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  1. Article ; Online: Open Search Strategy for Inferring the Masses of Cross-Link Adducts on Proteins.

    Slavin, Moriya / Tayri-Wilk, Tamar / Milhem, Hala / Kalisman, Nir

    Analytical chemistry

    2020  Volume 92, Issue 24, Page(s) 15899–15907

    Abstract: Development of new reagents for protein cross-linking is constantly ongoing. The chemical formulas for the linker adducts formed by these reagents are usually deduced from expert knowledge and then validated by mass spectrometry. Clearly, it would be ... ...

    Abstract Development of new reagents for protein cross-linking is constantly ongoing. The chemical formulas for the linker adducts formed by these reagents are usually deduced from expert knowledge and then validated by mass spectrometry. Clearly, it would be more rigorous to infer the chemical compositions of the adducts directly from the data without any prior assumptions on their chemistries. Unfortunately, the analysis tools that are currently available to detect chemical modifications on linear peptides are not applicable to the case of two cross-linked peptides. Here, we show that an adaptation of the open search strategy that works on linear peptides can be used to characterize cross-link modifications in pairs of peptides. We benchmark our approach by correctly inferring the linker masses of two well-known reagents, DSS and formaldehyde, to accuracies of a few parts per million. We then investigate the cross-linking chemistries of two poorly characterized reagents: EMCS and glutaraldehyde. In the case of EMCS, we find that the expected cross-linking chemistry is accompanied by a competing chemistry that targets other amino acid types. In the case of glutaraldehyde, we find that the chemical formula of the dominant linker is C
    MeSH term(s) Animals ; Cattle ; Cross-Linking Reagents/chemistry ; Glutaral/chemistry ; Molecular Structure ; Particle Size ; Serum Albumin, Bovine/chemistry ; Surface Properties
    Chemical Substances Cross-Linking Reagents ; Serum Albumin, Bovine (27432CM55Q) ; Glutaral (T3C89M417N)
    Language English
    Publishing date 2020-11-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.0c03292
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4033: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Low-Dose Colchicine Attenuates Sepsis-Induced Liver Injury: A Novel Method for Alleviating Systemic Inflammation.

    Kenig, Ariel / Keidar-Haran, Tal / Azmanov, Henny / Kessler, Asa / Kolben, Yotam / Tayri-Wilk, Tamar / Kalisman, Nir / Weksler-Zangen, Sarah / Ilan, Yaron

    Inflammation

    2023  Volume 46, Issue 3, Page(s) 963–974

    Abstract: Sepsis is a significant public health challenge. The immune system underlies the pathogenesis of the disease. The liver is both an active player and a target organ in sepsis. Targeting the gut immune system using low-dose colchicine is an attractive ... ...

    Abstract Sepsis is a significant public health challenge. The immune system underlies the pathogenesis of the disease. The liver is both an active player and a target organ in sepsis. Targeting the gut immune system using low-dose colchicine is an attractive method for alleviating systemic inflammation in sepsis without inducing immunosuppression. The present study aimed to determine the use of low-dose colchicine in LPS-induced sepsis in mice. C67B mice were injected intraperitoneal with LPS to induce sepsis. The treatment group received 0.02 mg/kg colchicine daily by gavage. Short and extended models were performed, lasting 3 and 5 days, respectively. We followed the mice for biochemical markers of end-organ injury, blood counts, cytokine levels, and liver pathology and conducted proteomic studies on liver samples. Targeting the gut immune system using low-dose colchicine improved mice's well-being measured by the murine sepsis score. Treatment alleviated the liver injury in septic mice, manifested by a significant decrease in their liver enzyme levels, including ALT, AST, and LDH. Treatment exerted a trend to reduce creatinine levels. Low-dose colchicine improved liver pathology, reduced inflammation, and reduced the pro-inflammatory cytokine TNFα and IL1-β levels. A liver proteomic analysis revealed low-dose colchicine down-regulated sepsis-related proteins, alpha-1 antitrypsin, and serine dehydratase. Targeting the gut immune system using low-dose colchicine attenuated liver injury in LPS-induced sepsis, reducing the pro-inflammatory cytokine levels. Low-dose colchicine provides a safe method for immunomodulation for multiple inflammatory disorders.
    MeSH term(s) Mice ; Animals ; Colchicine/therapeutic use ; Lipopolysaccharides/pharmacology ; Proteomics ; Chemical and Drug Induced Liver Injury, Chronic/metabolism ; Chemical and Drug Induced Liver Injury, Chronic/pathology ; Liver/metabolism ; Inflammation/metabolism ; Sepsis/complications ; Sepsis/drug therapy ; Cytokines/metabolism ; Mice, Inbred C57BL
    Chemical Substances Colchicine (SML2Y3J35T) ; Lipopolysaccharides ; Cytokines
    Language English
    Publishing date 2023-01-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 434408-x
    ISSN 1573-2576 ; 0360-3997
    ISSN (online) 1573-2576
    ISSN 0360-3997
    DOI 10.1007/s10753-023-01783-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1401: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins.

    Tayri-Wilk, Tamar / Slavin, Moriya / Zamel, Joanna / Blass, Ayelet / Cohen, Shon / Motzik, Alex / Sun, Xue / Shalev, Deborah E / Ram, Oren / Kalisman, Nir

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 3128

    Abstract: Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate ... ...

    Abstract Whole-cell cross-linking coupled to mass spectrometry is one of the few tools that can probe protein-protein interactions in intact cells. A very attractive reagent for this purpose is formaldehyde, a small molecule which is known to rapidly penetrate into all cellular compartments and to preserve the protein structure. In light of these benefits, it is surprising that identification of formaldehyde cross-links by mass spectrometry has so far been unsuccessful. Here we report mass spectrometry data that reveal formaldehyde cross-links to be the dimerization product of two formaldehyde-induced amino acid modifications. By integrating the revised mechanism into a customized search algorithm, we identify hundreds of cross-links from in situ formaldehyde fixation of human cells. Interestingly, many of the cross-links could not be mapped onto known atomic structures, and thus provide new structural insights. These findings enhance the use of formaldehyde cross-linking and mass spectrometry for structural studies.
    MeSH term(s) Amino Acids/chemistry ; Cell Line, Tumor ; Cross-Linking Reagents/chemistry ; Formaldehyde/chemistry ; Humans ; Mass Spectrometry ; Molecular Docking Simulation ; Protein Interaction Mapping/methods ; Proteins/chemistry ; Proteins/metabolism
    Chemical Substances Amino Acids ; Cross-Linking Reagents ; Proteins ; Formaldehyde (1HG84L3525)
    Language English
    Publishing date 2020-06-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-16935-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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