An E1‐Catalyzed Chemoenzymatic Strategy to Isopeptide‐N‐Ethylated Deubiquitylase‐Resistant Ubiquitin Probes

Triazole‐based deubiquitylase (DUB)‐resistant ubiquitin (Ub) probes have recently emerged as effective tools for the discovery of Ub chain‐specific interactors in proteomic studies, but their structural diversity is limited. A new family of DUB‐resistant Ub probes is reported based on isopeptide‐N‐ethylated dimeric or polymeric Ub chains, which can be efficiently prepared by a one‐pot, ubiquitin‐activating enzyme (E1)‐catalyzed condensation reaction of recombinant Ub precursors to give various homotypic and even branched Ub probes at multi‐milligram scale. Proteomic studies using label‐free quantitative (LFQ) MS indicated that the isopeptide‐N‐ethylated Ub probes may complement the triazole‐based probes in the study of Ub interactome. Our study highlights the utility of modern protein synthetic chemistry to develop structurally and new families of tool molecules needed for proteomic studies.     

Activity‐Based Probes Developed by Applying a Sequential Dehydroalanine Formation Strategy to Expressed Proteins Reveal a Potential α‐Globin‐Modulating Deubiquitinase

We report a general and novel semisynthetic strategy for the preparation of ubiquitinated protein‐activity‐based probes on the basis of sequential dehydroalanine formation on expressed proteins. We applied this approach to construct a physiologically and therapeutically relevant ubiquitinated α‐globin probe, which was used for the enrichment and proteomic identification of α‐globin‐modulating deubiquitinases. We found USP15 as a potential deubiquitinase for the modulation of α‐globin, an excess of which aggravates β‐thalassemia symptoms. This development opens new opportunities for activity‐based‐probe design to shed light on the important aspects underlying ubiquitination and deubiquitination in health and disease.     

Efficient Semi-Synthesis of Atypical Ubiquitin Chains and Ubiquitin-Based Probes Forged by Thioether Isopeptide Bonds

The development of powerful and general methods to acquire ubiquitin (Ub) chains has prompted the deciphering of Ub-mediated processes. Herein, the cysteine-aminoethylation assisted chemical ubiquitination (CAACU) strategy is extended and improved to enable the efficient semi-synthesis of atypical Ub chain analogues and Ub-based probes. Combining the Cys aminoethylation and the auxiliary-mediated protein ligation, several linkage- and length-defined atypical Ub chains including di-Ubs, K27C-linked tri-Ub, K11/K48C-branched tri-Ub, and even the SUMOlated Ub are successfully prepared from recombinantly expressed starting materials at about a 9–20 mg L⁻¹ expression level. In addition, the utility of this strategy is demonstrated with the synthesis of a novel non-hydrolyzable di-Ub PA probe, which may provide a new useful tool for the mechanistic studies of deubiquitinase (DUB) recognition.     

Fluorescently Labelled ATP Analogues for Direct Monitoring of Ubiquitin Activation

Simple and robust assays to monitor enzymatic ATP cleavage with high efficiency in real-time are scarce. To address this shortcoming, we developed fluorescently labelled adenosine tri-, tetra- and pentaphosphate analogues of ATP. The novel ATP analogues bear — in contrast to earlier reports — only a single acridone-based dye at the terminal phosphate group. The dye's fluorescence is quenched by the adenine component of the ATP analogue and is restored upon cleavage of the phosphate chain and dissociation of the dye from the adenosine moiety. Thereby the activity of ATP-cleaving enzymes can be followed in real-time. We demonstrate this proficiency for ubiquitin activation by the ubiquitin-activating enzymes UBA1 and UBA6 which represents the first step in an enzymatic cascade leading to the covalent attachment of ubiquitin to substrate proteins, a process that is highly conserved from yeast to humans. We found that the efficiency to serve as cofactor for UBA1/UBA6 very much depends on the length of the phosphate chain of the ATP analogue: triphosphates are used poorly while pentaphosphates are most efficiently processed. Notably, the novel pentaphosphate-harbouring ATP analogue supersedes the efficiency of recently reported dual-dye labelled analogues and thus, is a promising candidate for broad applications.     

Structural Diversity of Ubiquitin E3 Ligase

The post-translational modification of proteins regulates many biological processes. Their dysfunction relates to diseases. Ubiquitination is one of the post-translational modifications that target lysine residue and regulate many cellular processes. Three enzymes are required for achieving the ubiquitination reaction: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3). E3s play a pivotal role in selecting substrates. Many structural studies have been conducted to reveal the molecular mechanism of the ubiquitination reaction. Recently, the structure of PCAF_N, a newly categorized E3 ligase, was reported. We present a review of the recent progress toward the structural understanding of E3 ligases.     

F-发光探针的设计策略和应用研究

氟离子在人类的生产生活以及生态平衡等方面都起着非常重要的作用。生理上,人体中大部分的氟存在于牙齿和骨骼,氟化物与人体生命活动以及牙齿骨骼组织代谢密切相关,氟离子缺乏或摄入过量都会导致严重的健康问题。生态中,用含氟水灌溉,含氟尘埃沉降,以及土壤中的空气与受氟污染大气的交换,都会使土壤和地下水受到污染。因此,对生理以及自然环境中氟离子的定量检测和控制有重要意义。由于传统检测方法的局限性,具有选择性好、可视化检测以及原位无损等优点的发光检测技术成为物质检测与分析领域的热点,基于发光检测技术的氟离子发光探针的设计方法也引起了科研工作者极大的研究兴趣,并将其运用在生物检测或者实际的生活产品中。本综述总结了近五年来基于不同种类及检测机理设计的氟离子探针的研究进展,同时对探针的负载和应用方式进行了深入分析,最后对氟离子发光探针的发展方向进行了展望。     

Chemical Synthesis of Phosphorylated Ubiquitin and Diubiquitin Exposes Positional Sensitivities of E1‐E2 Enzymes and Deubiquitinases

Modification of ubiquitin by phosphorylation extends the signaling possibilities of this dynamic signal, as it could affect the activity of ligases and the processing of ubiquitin chains by deubiquitinases. The first chemical synthesis of phosphorylated ubiquitin and of Lys63‐linked diubiquitin at the proximal, distal or both ubiquitins is reported. This enabled the examination of how such a modification alters E1‐E2 activities of the ubiquitination machinery. It is found that E1 charging was not affected, while the assembly of phosphorylated ubiquitin chains was differentially inhibited with E2 enzymes tested. Moreover, this study shows that phosphorylation interferes with the recognition of linkage specific antibodies and the activities of several deubiquitinases. Notably, phosphorylation in the proximal or distal ubiquitin unit has differential effects on specific deubiquitinases. These results support a unique role of phosphorylation in the dynamics of the ubiquitin signal.     

Reversal of Solvatochromism: A New Strategy to Construct Activatable Two-photon Fluorescent Probes for Sensing

Two-photon (TP) imaging with a donor-acceptor (D?A) type fluorophore is an emerging tool for bioimaging and sensing. However, current TP probes suffer from serious solvatochromic quenching in aqueous solution due to their strong intramolecular charge transfer (ICT) in excited states. In this work, based on solvatochromism reversal, we report a novel strategy to develop TP probes for bioimaging. Specifically, compared with the normal two-photon probes that showed a fluorescence off with ICT suppressed, the novel probes exhibited strong fluorescence in the aqueous solution when their ICT was inhibited. This strategy not only provides a new way for the design of high-performance TP probes, but also expands the biological analysis toolbox for use in living systems.     

Interrogating Substrate Selectivity and Composition of Endogenous Histone Deacetylase Complexes with Chemical Probes

Histone deacetylases (HDACs) regulate the function and activity of numerous cellular proteins by removing acetylation marks from regulatory lysine residues. We have developed peptide‐based HDAC probes that contain hydroxamate amino acids of various lengths to replace modified lysine residues in the context of known acetylation sites. The interaction profiles of all human HDACs were studied with three sets of probes, which derived from different acetylation sites, and sequence context was found to have a strong impact on substrate recognition and composition of HDAC complexes. By investigating K382 acetylation of the tumor suppressor p53 as an example, we further demonstrate that the interaction profiles reflect the catalytic activities of respective HDACs. These results underline the utility of the newly established probes for deciphering not only activity, but also substrate selectivity and composition of endogenous HDAC complexes, which can hardly be achieved otherwise.     

Cell‐ and Tissue‐Based Proteome Profiling and Bioimaging with Probes Derived from a Potent AXL Kinase Inhibitor

AXL has been defined as a novel target for cancer therapeutics. However, only a few potent and selective inhibitors targeting AXL are available to date. Recently, our group has developed a lead compound, 9im, capable of displaying potent and specific inhibition of AXL. To further identify the cellular on/off targets, in this study, competitive affinity‐based proteome profiling was carried out, leading to the discovery of several unknown cellular targets such as BCAP31, LPCAT3, POR, TM9SF3, SCCPDH and CANX. In addition, trans‐cyclooctene (TCO) and acedan‐containing probes were developed to image the binding between 9im and its target proteins inside live cells and tumor tissues. These probes would be useful tools in the detection of AXL in various biosystems.     

A Sequential Dual‐Lock Strategy for Photoactivatable Chemiluminescent Probes Enabling Bright Duplex Optical Imaging

Chemiluminescence (CL)‐based technologies have revolutionized in vivo monitoring of biomolecules. However, significant technical hurdles have limited the achievement of trigger‐controlled, bright, and enriched CL signal. Herein, a dual‐lock strategy uses sequence‐dependent triggers for bright optical imaging with real‐time fluorescent signal and ultra‐sensitive CL signal. These probes can obtain an analyte‐triggered accumulation of stable pre‐chemiluminophore with aggregation‐induced emission (AIE), and then the pre‐chemiluminophore exhibits a rapid photooxidation process (1,2‐dioxetane generation) by TICT‐based free‐radical addition, thereby achieving an enrichment and bright CL signal. The dual‐lock strategy expands the in vivo toolbox for highly accurate analysis and has for the first time allowed access to accurately sense and trace biomolecules with high‐resolution, dual‐mode of chemo‐fluoro‐luminescence, and three‐dimensional (3D) imaging in living animals.     

BODIPY-Based Fluorescent Probes for Biothiols

Fluorescent probes for biothiols have aroused increasing interest owing to their potential to enable better understanding of the diverse physiological and pathological processes related to the biothiol species. BODIPY fluorophores exhibit excellent optical properties, which can be readily tailored by introducing diverse functional units at various positions of the BODIPY core. In the present review, the development of fluorescent probes based on BODIPYs for the detection of biothiols are systematically summarized, with emphasis on the preferable detection of individual biothiols, as well as simultaneous discrimination among cysteine (Cys), homocysteine (Hcy), reduced glutathione (GSH). In addition, organelle-targeting probes for biothiols are also highlighted. The general design principles, various recognition mechanisms, and biological applications are elaboratively discussed, which could provide a useful reference to researchers worldwide interested in this area.     

When Molecular Probes Meet Self‐Assembly: An Enhanced Quenching Effect

We demonstrate that the incorporation of one or two amino acids of phenylalanine (F) or 4‐fluoro phenylalanine (^fF) will greatly lower the background fluorescence intensities of conventional quenched probes with quenchers. This enhanced quenching effect was due to the synergetic effect of the aggregation caused quenching and the presence of a quencher. Such strategy will not greatly affect the enzyme recognition properties to the probes. We also demonstrated that our self‐assembled nanoprobe with the enhanced quenching effect showed a better performance in cells for the detection of cell apoptosis than the unassembled probes. Our study demonstrates that using molecular self‐assembly can optimize and improve the performance of molecular probes and it provides a simple but very useful strategy to boost the signal‐to‐noise ratios of fluorescence probes.     

Development of ADPribosyl Ubiquitin Analogues to Study Enzymes Involved in Legionella Infection

Legionnaires’ disease is caused by infection with the intracellularly replicating Gram-negative bacterium Legionella pneumophila. This pathogen uses an unconventional way of ubiquitinating host proteins by generating a phosphoribosyl linkage between substrate proteins and ubiquitin by making use of an ADPribosylated ubiquitin (Ub^ADPr) intermediate. The family of SidE effector enzymes that catalyze this reaction is counteracted by Legionella hydrolases, which are called Dups. This unusual ubiquitination process is important for Legionella proliferation and understanding these processes on a molecular level might prove invaluable in finding new treatments. Herein, a modular approach is used for the synthesis of triazole-linked Ub^ADPr, and analogues thereof, and their affinity towards the hydrolase DupA is determined and hydrolysis rates are compared to natively linked Ub^ADPr. The inhibitory effects of modified Ub on the canonical eukaryotic E1-enzyme Uba1 are investigated and rationalized in the context of a high-resolution crystal structure reported herein. Finally, it is shown that synthetic Ub^ADPr analogues can be used to effectively pull-down overexpressed DupA from cell lysate.     

Dissecting Ubiquitin Signaling with Linkage‐Defined and Protease Resistant Ubiquitin Chains

Ubiquitylation is a complex posttranslational protein modification and deregulation of this pathway has been associated with different human disorders. Ubiquitylation comes in different flavors: Besides mono‐ubiquitylation, ubiquitin chains of various topologies are formed on substrate proteins. The fate of ubiquitylated proteins is determined by the linkage‐type of the attached ubiquitin chains, however, the underlying mechanism is poorly characterized. Herein, we describe a new method based on codon expansion and click‐chemistry‐based polymerization to generate linkage‐defined ubiquitin chains that are resistant to ubiquitin‐specific proteases and adopt native‐like functions. The potential of these artificial chains for analyzing ubiquitin signaling is demonstrated by linkage‐specific effects on cell‐cycle progression.     

反应型罗丹明类荧光探针

相比于基于非共价键的超分子相互作用的传统荧光探针,反应型荧光探针的识别过程不是通过配位和氢键的相互作用,而是通过与目标物发生化学反应,使得光谱性质或颜色改变,生成不同结构的光活性化合物。近年来,反应型荧光探针主要有三种化学反应类型:底物与受体通过共价键连接;底物作为催化剂,与受体发生不可逆的反应;基于置换反应使底物与受体络合。正是反应型荧光探针利用选择反应的优势识别特定物质,因而提供了方便、快捷、专一的分析检测目标物的方法,具有很高的灵敏度和选择性,受到越来越多的关注。本文综述了近六年来基于反应型罗丹明荧光探针用于检测金属阳离子、活性氧化物和阴离子诱导β-内酰胺开环的最新研究进展,评述其结构和检测性能之间的关系,并展望这类荧光探针的应用前景与发展趋势。     

N-取代马来酰亚胺巯基荧光探针的研究进展

评述了测这含－SH生物活性物质和肽、蛋白质等的N－聚代马来酰亚胺荧光探针的种类、性能、原理、应用及其进展。