The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family

The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.     

Ubiquitin Ligases at the Heart of Skeletal Muscle Atrophy Control

Skeletal muscle loss is a detrimental side-effect of numerous chronic diseases that dramatically increases mortality and morbidity. The alteration of protein homeostasis is generally due to increased protein breakdown while, protein synthesis may also be down-regulated. The ubiquitin proteasome system (UPS) is a master regulator of skeletal muscle that impacts muscle contractile properties and metabolism through multiple levers like signaling pathways, contractile apparatus degradation, etc. Among the different actors of the UPS, the E3 ubiquitin ligases specifically target key proteins for either degradation or activity modulation, thus controlling both pro-anabolic or pro-catabolic factors. The atrogenes MuRF1/TRIM63 and MAFbx/Atrogin-1 encode for key E3 ligases that target contractile proteins and key actors of protein synthesis respectively. However, several other E3 ligases are involved upstream in the atrophy program, from signal transduction control to modulation of energy balance. Controlling E3 ligases activity is thus a tempting approach for preserving muscle mass. While indirect modulation of E3 ligases may prove beneficial in some situations of muscle atrophy, some drugs directly inhibiting their activity have started to appear. This review summarizes the main signaling pathways involved in muscle atrophy and the E3 ligases implicated, but also the molecules potentially usable for future therapies.     

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.     

Synthesis of novel glutarimide derivatives via the Ugi multicomponent reaction: affinity towards the E3 ubiquitin ligase substrate receptor Cereblon

The glutarimide moiety, common in many immuno-modulatory drugs, was decorated with lactam and diamide side chains via two variants of the Ugi reaction, namely, with isocyanide, aldehyde and acid or with isocyanide and oxo acid. The resulting diastereomerically pure compounds were evaluated for their affinity towards the E3 ubiquitin ligase substrate receptor Cereblon.     

A Pro-Fluorescent Ubiquitin-Based Probe to Monitor Cysteine-Based E3 Ligase Activity

Protein post-translational modification with ubiquitin (Ub) is a versatile signal regulating almost all aspects of cell biology, and an increasing range of diseases is associated with impaired Ub modification. In this light, the Ub system offers an attractive, yet underexplored route to the development of novel targeted treatments. A promising strategy for small molecule intervention is posed by the final components of the enzymatic ubiquitination cascade, E3 ligases, as they determine the specificity of the protein ubiquitination pathway. Here, we present UbSRhodol, an autoimmolative Ub-based probe, which upon E3 processing liberates the pro-fluorescent dye, amenable to profile the E3 transthiolation activity for recombinant and in cell-extract E3 ligases. UbSRhodol enabled detection of changes in transthiolation efficacy evoked by enzyme key point mutations or conformational changes, and offers an excellent assay reagent amenable to a high-throughput screening setup allowing the identification of small molecules modulating E3 activity.     

基于分子信标实时监测大肠杆菌DNA连接酶催化的DNA连接过程

报道了一种对DNA连接过程进行实时监测的方法,利用分子信标核酸探针作为DNA连接反应的模板和检测探针,实时监测了 E.coli DNA连接酶催化的DNA连接反应,克服了传统的凝胶电泳技术操作复杂、周期长及无法实时监测DNA连接过程的缺点,为核酸连接过程的实时监测和连接酶催化机理的研究提供了更为丰富的信息.在此基础上,发展了一种快速、准确测定 E.coli DNA连接酶的方法,线性响应范围为4.0×10^-6～2.0×10^-4U/μL,检测下限为4.0×10^-6U/μL.     

Identification of Proteins Interacting with Ubiquitin Chains

Ubiquitylation, the modification of proteins with ubiquitin (Ub), is one of the most versatile post‐translational modifications in eukaryotic cells. Since Ub also serves as its own substrate, proteins can be modified by numerous different Ub chains, in which the individual moieties are linked via one or several of the seven lysines of Ub. Homogeneous Ub chains, in which the moieties are sequentially linked via the same residue, have been most extensively studied. However, due to their restricted availability, the functions of Ub chains linked via K27, K29, or K33 are poorly understood. We have developed an approach that, for the first time, allows the generation of all seven homogeneous Ub chains in large quantities. The potential of our approach is demonstrated by the identification of previously unknown interaction partners of K27‐, K29‐, and K33‐linked Ub chains by affinity‐based proteomics.     

The Length of a Ubiquitin Chain: A General Factor for Selective Recognition by Ubiquitin‐Binding Proteins

The attachment of ubiquitin (Ub) chains of various length to proteins is a prevalent posttranslational modification in eukaryotes. The fate of a modified protein is determined by Ub‐binding proteins (UBPs), which interact with Ub chains in a linkage‐selective manner. However, the impact and functional consequences of chain length on the binding selectivity of UBPs remain mostly elusive. We have generated Ub chains of defined length and linkage by using click chemistry and GELFrEE fractionation. These defined polymers were used in affinity‐based enrichment assays to identify length‐ and linkage‐selective interaction partners on a proteome‐wide scale. For the first time, it is revealed that the length of a Ub chain generally has a major impact on its ability to be selectively recognized by UBPs.     

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.     

Synthetic approaches to constructing proteolysis targeting chimeras (PROTACs)

The development of various heterobifunctional constructs dubbed PRoteolysis-TArgeting Chimeras (PROTACs) has gained a significant impetus in the last few years. A viable alternative to the traditional occupancy-based inhibition of aberrantly hyperactive proteins, PROTACs operate by an event-based catalytic mechanism bringing together the protein of interest (POI, to be degraded) and E3 ubiquitin ligases. The formation of the ternary complex ‘POI–PROTAC–E3 ubiquitin ligase’ is the critical step which leads to the ubiquitination of the POI and its proteasomal degradation. The current Focused Review aims to highlight the syntheses of selected innovative PROTAC-type degraders of the therapeutically important protein targets as well as some notable chemical aspects of PROTAC construction. The overview is focusing on PROTACs aimed at recruiting Cereblon, the most exploited E3 ligase for targeted protein degradation.     

X射线晶体学和电子晶体学在分子筛结构表征中的应用

分子筛是一类具有规则孔道或笼结构的晶态微孔材料, 在吸附、 分离和催化中都表现出了优异的性能. 为了探索其结构与性质的关系, 在原子尺度上研究分子筛的微观结构是十分必要的. 本综述介绍了一系列与X射线晶体学和电子晶体学相关的表征技术（倒易空间和正空间）在分子筛结构表征中的应用. 随后, 基于分子筛的结构表征方法和化学组成, 对2007年之后发现的85种新分子筛进行了系统总结, 对其中9种具有独特合成方法或结构特征的分子筛进行了详细介绍.     

Structural elucidation of the binding and inhibitory properties of lanthanide (III) ions at the 3'-5' exonucleolytic active site of the Klenow fragment

BACKGROUND: Biochemical and biophysical experiments have shown that two catalytically essential divalent metal ions (termed 'A' and 'B') bind to the 3'-5' exonuclease active site of the Klenow fragment (KF) of Escherichia coli DNA polymerase I. X-ray crystallographic studies have established the normal positions in the KF 3'-5' exonuclease (KF exo) active site of the two cations and the single-stranded DNA substrate. Lanthanide (III) luminescence studies have demonstrated, however, that only a single europium (III) ion (Eu3+) binds to the KF exo active site. Furthermore, Eu3+ does not support catalysis by KF exo or several other two-metal-ion phosphoryl-transfer enzymes. RESULTS: A crystal structure of KF complexed with both Eu3+ and substrate single-stranded oligodeoxynucleotide shows that a lone Eu3+ is bound near to metal-ion site A. Comparison of this structure to a relevant native structure reveals that the bound Eu3+ causes a number of changes to the KF exo active site. The scissile phosphate of the substrate is displaced from its normal position by about 1 A when Eu3+ is bound and the presence of Eu3+ in the active site precludes the binding of the essential metal ion B. CONCLUSIONS: The substantial, lanthanide-induced differences in metal-ion and substrate binding to KF exo account for the inhibition of this enzyme by Eu3+. These changes also explain the inability of KF exo to bind more than one cation in the presence of lanthanides. The mechanistic similarity between KF exo and other two-metal-ion phosphoryl-transfer enzymes suggests that the principles of lanthanide (III) ion binding and inhibition ascertained from this study will probably apply to most members of this class of enzymes.     

Conformational analysis 29: Preparation and1H and13C NMR,FTIR, MS,and crystallographic conformational and configurational study of 3-Oxo-1,3-oxathiane and its monomethyl derivatives

3-Oxo-1,3-oxathiane (1) and its monomethyl derivatives were prepared by oxidation of the corresponding 1,3-oxathianes. The structural analysis was carried out by¹H and¹³C NMR, FTIR, and mass spectrometry. At 298 K compound1 was a 1 1 (at 173 K a 3 1) mixture of the SO(ax) and SO(eq) chair forms. The major oxidation products of methyl 1,3-oxathianes attained exclusively the SO(ax), Me(eq) chair forms except that of the 5-methyl derivative, which consisted of 7% of the SO(eq), Me(ax) chair conformation in CDCl₃ solution. The minor products of oxidation existed in anancomeric SO(eq), Me(eq) chair conformations. The oxidation of 2-methyl- 1,3-oxathiane, however, led to 3,3-dioxo derivative (6) in addition to thetrans [SO(eq)] monoxide. The crystal structures of6 andtrans-3-oxo-5-methyl-1,3-oxathiane were solved by X-ray diffractometry.     

Stable Lewis Base Adducts of Tetrahalodiboranes: Synthetic Methods and Structural Diversity

A series of 22 new bis(phosphine), bis(carbene), and bis(isonitrile) tetrahalodiborane adducts has been synthesized, either by direct adduct formation with highly sensitive B₂X₄ precursors (X=Cl, Br, I) or by ligand exchange at stable B₂X₄(SMe₂)₂ precursors (X=Cl, Br) with labile dimethylsulfide ligands. The isolated compounds have been fully characterized using NMR spectroscopy, elemental analysis, and, for 20 of these compounds, single-crystal X-ray diffraction, revealing an unexpected variation in the bonding motifs. In addition to the classical B₂X₄L₂ diborane(4) bis-adducts, certain more sterically demanding carbene ligands induce a halide displacement which led to the first halide-bridged monocationic diboron species, [B₂X₃L₂]A (A=BCl₄, Br, I). Furthermore, low-temperature 1:1 reactions of B₂Cl₄ with sterically demanding N-heterocyclic carbenes led to the formation of kinetically unstable mono-adducts, one of which was structurally characterized. A comparison of the NMR spectra and structural data of new and literature-known bis-adducts shows several trends pertaining to the nature of the halides and the stereoelectronic properties of the Lewis bases employed.     

黄芩素A环的结构修饰

以传统中药黄芩的主要活性成分黄芩苷及其乙酰化产物6,7-二乙酰氧基黄芩素为原料,通过碘代、硝化及硝基还原胺化反应在A环的C-8上引入碘原子、硝基及胺基,并对黄芩素A环上的3个酚羟基进行了选择性二甲醚化及全甲醚化,制备了A环修饰的6种黄芩素衍生物,表征了它们的结构,讨论了合成方法的特点。     

Electron and X‐Ray Methods of Ultrafast Structural Dynamics: Advances and Applications

In this contribution, we highlight the state of the art in the determination of structures with ultrafast electrons and X‐rays. We provide our perspectives and reflections on the principles, techniques and methods, and on applications from different disciplines, with some focus on physical, chemical and biological structures. Although this article is not a survey of all the work done with these techniques, it provides a comprehensive referencing to current research.     

Preparation,Thermolysis, and Photolysis of Some New Thiophosphoramidates Derived from 3-Methyl-2-Benzothiazolinone Hydrazone

3-Methyl-2-benzothiazolinone hydrazone (1) reacts with dialkyl phosphorothiochloridates 2a,b in the presence of a base, to give the respective dialkylthiophosphorylated hydrazones 3a,b. Upon thermolysis, compound 3b yields bi(3-methylbenzothiazole-2-iminyl) (4). Exposure of 3b to sunlight in methanol results in the formation of 3-methyl-2-benzothiazolinone (5). When the same experiment was carried on the starting hydrazone 1, bis(3-methyl- benzothiazole-2-iminyl)diazine (6) was formed. Elemental analyses and spectroscopic details are presented for the new compounds.

Supplemental materials are available for this article. Go to the publisher's online edition of Phosphorus, Sulfur, and Silicon and the Related Elements to view the free supplemental file.     

Conformational analysis and steric effects of substituents in derivatives of 3-oxo-, 3-imino-, and 3-methylenecyclohexene

The equilibrium conformations and the inversion barriers of the rings in 3-oxo-, 3-imino-, 3-methylenecyclohexenes and in their methyl,tert-butyl, and phenyl derivatives were calculated by molecular mechanics. The unsubstituted molecules adopt a sofa conformation. The nonbonded interactions between substituents at positions 2 and 4 and the exocyclic double bond lead to a change in the conformation of the ring to a half-chair. The effect is enhanced as the volume of the substituent increases in the series of the oxo, imino, and methylene derivatives. Substituents at other positions of the ring affect only slightly the equilibrium conformation. The results of calculations were confirmed by X-ray structural analysis of 2-(4-benzoyloxybenzyl)-6-isopropyl-3-methylcyclohex-2-enone. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 1995–2000, November, 1997.