Hexicon 2: Automated Processing of Hydrogen-Deuterium Exchange Mass Spectrometry Data with Improved Deuteration Distribution Estimation

Hydrogen–deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.

Dynamics simulation and reaction pathway analysis of characteristics of soot particles in ethylene oxidation at high temperature

Soot particles characteristics were investigated numerically for high temperature oxidation of C₂H₄/O₂/N₂ (C/O ratio of 2.2) in a closed jet-stirred/plug-flow reactor (JSR/PFR) system. Based on the growth mechanism of polycyclic aromatic hydrocarbons (PAHs), two mechanisms were used to explore the formation pathways of soot precursors and soot. Numerical results were compared with the experimental and reference data. The simulation results show that the value predicted for small molecule intermediates within A1 gives a strong regularity, consistent trend with reference data. However, with the hydrogen-abstraction-carbon-addition (HACA) growth mechanism, the predicted value for beyond-A1 PAH macromolecules and soot volume fraction are smaller than the experimental data. The results also show that the predicted soot volume fraction is in good agreement with experimental data when a combination of the HACA and PAHs condensation (HACA + PAH-PAH) growth mechanisms is used. Analyses of the A1 sensitivity and reaction pathway elucidated that A1 are mainly formed from C₂H₃, C₂H₂, C₃H₃, C₆H₅OH, A1C₂H and A1-. The reaction 2C₃H₃ → A1 is the dominant route of benzene formation. The prediction results and an analysis of the A3 reaction pathway indicate that the growth process from benzene to larger aromatic hydrocarbons (beyond two-ring polycyclic aromatic hydrocarbons [PAHs]) goes by two pathways, i.e., HACA combined with the PAH-PAH radical recombination and addition reaction growth mechanisms.     

Catalytic epoxidation of alkenes over supported manganese oxide with hydrogen peroxide: effect of supports and manganese loading

Manganese oxides supported on γ-Al₂O₃, amorphous SiO₂, MCM-41, and TiO₂ prepared by an impregnation method were used as heterogeneous catalysts for epoxidation of alkenes with 30 % H₂O₂ in the presence of NaHCO₃ aqueous solution. The effect of support and manganese loading on their activity was studied. The 1.3-MnO _x /γ-Al₂O₃ exhibited superior epoxidazing activity of styrene, compared with other supported MnO _x . Hydrogen temperature-programmed reduction, UV–vis and ESR analyses suggested that Mn²⁺ (catalytic activity species) dominated in 1.3 % MnO _x /γ-Al₂O₃ due to a strong interaction between MnO _x and γ-Al₂O₃. Recycling studies showed the catalyst was a heterogeneous one and retained its activity after recycling four times.     

Enzymatic Building-Block Synthesis for Solid-Phase Automated Glycan Assembly

Automated chemical oligosaccharide synthesis is an attractive concept that has been successfully applied to a large number of target structures, but requires excess quantities of suitably protected and activated building blocks. Herein we demonstrate the use of biocatalysis to supply such reagents for automated synthesis. By using the promiscuous NmLgtB-B β1-4 galactosyltransferase from Neisseria meningitidis we demonstrate fast and robust access to the LacNAc motif, common to many cell-surface glycans, starting from either lactose or sucrose as glycosyl donors. The enzymatic product was shown to be successfully incorporated as a complete unit into a tetrasaccharide target by automated assembly.     

Divergent Total Synthesis of Euphoranginol C,Euphoranginone D,ent-Trachyloban-3β-ol,ent-Trachyloban-3-one,Excoecarin E,and ent-16α-Hydroxy-atisane-3-one

A divergent synthetic approach to biogenetically related diterpenoids such as ent-kauranes, ent-trachylobanes, ent-beyerane, and ent-atisane has been developed. The unified synthetic route involves the De Mayo reaction to rapidly generate the bicyclo[3.2.1]-octane moiety of ent-kaurane. The key reactions also include bioinspired nucleophilic cyclopropanation generating the [3.2.1.0^2,7]-tricyclic core of ent-trachylobane and regioselective cyclopropane fragmentation furnishing ent-beyerane and ent-atisane through the nucleophilic attack and protonation of the cyclopropane ring. This strategy enables the asymmetric total syntheses of six diterpenoids from the commercially available geraniol.     

Bioorthogonal Ligation and Cleavage by Reactions of Chloroquinoxalines with ortho-Dithiophenols

A bioorthogonal ligation and cleavage method via reactions of chloroquinoxalines (CQ) and ortho-dithiophenols (DT) is presented. Double nucleophilic substitutions of ortho-dithiophenols to chloroquinoxalines provide conjugates containing tetracyclic benzo[5,6][1,4]dithiino[2,3-b]quinoxaline with strong built-in fluorescence together with release of the other functional molecules. Three cleavable linkers were designed and successfully used in release of the molecules containing biotin from the protein conjugates. The CQ-DT bioorthogonal reactions can be applied for the bioorthogonal ligations, bioorthogonal cleavages, and trans-tagging of proteins, and show advantages of readily accessible unnatural orthogonal groups, appealing reaction kinetics (k₂≈1.3 m ⁻¹ s⁻¹), excellent biocompatibility of orthogonal groups, and high stability of conjugates. This complements previous bioorthogonal reactions and is a new route for protein-fishing applications and in-gel fluorescence analysis.     

Rationally Designed Three-Layered Cu2S@Carbon@MoS2 Hierarchical Nanoboxes for Efficient Sodium Storage

Hybrid materials, integrating the merits of individual components, are ideal structures for efficient sodium storage. However, the construction of hybrid structures with decent physical/electrochemical properties is still challenging. Now, the elaborate design and synthesis of hierarchical nanoboxes composed of three-layered Cu₂S@carbon@MoS₂ as anode materials for sodium-ion batteries is reported. Through a facile multistep template-engaged strategy, ultrathin MoS₂ nanosheets are grown on nitrogen-doped carbon-coated Cu₂S nanoboxes to realize the Cu₂S@carbon@MoS₂ configuration. The design shortens the diffusion path of electrons/Na⁺ ions, accommodates the volume change of electrodes during cycling, enhances the electric conductivity of the hybrids, and offers abundant active sites for sodium uptake. By virtue of these advantages, these three-layered Cu₂S@carbon@MoS₂ hierarchical nanoboxes show excellent electrochemical properties in terms of decent rate capability and stable cycle life.     

用于细胞和组织中弗林蛋白酶特异性成像的双光子荧光探针研究

弗林蛋白酶是前体蛋白转化酶家族中最具特色的酶之一,具有重要的生物学功能,其表达量水平与许多疾病有密切的关系,如癌症的发生和发展与弗林蛋白酶表达水平有着密切关联.目前文献中报道了一些单光子荧光探针用于弗林蛋白酶的检测,但这些探针不能应用于深层组织成像,且弗林蛋白酶在肿瘤发展过程的作用仍没有得到很好地研究.针对这些问题,本工作构建了一种新型双光子荧光探针Nap-F用于细胞和肿瘤组织内弗林蛋白酶的检测与双光子成像.Nap-F是由经典双光子荧光染料1,8-萘酰亚胺、弗林蛋白酶特异性多肽序列RVRR和自消除连接体整合而成.实验结果表明Nap-F对弗林蛋白酶具有很好的特异性,能够定量检测弗林蛋白酶的活性.在飞秒激光820 nm激发下,Nap-F能有效降低生物背景,并提高组织穿透深度,适用于细胞和组织的双光子成像.Nap-F成功地实现了几种活细胞中弗林蛋白酶的双光子成像,揭示了癌细胞和表达缺陷细胞中弗林蛋白酶含量的差异.更重要的是,我们将该探针用于CoCl₂固定HIF-1构建的肿瘤细胞缺氧模型成像,实验结果表明弗林蛋白酶的表达与肿瘤细胞缺氧程度存在正相关性.     

Fabrication of Heterostructured Fe2TiO5–TiO2 Nanocages with Enhanced Photoelectrochemical Performance for Solar Energy Conversion

Photocatalysts with well‐designed compositions and structures are desirable for achieving highly efficient solar‐to‐chemical energy conversion. Heterostructured semiconductor photocatalysts with advanced hollow structures possess beneficial features for promoting the activity towards photocatalytic reactions. Here we develop a facile synthetic strategy for the fabrication of Fe₂TiO₅–TiO₂ nanocages (NCs) as anode materials in photoelectrochemical (PEC) water splitting cells. A hydrothermal reaction is performed to transform MIL‐125(Ti) nanodisks (NDs) to Ti–Fe–O NCs, which are further converted to Fe₂TiO₅–TiO₂ NCs through a post annealing process. Owing to the compositional and structural advantages, the heterostructured Fe₂TiO₅–TiO₂ NCs show enhanced performance for PEC water oxidation compared with TiO₂ NDs, Fe₂TiO₅ nanoparticles (NPs) and Fe₂TiO₅–TiO₂ NPs.     

Rationally Designed Three‐Layered Cu2S@Carbon@MoS2 Hierarchical Nanoboxes for Efficient Sodium Storage

Hybrid materials, integrating the merits of individual components, are ideal structures for efficient sodium storage. However, the construction of hybrid structures with decent physical/electrochemical properties is still challenging. Now, the elaborate design and synthesis of hierarchical nanoboxes composed of three‐layered Cu₂S@carbon@MoS₂ as anode materials for sodium‐ion batteries is reported. Through a facile multistep template‐engaged strategy, ultrathin MoS₂ nanosheets are grown on nitrogen‐doped carbon‐coated Cu₂S nanoboxes to realize the Cu₂S@carbon@MoS₂ configuration. The design shortens the diffusion path of electrons/Na⁺ ions, accommodates the volume change of electrodes during cycling, enhances the electric conductivity of the hybrids, and offers abundant active sites for sodium uptake. By virtue of these advantages, these three‐layered Cu₂S@carbon@MoS₂ hierarchical nanoboxes show excellent electrochemical properties in terms of decent rate capability and stable cycle life.