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    Tytuł:
    Narzędzia chemiczne do badania enzymów proteolitycznych przy użyciu cytometrii masowej
    Mass cytometry-compatible chemical probes for the investigation of proteolytic enzymes
    Autorzy:
    Groborz, Katarzyna
    Powiązania:
    https://bibliotekanauki.pl/articles/2200437.pdf
    Data publikacji:
    2022
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    markery chemiczne
    cytometria masowa
    enzymy proteolityczne
    nowotwór
    śmierć komórki
    activity-based probes
    mass cytometry
    proteolytic enzymes
    cancer
    cell death
    Opis:
    Mass cytometry is one of the newest and most high-throughput technologies that allows for the investigation of complex biological systems at single cell level. It relies on the use of stable metal isotopes as labels of specific cell markers and therefore, allows for simultaneous analysis of more than 40 parameters at single cell level. In order to fully explore the potential of mass cytometry, researchers are trying to develop new experimental setups based on the application of pure metal isotopes in biological studies. The incorporation of antibodies into mass cytometry setups, while extremely selective and well-validated, limits the analysis as it shows the whole protein pool present in the cell. In our group, we developed new technology that allows for the identification of active forms of proteins-the ones that actively participate in cell signaling pathways. Activity-based probes are the most valuable tools for enzyme activity profiling and for years now they have been in the center of the method called Activity-Based Protein Profiling. Classic activity-based probes consist of three parts: a warhead (electrophilic binding group that covalently modifies enzyme active site), linker (specific peptide sequence or non-specific carbon chain) and the fluorescent tag that allows for enzyme detection and localization inside the cell. Spectral properties of commercially available fluorophores allow for the detection of up to dozen different cell parameters, with the use of various techniques such as confocal microscopy or flow cytometry. To increase the number of analyzed parameters, we designed activity-based probes that possess DOTA chelating moiety that is able to trap one metal atom per one probe. The combination of mass cytometry with highly selective activity-based probes allowed for the development of new technology that grants the possibility of multiparametric analysis of complex biological samples such as blood or cancer tissue. The new type of activity-based probes (so-called TOF-probes) incorporate various inhibitor scaffolds designed with HyCoSuL technology (Hybrid Combinatorial Substrate Libraries). These compounds possess a variety of unnatural amino acids in their structures, which significantly increases their selectivity toward proteases of interest.
    Źródło:
    Wiadomości Chemiczne; 2022, 76, 11-12; 864-880
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Sondy fluorescencyjne typu „light up” do detekcji i obrazowania G-kwadrupleksów in vitro i in vivo. Cz. 1 i 2
    Light up fluorescent probes for detection and visualizing the G-quadruplexes in vitro and in vivo. Part 1 and 2
    Autorzy:
    Baranowski, Daniel
    Powiązania:
    https://bibliotekanauki.pl/articles/1409732.pdf
    Data publikacji:
    2020
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    G-kwadrupleks
    fluorescencja
    ligandy wiążące się do G-kwadrupleksu
    sondy fluorescencyjne
    obrazowanie komórkowe
    detekcja in vitro
    G-quadruplex
    Fluorescence
    G-quadruplex binding ligand
    Fluorescent probes
    cellular imaging
    in vitro detection
    Opis:
    G-quadruplexes are non-canonical guanosine rich four stranded nucleic acids structures consisting of at least two or more G-tetrads stabilized by an array of Hoogsteen hydrogend bonds and monovalent cations. The distinguishing feature of the G-quadruplexes is their high thermal stability and structural polymorphism in aqueous media. In parallel, a great number of GQ structures have been extensively surveyed ex vivo by means of biophysical techniques such as nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD) spectroscopy, and X-ray crystallography. Accumulating evidence suggesting that G-quadruplexes play essential role in a numerous biological processes in vivo, including DNA replication and transcription, RNA translation as well as genomic maintenance. Consequently, G-quadruplexes has attracted attention as therapeutic targets in cancer or hereditary diseases as well as molecular target in cellular biology. Study on G-quadruplexes:ligand interaction by NMR, CD, UV and fluorescence spectroscopy in vitro or in vivo has become an intensive research work area of many groups in recent years. Nowadays, there are available large amount of organic compounds that selectively bind to G-quadruplexes and their photophysical and kinetic properties were comprehensively characterized but only few of them are endowed with fluorescence properties that could be applicable as fluorescent probes in cellular biology or in vitro detection. Interestingly, the group of these fluorescent probes is characterized by a vast structural diverisity resulting from the different way of interaction with G-quadruplexes as well as G-quadruplex polymorphism. This review focuses on the G-quadruplex-selective light up fluorescent probes that have been employed for in vitro detection as well as cellular imaging along with a summary of the key photophysical, biophysical, and biological properties of reported examples.
    Źródło:
    Wiadomości Chemiczne; 2020, 74, 11-12; 883-901
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Badania FTIR-ATR i fluorescencyjne układów białkowo-lipidowych
    FTIR-ATR and fluorescence studies of protein-lipid systems
    Autorzy:
    Litwińczuk-Mammadova, A.
    Cieślik-Boczula, K.
    Rospenk, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/172158.pdf
    Data publikacji:
    2017
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    spektroskopia FTIR-ATR
    spektroskopia fluorescencyjna
    anizotropia
    efekt REES
    wygaszanie fluorescencji
    model stanów dyskretnych Trp
    sonda fluorescencyjna
    białko
    lipid
    FTIR-ATR spectroscopy
    fluorescence spectroscopy
    anisotropy
    REES effect
    fluorescence quenching
    fluorescent probes
    protein
    Opis:
    Lipid-protein systems paly curtail roles in living systems [49]. Hence, a determination of their structure at different levels of organization is still one of the most important tasks in many research projects. A study of lipid-protein systems is based on many physicochemical techniques, such as spectroscopy of FTIR, Raman, fluorescence, NMR, EPR, as well as DLS, DSC and TEM methods. In the presented paper tow of the most frequently used methods, that is FTIR and fluorescence spectroscopy, will be discussed in details. They are characterized by a relatively low cost of sample preparation, a short measuring time, and they give a huge number of structural and physicochemical information about lipid-protein systems. In the FTIR-ATR spectroscopy many of vibrational bands are commonly used as very precise vibrational indicators of structural changes in lipids and proteins (Fig. 1) [1–6]. They allows to characterize lipid and protein components separately in mixed systems. Additionally, structural changes in lipid membranes can be monitored in one FTIR-ATR experiment simultaneously in a region of hydrophilic lipid head-groups (Fig. 5) [17, 18], in a hydrophobic part composed of hydrocarbon lipid chains (see Figures 2 and 3) [7–9], and in a lipid membrane interface represented by ester lipid groups (Fig. 4) [4, 6, 11, 12]. A secondary structure of proteins and peptides in different experimental conditions can be defined in the FTIR-ATR spectroscopy on the base of amide I bands (Fig. 6 and Tabs 1, 2 and 3) [20–22]. A fluorescence spectroscopy is a complementary methods to FTIR spectroscopy in a study of lipid-protein systems. It competes information about time-dependent and very fast (in a scale of femtoseconds) structural processes in both lipids [41–45] and proteins [23, 27, 48]. The folding, denaturation, and aggregation of proteins and lipid membranes accompanied by changes in an order, packing and hydration of the system under study [23, 27, 41–45, 48].
    Źródło:
    Wiadomości Chemiczne; 2017, 71, 1-2; 109-132
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Nienaturalne aminokwasy jako strategia do otrzymywania substratów, inhibitorów i niskocząsteczkowych sond aktywności dla enzymów proteolitycznych
    Unnatural amino acids as achemical tool for the development of protease substrates, inhibitors and activity - baseproblems
    Autorzy:
    Poręba, Marcin
    Kasperkiewicz-Wasilewska, Paulina
    Rut, Wioletta
    Drąg, Marcin
    Powiązania:
    https://bibliotekanauki.pl/articles/2200587.pdf
    Data publikacji:
    2022
    Wydawca:
    Polskie Towarzystwo Chemiczne
    Tematy:
    proteolytic enzymes
    substrate specificity
    unnatural amino acids
    substrates
    inhibitors
    activity-based probes
    caspases
    cathepsins
    neuthrophil serine proteases
    proteasome
    SARS-CoV-2 proteases
    enzymy proteolityczne
    specyficzność substratowa
    nienaturalne aminokwasy
    niskocząsteczkowe sondy aktywności
    kaspazy
    katepsyny
    proteasom
    proteazy wirusa SARS-CoV-2
    Opis:
    Proteolytic enzymes are molecular scissors that are responsible for the amide bond breakdown in peptide and protein substrates. Over the years, the view on proteases has been considerably changed from non-specific digestive enzymes to sophisticated biocatalysts, which by performing limited proteolysis control virtually all biological processes. In order to better understand how proteases work and what are their biologically relevant target substrates, it is indispensable to determine their catalytic preferences. This knowledge can be further utilized to develop selective substrates, inhibitors and activity-based probes (ABPs) enabling the monitoring of proteases activity in various settings, from in vitro analysis on recombinant enzymes or cell lysates to ex vivo and in vivo imaging at the single cell level. Among many chemical-based approaches that have been developed and applied over the years, the Hybrid Combinatorial Substrate Library (HyCoSuL) technology has emerged as one of the most powerful one. HyCoSuL is a combinatorial peptide-based library of fluorogenic substrates, that comprise natural and unnatural amino acids, that can deeply explore the chemical space in proteases active site, providing a structural framework for the development of highly-selective chemical tools. In this review we present the most prominent examples of proteolytic enzymes that have been profiled with HyCoSuL approach yielding selective substrates, potent inhibitors, and very sensitive activity-based probes.
    Źródło:
    Wiadomości Chemiczne; 2022, 76, 5-6; 433--454
    0043-5104
    2300-0295
    Pojawia się w:
    Wiadomości Chemiczne
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-4 z 4

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