, the challenging issues and some perspective insights in the future development of hydrogen spillover-based electrocatalysts are also systematically discussed.     

Zinc is an essential cofactor for type I isopentenyl diphosphate:dimethylallyl diphosphate isomerase

Isopentenyl diphosphate (IPP) isomerase catalyzes the interconversion of IPP and dimethylallyl diphosphate (DMAPP). This is an essential reaction in the mevalonate pathway for biosynthesis of isoprenoid compounds. A crystal structure of Escherichia coli type I IPP isomerase shows a his3glu2 octahedral metal binding site (Durbecq, V. et al. EMBO, 2001, 20, 1530-1537). A metal ion analysis of recombinant E. coli type I IPP isomerase purified from metal-free buffer or buffer containing 10 muM ZnCl2 and 10 muM MnCl2 indicated that the protein contained one atom of Zn2+ per molecule. The metal content and the activity of the enzyme did not change when dialyzed for 6 h against metal-free buffer but rapidly decreased upon dialysis against buffer containing o-phenanthroline. Structural and catalytic roles for Zn2+ are discussed.     

Conserved motif VIII of murine DNA methyltransferase Dnmt3a is essential for methylation activity

Background

Dnmt3a is a DNA methyltransferase that establishes de novo DNA methylation in mammals. The structure of the Dnmt3a C-terminal domain is similar to the bacterial M. HhaI enzyme, a well-studied prokaryotic DNA methyltransferase. No X-ray structure is available for the complex of Dnmt3a with DNA and the mechanistic details of DNA recognition and catalysis by mammalian Dnmts are not completely understood.

Results

Mutant variants of the catalytic domain of the murine Dnmt3a carrying substitutions of highly conserved N167, R200, and R202 have been generated by site directed mutagenesis and purified. Their methylation activity, DNA binding affinity, ability to flip the target cytosine out of the DNA double helix and covalent complex formation with DNA have been examined. Substitutions of N167 lead to reduced catalytic activity and reduced base flipping. Catalytic activity, base flipping, and covalent conjugate formation were almost completely abolished for the mutant enzymes with substitutions of R200 or R202.

Conclusions

We conclude that R202 plays a similar role in catalysis in Dnmt3a-CD as R232 in M.SssI and R165 in M.HhaI, which could be positioning of the cytosine for nucleophilic attack by a conserved Cys. R200 of Dnmt3a-CD is important in both catalysis and cytosine flipping. Both conserved R200 and R202 are involved in creating and stabilizing of the transient covalent intermediate of the methylation reaction. N167 might contribute to the positioning of the residues from the motif VI, but does not play a direct role in catalysis.

     

Hydrogen peroxide is responsible for UVA-induced DNA damage measured by alkaline comet assay in HaCaT keratinocytes

We investigated the role of different reactive oxygen species (ROS) in ultraviolet A (UVA)-induced DNA damage in a human keratinocyte cell line, HaCaT. UVA irradiation increased the intracellular levels of hydrogen peroxide (H2O2), detected by a fluorescent probe carboxydichlorodihydrofluorescein, and caused oxidative DNA damage, single strand-breaks and alkali-labile sites, measured by alkaline single cell gel electrophoresis (comet assay). Superoxide anion (O2*-) was a likely substrate for H2O2 production since diethyldithiocarbamate (DDC), a superoxide dismutase blocker, decreased the level of intracellular H2O2. Hydrogen peroxide was shown to play a central role in DNA damage. Increasing the intracellular levels of H2O2 with aminotriazole (AT) (a catalase blocker) and buthionine sulfoximine (BSO) (an inhibitor of glutathione synthesis) potentiated the UVA-induced DNA damage. Exogenous H2O2 was also able to induce DNA damage. Since H2O2 alone is not able to damage DNA directly, we investigated the significance of the H2O2-derived hydroxyl radical (*OH). Addition of FeSO4, that stimulates *OH formation from H2O2 (Fenton reaction) resulted in a twofold increase of DNA-damage. Desferrioxamine, an iron chelator that blocks the Fenton reaction, prevented UVA-induced DNA damage. We also employed a panel of less specific antioxidants and enzyme modulators. Sodium selenite (Na-Se) present in glutathione peroxidase and thioredoxin reductase and addition of glutathione (GSH) prevented DNA-damage. Tocopherol potently prevented UVA-and H2O2-induced DNA damage and reduced intracellular H2O2 -levels. Ascorbic acid reduced H2O2 production, but only partly prevented DNA damage. Singlet oxygen (1O2) did not seem to play an important role in the UVA-induced DNA-damage since the specific 1O2 scavenger sodium azide (NaN3) and the less specific 1O2 scavenger beta-carotene did not markedly prevent either DNA-damage or H2O2 production. In conclusion the conversion of H2O2 to *OH appears to be the most important step in UVA-induced generation of strand breaks and alkali-labile sites and the bulk H2O2 appears to originate from O2*- generated by UVA irradiation.     

用于光催化分解硫化氢制氢的金属硫化物

硫化氢(H₂S)作为一种剧毒、恶臭的强腐蚀性气体,广泛来源于人类活动和自然界,对动植物生存和环境都具有较大的危害。光催化分解H₂S制氢是一种理想的H₂S处理技术,可以同时实现H₂S的转移和清洁能源氢气的产生。近年来,金属硫化物由于其优异的可见光响应、恰当的能带结构和对H₂S有高的稳定性,因此被广泛地应用于光催化分解H₂S制氢。本文对近年来国内外金属硫化物驱动H₂S资源化利用制氢领域取得的重要进展进行了概述和总结,探讨了不同反应媒介下光催化分解H₂S制氢机制;特别关注了一些为实现高效稳定光催化H₂S资源化利用制氢的优异调控策略;最后,对H₂S资源化利用的挑战和前景进行了展望。     

Designing for sustainability with biocatalytic and chemoenzymatic cascade processes

Cascade reactions have been widely recognized to cut costs, decrease solvent usage, and reduce cycle times in chemical processes. Recently, biocatalytic cascades have altered how we design synthetic routes to complex molecules to achieve sustainable commercial processes for pharmaceutical, agricultural, and fine chemical industries. With advancements in protein engineering and an increase in the number of enzyme classes available to chemists, industrial and academic groups alike have endeavored to expand the scope of biocatalysis from single reactions to multi-enzyme cascades to rapidly build complex molecular structures. Recent reports have drawn inspiration from biosynthetic pathways and have applied engineered enzymes to in vitro enzymatic cascades. Furthermore, combining transition-metal catalysis and enzymes in one-pot chemoenzymatic cascades likewise serves to broaden the scope of biocatalysis, enabling traditional chemical reactions to be performed under mild aqueous conditions. In this article, we review recent biocatalytic and chemoenzymatic cascades from 2019 to 2021.     

Inorganic Membranes for Hydrogen Separation

Hydrogen, one of the most promising energy carriers for the future, is currently produced mainly by natural gas reforming or coal gasification, where mixtures containing H₂, CO₂ and contaminants like CO, H₂S and CH₄ are obtained. Among other methods, membrane technology has received special attention due to its potential efficiency for hydrogen separation, simplicity of operation, low energy consumption, and because it is environmentally friendly. For this application, the inorganic membranes can be essentially divided into five main families: metallic and proton conducting (dense phases), and silica, zeolite and carbon molecular sieve (porous solids). Over the past 20 years, palladium-based membranes have been the most studied and implemented at industrial level; however, recent advances in other membrane types have received a great deal of attention. This article critically reviews more than 520 publications, highlighting the latest research developments on inorganic membranes for the recovery and purification of hydrogen, with emphasis on their structural characteristics, synthesis, commercial application, drawbacks and challenges. Furthermore, a large compilation of data is provided in Supplementary Material divided according to membrane type.     

纳米限域的储氢材料

氢能作为洁净、理想的二次能源,已受到世界各国的广泛关注。然而,氢的储存技术仍然是制约氢能商业化应用的关键技术。利用储氢材料进行储氢被认为是一种安全、高效的固态储氢方式。因此,开发新型高容量的储氢材料与储氢技术成为氢能领域研究的热点之一。纳米限域是将材料填充到纳米孔道里,利用材料和纳米孔道的相互作用促进反应的进行,为化学反应提供一个独特的微环境。近年来,纳米限域逐渐发展成为改善储氢材料热力学和动力学的新方法。本文综述了纳米限域的储氢材料的研究进展,从纳米限域的储氢材料制备、储氢性能、反应机理和存在的问题等方面进行讨论,并指出了纳米限域储氢材料的发展趋势。     

人工光合成制氢

氢气的燃烧热值高(285.8 kJ/mol),且燃烧时只生成水不生成任何污染物,被认为是理想的能源载体。模拟自然界光合作用系统活性中心的结构和功能,利用光催化分解水制取氢气是将太阳能转换为化学能的重要方式,也是人工光合成的重要内容。本文对近年来国内外人工光合成制氢领域取得的重要进展进行了总结,并对人工光合成制氢的发展趋势和前景进行了展望。     

Tyrosine 105 of Paucimonas lemoignei PHB depolymerase PhaZ7 is essential for polymer binding

The 3-dimensional structure of the Paucimonas lemoignei poly(3-hydroxybutyrate) (PHB) depolymerase PhaZ7 has significant similarity to Bacillus subtilis lipase LipA but differs from the latter by the presence of an additional domain. Analysis of this lid-like domain revealed the presence of many hydrophobic amino acid residues including Tyr₁₀₅. In this study we constructed His-tag fusions of PhaZ7 for simplified purification and investigated the effect of amino acid exchange of eight tyrosine codons of the lid-like domain. Exchanges of Tyr₁₀₃, Tyr₁₇₂, Tyr₁₇₃, Tyr₂₀₃ or Tyr₂₀₄ to alanine or serine had no phenotype but muteins with substitution of Tyr₁₈₉, Tyr₁₉₀ and Tyr₁₀₅ to alanine showed a lag phase of the in vitro PHB depolymerase reaction. Replacement of Tyr₁₀₅ by glutamate further increased the lag phase. Binding assays of the purified PHB depolymerase proteins with the natural substrate, native PHB granules, revealed a significantly reduced binding ability of the Tyr₁₀₅Glu mutant compared to the wild type protein and confirmed that Tyr₁₀₅ is involved in interaction with the polymeric substrate.     

Multiplasmid DNA in agarose gel electrophoresis: Suitable dye and temperature is essential for prominent profiles

Nucleic acids dye Goldview is widely used in agarose gel electrophoresis (AGE). However, in this study, a sample of multiplasmid DNA (multi-pDNA) stained with Goldview analyzed by AGE showed its instability at low temperature. Three types of DNA samples were analyzed, including linear DNA (ladder), single-plasmid DNA (single-pDNA), and multi-pDNA, electrophoretic conditions were optimized by adjusting the dye, the buffer, and the temperature (1–50°C). The results showed that the light intensity of Gelred is 2.2-times higher than that of Goldview in staining multi-pDNA. Compared with the single-pDNA and the linear DNA, the multi-pDNA stained with Goldview was greatly affected by temperature. This short communication indicated that Gelred is a highly applicable dye for analyzing multiplasmid samples. The degree and the way of binding of Goldview to multi-pDNA are greatly affected by temperature.