An Organotrifluoroborate for Broadly Applicable One‐Step 18F‐Labeling

A new zwitterionic organotrifluoroborate is appended to three radiosynthons that afford undergo facile bioconjugation to several clinically relevant peptides and one enzyme inhibitor. Molecularly complex bioconjugates are ¹⁸F‐labeled in a single aqueous step in rapid time (<15 min) without HPLC purification to afford tracers in good yields (>200 mCi, 20–40 %) at high specific activity (≥3 Ci/μmol) and at >98 % purity. PET imaging shows in vivo stability and tumor uptake.     

An Isotope‐Coded Fluorogenic Cross‐Linker for High‐Performance Target Identification Based on Photoaffinity Labeling

A photoaffinity labeling (PAL)‐based method for the rapid identification of target proteins is presented in which a high‐performance chemical tag, an isotope‐coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage. The combination of PAL and heterogeneous target‐selecting techniques significantly reduces the amount of time and protein required for identification. An additional photocleavable moiety successfully accelerated proteomic analysis using cell lysate. This method is a widely applicable approach for the rapid and accurate identification of interacting proteins.     

金属标记结合高效液相色谱-选择离子监测质谱的蛋白质绝对定量新方法

建立了金属标记结合高效液相色谱-选择性离子监测质谱(SIM)的蛋白质绝对定量新方法。实验考察了金属标记效率、金属标记的稳定性、标记后肽段的色谱保留和质谱行为、新定量方法的线性范围和准确度。实验结果表明金属标记具有标记效率高,稳定性好,色谱保留行为一致等优点。另外,金属标记-选择离子监测质谱绝对定量方法灵敏度高,其定量限低至1 fmol,线性范围为1~500 fmol,线性范围内R2值大于0.99,具有良好的线性关系;经过测量,标准肽段的回收率为117.01%,说明该方法具有较高的准确度。将该方法应用于腾冲嗜热菌中烯醇酶蛋白的定量分析,相对标准偏差为5.47%,表明该方法的精密度高。以上结果表明该方法可以用于生物样本中的蛋白质的绝对定量分析,为比较简单的生物样本中蛋白质的绝对定量方法提供了一种新的选择。     

Chromophore-Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells

The spatial arrangement of chromosome within the nucleus is linked to genome function and gene expression regulation. Existing genome-wide mapping methods often rely on chemically crosslinking DNA with protein baits, which raises concerns of artifacts being introduced during cell fixation. By genetically targeting a photosensitizer protein to specific subnuclear locations, we achieved blue-light-activated labeling of local DNA with a bioorthogonal functional handle for affinity purification and sequence identification through next-generation sequencing. When applied to the nuclear lamina in human embryonic kidney 293T cells, it revealed lamina-associated domains (LADs) that cover 37.6 % of the genome. These LADs overlap with heterochromatin hallmarks and are depleted with CpG islands. This simple labeling method avoids the harsh treatment of chemical crosslinking and is generally applicable to the genome-wide high-resolution mapping of the spatial chromosome organization in living cells.     

LC-MS Quantification of Site-Specific Phosphorylation Degree by Stable-Isotope Dimethyl Labeling Coupled with Phosphatase Dephosphorylation

Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation degrees is still a challenging task due to its dynamic nature and the lack of an internal standard simultaneously available for the samples differently prepared for various phosphorylation extents. In this study, stable-isotope dimethyl labeling coupled with phosphatase dephosphorylation (DM + deP) was tried to determine the site-specific degrees of phosphorylation in proteins. Firstly, quantitation accuracy of the (DM + deP) approach was confirmed using synthetic peptides of various simulated phosphorylation degrees. Afterwards, it was applied to evaluate the phosphorylation stoichiometry of milk caseins. The phosphorylation degree of Ser130 on α-S1-casein was also validated by absolute quantification with the corresponding synthetic phosphorylated and nonphosphorylated peptides under a selected reaction monitoring (SRM) mode. Moreover, this (DM + deP) method was used to detect the phosphorylation degree change of Ser82 on the Hsp27 protein of HepG2 cells caused by tert-butyl hydroperoxide (t-BHP) treatment. The results showed that the absolute phosphorylation degree obtained from the (DM + deP) approach was comparable with the relative quantitation resulting from stable-isotope dimethyl labeling coupled with TiO₂ enrichment. This study suggested that the (DM + deP) approach is promising for absolute quantification of site-specific degrees of phosphorylation in proteins, and it may provide more convincing information than the relative quantification method.     

Visualization and In Situ Ablation of Intracellular Bacterial Pathogens through Metabolic Labeling

Protected by the host cells, the hidden intracellular bacteria are typically difficult to kill by common antibiotics and cannot be visualized without complex cellular pretreatments. Herein, we successfully developed a bacteria‐metabolizable dual‐functional probe TPEPy‐d ‐Ala, which is based on d ‐alanine and a photosensitizer with aggregation‐induced emission for fluorescence turn‐on imaging of intracellular bacteria in living host cells and photodynamic ablation in situ. Once metabolically incorporated into bacterial peptidoglycan, the intramolecular motions of TPEPy‐d ‐Ala are inhibited, leading to an enhanced fluorescent signal, which allows the clear visualization of the intracellular bacteria. Moreover, TPEPy‐d ‐Ala can effectively ablate the labeled intracellular bacteria in situ owing to covalent ligation to peptidoglycan, yielding a low intracellular minimum inhibitory concentration (MIC) of 20±0.5 μg mL^?1, much more efficient than that of a commonly used antibiotic, vancomycin.     

Ruthenium coordination preferences in imidazole‐containing systems revealed by electrospray ionization mass spectrometry and molecular modeling: Possible cues for the surprising stability of the Ru (III)/tris (hydroxymethyl)‐aminomethane/imidazole complexes

Ruthenium is a platinoid that exhibits a range of unique chemical properties in solution, which are exploited in a variety of applications, including luminescent probes, anticancer therapies, and artificial photosynthesis. This paper focuses on a recently demonstrated ability of this metal in its +3 oxidation state to form highly stable complexes with tris (hydroxymethyl)aminomethane (H₂NC(CH₂OH)₃, Tris‐base or T) and imidazole (Im) ligands, where a single Ru^III cation is coordinated by two molecules of each T and Im. High‐resolution electrospray ionization mass spectrometry (ESI MS) is used to characterize Ru^III complexes formed by placing a Ru^II complex [(NH₃)₅Ru^IICl]Cl in a Tris buffer under aerobic conditions. The most abundant ionic species in ESI MS represent mononuclear complexes containing an oxidized form of the metal, ie, [X_nRu^IIIT₂ – 2H]⁺, where X could be an additional T (n = 1) or NH₃ (n = 0‐2). Di‐ and tri‐metal complexes also give rise to a series of abundant ions, with the highest mass ion representing a metal complex with an empirical formula Ru₃C₂₄O₂₁N₆H₆₆ (interpreted as cyclo(T₂RuO)₃, a cyclic oxo‐bridged structure, where the coordination sphere of each metal is completed by two T ligands). The empirical formulae of the binuclear species are consistent with the structures representing acyclic fragments of cyclo(T₂RuO)₃ with addition of various combinations of ammonia and dioxygen as ligands. Addition of histidine in large molar excess to this solution results in complete disassembly of poly‐nuclear complexes and gives rise to a variety of ionic species in the ESI mass spectrum with a general formula [Ru^IIIHis_kT_m (NH₃)_n ? 2H]⁺, where k = 0 to 2, m = 0 to 3, and n = 0 to 4. Ammonia adducts are present for all observed combinations of k and m, except k = m = 2, suggesting that [His₂Ru^IIIT₂ ? 2H]⁺ represents a complex with a fully completed coordination sphere. The observed cornucopia of Ru^III complexes formed in the presence of histidine is in stark contrast to the previously reported selective reactivity of imidazole, which interacts with the metal by preserving the RuT₂ core and giving rise to a single abundant ruthenium complex (represented by [Im₂Ru^IIIT₂ ? 2H]⁺ in ESI mass spectra). Surprisingly, the behavior of a hexa‐histidine peptide (HHHHHH) is similar to that of a single imidazole, rather than a single histidine amino acid: The RuT₂ core is preserved, with the following ionic species observed in ESI mass spectra: [HHHHHH·(Ru^IIIT₂)_m ? (3m‐1)H]⁺ (m = 1‐3). The remarkable selectivity of the imidazole interaction with the Ru^IIIT₂ core is rationalized using energetic considerations at the quantum mechanical level of theory.     

SLIM: A Short‐Linked,Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.     

Aromatic 19F–13C TROSY—[19F, 13C]‐Pyrimidine Labeling for NMR Spectroscopy of RNA

We present the access to [5‐¹⁹F, 5‐¹³C]‐uridine and ‐cytidine phosphoramidites for the production of site‐specifically modified RNAs up to 65 nucleotides (nts). The amidites were used to introduce [5‐¹⁹F, 5‐¹³C]‐pyrimidine labels into five RNAs—the 30 nt human immunodeficiency virus trans activation response (HIV TAR) 2 RNA, the 61 nt human hepatitis B virus ? (hHBV ?) RNA, the 49 nt SAM VI riboswitch aptamer domain from B. angulatum, the 29 nt apical stem loop of the pre‐microRNA (miRNA) 21 and the 59 nt full length pre‐miRNA 21. The main stimulus to introduce the aromatic ¹⁹F–¹³C‐spin topology into RNA comes from a work of Boeszoermenyi et al., in which the dipole‐dipole interaction and the chemical shift anisotropy relaxation mechanisms cancel each other leading to advantageous TROSY properties shown for aromatic protein sidechains. This aromatic ¹³C–¹⁹F labeling scheme is now transferred to RNA. We provide a protocol for the resonance assignment by solid phase synthesis based on diluted [5‐¹⁹F, 5‐¹³C]/[5‐¹⁹F] pyrimidine labeling. For the 61 nt hHBV ? we find a beneficial ¹⁹F–¹³C TROSY enhancement, which should be even more pronounced in larger RNAs and will facilitate the NMR studies of larger RNAs. The [¹⁹F, ¹³C]‐labeling of the SAM VI aptamer domain and the pre‐miRNA 21 further opens the possibility to use the biorthogonal stable isotope reporter nuclei in in vivo NMR to observe ligand binding and microRNA processing in a biological relevant setting.