Synthesis and multiple STED imaging applications of four, red-emitting (610–670 nm), tetrazine-functionalized fluorescent probes (CBRD = Chemical Biology Research group Dye 1–4) with large Stokes-shift is presented. Present studies revealed the super-resolution microscopy applicability of the probes as demonstrated through bioorthogonal labeling scheme of cytoskeletal proteins actin and keratin-19, and mitochondrial protein TOMM20. Furthermore, super-resolved images of insulin receptors in live-cell bioorthogonal labeling schemes through a genetically encoded cyclooctynylated non-canonical amino acid are also presented. The large Stokes-shifts and the wide spectral bands of the probes enabled the use of two common depletion lasers (660 nm and 775 nm). The probes were also found suitable for super-resolution microscopy in combination with two-photon excitation (2P-STED) resulting in improved spatial resolution. One of the dyes was also used together with two commercial dyes in the three-color STED imaging of intracellular structures.

Protein post-translational modifications (PTMs) play a critical role in the regulation of protein catalytic activity, localization, and protein–protein interactions. Attachment of PTMs onto proteins significantly diversifies their structure and function, resulting in proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease-specific, is still a highly challenging task. Substoichiometric amounts and modifications of low abundant proteins necessitate the purification or enrichment of the modified proteins. Although the introduction of mass spectrometry-based chemical proteomic strategies has enabled the screening of protein PTMs with increased throughput, sample preparation remains highly time-consuming and tedious. Here, we report an optimized workflow for the enrichment of PTM proteins in a 96-well plate format, which could be extended to robotic automation. This platform allows us to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult-to-culture cell lines in a high-throughput manner. The presented SP2E protocol is robust and time- and cost-effective, as well as suitable for large-scale screening of proteoforms. The application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration, and cancer. This may contribute to an overall acceleration of the recently launched Human Proteoform Project.

Opines and opine‐type chemicals are valuable natural products with diverse biochemical roles, and potential synthetic building blocks of bioactive compounds. Their synthesis involves reductive amination of ketoacids with amino acids. This transformation has high synthetic potential in producing enantiopure secondary amines. Nature has evolved opine dehydrogenases for this chemistry. To date, only one enzyme has been used as biocatalyst, however, analysis of the available sequence space suggests more enzymes to be exploited in synthetic organic chemistry. This review summarizes the current knowledge of this underexplored enzyme class, highlights key molecular, structural, and catalytic features with the aim to provide a comprehensive general description of opine dehydrogenases, thereby supporting future enzyme discovery and protein engineering studies.

The identification and quantification of modified peptides are critical for the functional characterization of post‐translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom‐up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click‐chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide‐PTM quantification from various experimental conditions.

2020. decemberében a Pilis hegységhez tartozó egri vár másolatának egyik ÉNy-i ki­tettségű, habarccsal kötött homokkő falán öt páfrányfaj kicsiny populációjára bukkantunk. 15 tő Asplenium ceterach L. (s.str.), 1 tő Polystichum aculeatum (L.) Roth mellett 1 tő Asplenium trichomanes L., számos Asplenium ruta-muraria (L.) Hoffm. és egyetlen tő Dryopteris filix-mas (L.) Schott is előkerült. Az Asplenium ceterach s.str., a Pilis hegységre új faj, feltehetően a közeli, budai-hegységi (Remete-szurdok) állománynak legkésőbb 5–10 évvel ezelőtt megtelepedett származékáról lehet szó.

Protein post-translational modifications (PTMs) play a critical role in regulation of protein catalytic activity, localization and protein-protein interactions. An attachment of PTMs onto proteins significantly diversifies their structure and function resulting in so-called proteoforms. However, the sole identification of post-translationally modified proteins, which are often cell type and disease specific, is still a highly challenging task. Sub-stoichiometric amounts and modification of low abundant proteins necessitate purification or enrichment of the modified proteins. Although the introduction of the mass spectrometry-based chemical proteomic strategy has enabled to screen protein PTMs with increased throughput, sample preparation has remained highly time consuming and tedious. Here, we report an optimized workflow for enrichment of PTM proteins in 96-well plate format which can be possible extended to robotic automatization. This platform allows to significantly lower the input of total protein, which opens up the opportunity to screen specialized and difficult to culture cell lines in high-throughput manner. The presented SP2E protocol is robust, time- and cost-effective as well as suitable for large-scale screening of proteoforms. Application of the SP2E protocol will thus enable the characterization of proteoforms in various processes such as neurodevelopment, neurodegeneration and cancer and may contribute to an overall acceleration of the recently launched Human Proteoform Project.

Optoacoustic imaging, also known as photoacoustic imaging, promises micron-resolution noninvasive imaging in biology at much deeper penetration (>cm) depths than e.g. fluorescence. However, the loud, photostable, NIR-absorbing molecular contrast agents which would be needed for optoacoustic imaging of enzyme activity remain unknown: most organic molecular contrast agents are simply repurposed fluorophores, with severe shortcomings of photoinstability or phototoxicity under optoacoustic imaging conditions, which are consequences of their slow S1→S0 electronic relaxation rates. We now disclose that known fluorophores can be rationally modified to reach ultrafast S1→S0 rates, without much extra molecular complexity, simply by merging them with molecular switches. Here, we merge azobenzene switches to cyanine dyes to give ultrafast relaxation (<10 ps, >100-fold faster). Even without adapting instrument settings, these azohemicyanine optoacoustic imaging agents deliver outstanding improvements in signal longevity (>1000-fold increase of photostability) and signal loudness (here: >3-fold even at time zero). We show why this still-unexplored design strategy can offer even stronger performance in the future, as a simple method that will also increase the spatial resolution and the quantitative linearity of photoacoustic response even over extended longitudinal imaging. By bringing the world of molecular switches and rotors to bear on unsolved problems that have faced optoacoustic agents, this practical strategy may be a crucial step towards unleashing the full potential, in fundamental studies and in translational uses, of optoacoustic imaging.