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  1. Article ; Online: Peptimetric

    Erik Hartman / Simon Mahdavi / Sven Kjellström / Artur Schmidtchen

    Frontiers in Bioinformatics, Vol

    Quantifying and Visualizing Differences in Peptidomic Data

    2021  Volume 1

    Abstract: Finding new sustainable means of diagnosing and treating diseases is one of the most pressing issues of our time. In recent years, several endogenous peptides have been found to be both excellent biomarkers for many diseases and to possess important ... ...

    Abstract Finding new sustainable means of diagnosing and treating diseases is one of the most pressing issues of our time. In recent years, several endogenous peptides have been found to be both excellent biomarkers for many diseases and to possess important physiological roles which may be utilized in treatments. The detection of peptides has been facilitated by the rapid development of biological mass spectrometry and now the combination of fast and sensitive high resolution MS instruments and stable nano HP-LC equipment sequences thousands of peptides in one single experiment. In most research conducted with these advanced systems, proteolytically cleaved proteins are analyzed and the specific peptides are identified by software dedicated for protein quantification using different proteomics workflows. Analysis of endogenous peptides with peptidomics workflows also benefit from the novel sensitive and advanced instrumentation, however, the generated peptidomic data is vast and subsequently laborious to visualize and examine, creating a bottleneck in the analysis. Therefore, we have created Peptimetric, an application designed to allow researchers to investigate and discover differences between peptidomic samples. Peptimetric allows the user to dynamically and interactively investigate the proteins, peptides, and some general characteristics of multiple samples, and is available as a web application at https://peptimetric.herokuapp.com. To illustrate the utility of Peptimetric, we’ve applied it to a peptidomic dataset of 15 urine samples from diabetic patients and corresponding data from healthy subjects.
    Keywords peptidomics ; proteomics ; bioinformatics ; mass spectrometry ; biomarkers ; visualization ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 540
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Selective protein aggregation confines and inhibits endotoxins in wounds

    Jitka Petrlova / Erik Hartman / Ganna Petruk / Jeremy Chun Hwee Lim / Sunil Shankar Adav / Sven Kjellström / Manoj Puthia / Artur Schmidtchen

    iScience, Vol 26, Iss 10, Pp 107951- (2023)

    Linking host defense to amyloid formation

    2023  

    Abstract: Summary: Bacterial lipopolysaccharide (LPS) induces rapid protein aggregation in human wound fluid. We aimed to characterize these LPS-induced aggregates and their functional implications using a combination of mass spectrometry analyses, biochemical ... ...

    Abstract Summary: Bacterial lipopolysaccharide (LPS) induces rapid protein aggregation in human wound fluid. We aimed to characterize these LPS-induced aggregates and their functional implications using a combination of mass spectrometry analyses, biochemical assays, biological imaging, cell experiments, and animal models. The wound-fluid aggregates encompass diverse protein classes, including sequences from coagulation factors, annexins, histones, antimicrobial proteins/peptides, and apolipoproteins. We identified proteins and peptides with a high aggregation propensity and verified selected components through Western blot analysis. Thioflavin T and Amytracker staining revealed amyloid-like aggregates formed after exposure to LPS in vitro in human wound fluid and in vivo in porcine wound models. Using NF-κB-reporter mice and IVIS bioimaging, we demonstrate that such wound-fluid LPS aggregates induce a significant reduction in local inflammation compared with LPS in plasma. The results show that protein/peptide aggregation is a mechanism for confining LPS and reducing inflammation, further emphasizing the connection between host defense and amyloidogenesis.
    Keywords Immunology ; Bacteriology ; cell biology ; Science ; Q
    Subject code 630
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Electrophile-Induced Conformational Switch of the Human TRPA1 Ion Channel Detected by Mass Spectrometry

    Lavanya Moparthi / Sven Kjellström / Per Kjellbom / Milos R. Filipovic / Peter M. Zygmunt / Urban Johanson

    International Journal of Molecular Sciences, Vol 21, Iss 6667, p

    2020  Volume 6667

    Abstract: The human Transient Receptor Potential A1 (hTRPA1) ion channel, also known as the wasabi receptor, acts as a biosensor of various potentially harmful stimuli. It is activated by a wide range of chemicals, including the electrophilic compound N- ... ...

    Abstract The human Transient Receptor Potential A1 (hTRPA1) ion channel, also known as the wasabi receptor, acts as a biosensor of various potentially harmful stimuli. It is activated by a wide range of chemicals, including the electrophilic compound N-methylmaleimide (NMM), but the mechanism of activation is not fully understood. Here, we used mass spectrometry to map and quantify the covalent labeling in hTRPA1 at three different concentrations of NMM. A functional truncated version of hTRPA1 (Δ1-688 hTRPA1), lacking the large N-terminal ankyrin repeat domain (ARD), was also assessed in the same way. In the full length hTRPA1, the labeling of different cysteines ranged from nil up to 95% already at the lowest concentration of NMM, suggesting large differences in reactivity of the thiols. Most important, the labeling of some cysteine residues increased while others decreased with the concentration of NMM, both in the full length and the truncated protein. These findings indicate a conformational switch of the proteins, possibly associated with activation or desensitization of the ion channel. In addition, several lysines in the transmembrane domain and the proximal N-terminal region were labeled by NMM, raising the possibility that lysines are also key targets for electrophilic activation of hTRPA1.
    Keywords TRP channel ; TRPA1 ; wasabi receptor ; electrophile sensing ; N-methylmaleimide ; Iodoacetamide ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 572
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Method development and characterisation of the low-molecular-weight peptidome of human wound fluids

    Mariena JA van der Plas / Jun Cai / Jitka Petrlova / Karim Saleh / Sven Kjellström / Artur Schmidtchen

    eLife, Vol

    2021  Volume 10

    Abstract: The normal wound healing process is characterised by proteolytic events, whereas infection results in dysfunctional activations by endogenous and bacterial proteases. Peptides, downstream reporters of these proteolytic actions, could therefore serve as a ...

    Abstract The normal wound healing process is characterised by proteolytic events, whereas infection results in dysfunctional activations by endogenous and bacterial proteases. Peptides, downstream reporters of these proteolytic actions, could therefore serve as a promising tool for diagnosis of wounds. Using mass-spectrometry analyses, we here for the first time characterise the peptidome of human wound fluids. Sterile post-surgical wound fluids were found to contain a high degree of peptides in comparison to human plasma. Analyses of the peptidome from uninfected healing wounds and Staphylococcus aureus -infected wounds identify unique peptide patterns of various proteins, including coagulation and complement factors, proteases, and antiproteinases. Together, the work defines a workflow for analysis of peptides derived from wound fluids and demonstrates a proof-of-concept that such fluids can be used for analysis of qualitative differences of peptide patterns from larger patient cohorts, providing potential biomarkers for wound healing and infection.
    Keywords peptidomics ; wound fluid ; plasma ; bacterial infection ; peptide profiles ; biomarkers ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Publisher Correction

    Ganna Petruk / Manoj Puthia / Firdaus Samsudin / Jitka Petrlova / Franziska Olm / Margareta Mittendorfer / Snejana Hyllén / Dag Edström / Ann-Charlotte Strömdahl / Carl Diehl / Simon Ekström / Björn Walse / Sven Kjellström / Peter J. Bond / Sandra Lindstedt / Artur Schmidtchen

    Nature Communications, Vol 14, Iss 1, Pp 1-

    Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs

    2023  Volume 1

    Keywords Science ; Q
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Targeting Toll-like receptor-driven systemic inflammation by engineering an innate structural fold into drugs

    Ganna Petruk / Manoj Puthia / Firdaus Samsudin / Jitka Petrlova / Franziska Olm / Margareta Mittendorfer / Snejana Hyllén / Dag Edström / Ann-Charlotte Strömdahl / Carl Diehl / Simon Ekström / Björn Walse / Sven Kjellström / Peter J. Bond / Sandra Lindstedt / Artur Schmidtchen

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 20

    Abstract: Abstract There is a clinical need for conceptually new treatments that target the excessive activation of inflammatory pathways during systemic infection. Thrombin-derived C-terminal peptides (TCPs) are endogenous anti-infective immunomodulators ... ...

    Abstract Abstract There is a clinical need for conceptually new treatments that target the excessive activation of inflammatory pathways during systemic infection. Thrombin-derived C-terminal peptides (TCPs) are endogenous anti-infective immunomodulators interfering with CD14-mediated TLR-dependent immune responses. Here we describe the development of a peptide-based compound for systemic use, sHVF18, expressing the evolutionarily conserved innate structural fold of natural TCPs. Using a combination of structure- and in silico-based design, nuclear magnetic resonance spectroscopy, biophysics, mass spectrometry, cellular, and in vivo studies, we here elucidate the structure, CD14 interactions, protease stability, transcriptome profiling, and therapeutic efficacy of sHVF18. The designed peptide displays a conformationally stabilized, protease resistant active innate fold and targets the LPS-binding groove of CD14. In vivo, it shows therapeutic efficacy in experimental models of endotoxin shock in mice and pigs and increases survival in mouse models of systemic polymicrobial infection. The results provide a drug class based on Nature´s own anti-infective principles.
    Keywords Science ; Q
    Subject code 570
    Language English
    Publishing date 2023-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure

    Awad, Wael / Derek T. Logan / Gabriel Svensson Birkedal / Katrin Mani / Sven Kjellström

    Biochemistry. 2018 Feb. 20, v. 57, no. 7

    2018  

    Abstract: Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular ... ...

    Abstract Heparan sulfate proteoglycans are proteins substituted with one or more heparan sulfate (HS) polysaccharides, found in abundance at cell surfaces. HS chains influence the activity of many biologically important molecules involved in cellular communication and signaling. The exostosin (EXT) proteins are glycosyltransferases in the Golgi apparatus that assemble HS chains on HSPGs. The EXTL3 enzyme mainly works as an initiator in HS biosynthesis. In this work, human lumenal N-glycosylated EXTL3 (EXTL3ΔN) was cloned, expressed in human embryonic kidney cells, and purified. Various biophysical and biochemical approaches were then employed to elucidate the N-glycosylation sites and the function of their attached N-glycans. Furthermore, the stability and conformation of the purified EXTL3ΔN protein in solution have been analyzed. Our data show that EXTL3ΔN has N-glycans at least at two positions, Asn290 and Asn592, which seem to be critical for proper protein folding and/or release. EXTL3ΔN is quite stable, as high temperature (∼59 °C) was required for denaturation. Deconvolution of the EXTL3ΔN far-UV CD spectrum revealed a substantial fraction of β sheets (25%) with a minor proportion of α-helices (14%) in the secondary structure. Solution small-angle X-ray scattering and dynamic light scattering revealed an extended structure suggestive of a dimeric arrangement and consisting of two distinct regions, narrow and broad, respectively. This is consistent with bioinformatics analyses suggesting a 3-domain structure with two glycosyltransferase domains and a coiled-coil domain.
    Keywords bioinformatics ; biosynthesis ; denaturation ; glycosylation ; glycosyltransferases ; Golgi apparatus ; heparan sulfate ; humans ; kidney cells ; light scattering ; protein folding ; proteoglycans ; small-angle X-ray scattering ; temperature
    Language English
    Dates of publication 2018-0220
    Size p. 1166-1177.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.7b00557
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis

    Andreas Sonesson / Kornelia Przybyszewska / Sigrid Eriksson / Matthias Mörgelin / Sven Kjellström / Julia Davies / Jan Potempa / Artur Schmidtchen

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 12

    Abstract: Abstract Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by an impaired epidermal barrier, dysregulation of innate and adaptive immunity, and a high susceptibility to bacterial colonization and infection. In the present study, ...

    Abstract Abstract Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by an impaired epidermal barrier, dysregulation of innate and adaptive immunity, and a high susceptibility to bacterial colonization and infection. In the present study, bacterial biofilm was visualized by electron microscopy at the surface of AD skin. Correspondingly, Staphylococcus aureus (S. aureus) isolates from lesional skin of patients with AD, produced a substantial amount of biofilm in vitro. S. aureus biofilms showed less susceptibility to killing by the antimicrobial peptide LL-37 when compared with results obtained using planktonic cells. Confocal microscopy analysis showed that LL-37 binds to the S. aureus biofilms. Immuno-gold staining of S. aureus biofilm of AD skin detected the S. aureus derived protease staphopain adjacent to the bacteria. In vitro, staphopain B degraded LL-37 into shorter peptide fragments. Further, LL-37 significantly inhibited S. aureus biofilm formation, but no such effects were observed for the degradation products. The data presented here provide novel information on staphopains present in S. aureus biofilms in vivo, and illustrate the complex interplay between biofilm and LL-37 in skin of AD patients, possibly leading to a disturbed host defense, which facilitates bacterial persistence.
    Keywords Medicine ; R ; Science ; Q
    Subject code 616
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells

    Meliha Mehmeti / Caroline Bergenfelz / Eva Källberg / Camilla Rydberg Millrud / Per Björk / Fredrik Ivars / Bengt Johansson-Lindbom / Sven Kjellström / Ingemar André / Karin Leandersson

    Communications Biology, Vol 2, Iss 1, Pp 1-

    2019  Volume 13

    Abstract: Meliha Mehmeti et al. show that Wnt5a is a direct ligand of toll-like receptor 2 and 4 to act as an endogenous tolerance-associated molecular pattern, triggering innate immune tolerance in human myeloid cells. This study expands the functional repertoire ...

    Abstract Meliha Mehmeti et al. show that Wnt5a is a direct ligand of toll-like receptor 2 and 4 to act as an endogenous tolerance-associated molecular pattern, triggering innate immune tolerance in human myeloid cells. This study expands the functional repertoire of Wnt5a that is mainly known as a signalling protein involved in development and cancer.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2019-05-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses

    Mariena J. A. van der Plas / Ravi K. V. Bhongir / Sven Kjellström / Helena Siller / Gopinath Kasetty / Matthias Mörgelin / Artur Schmidtchen

    Nature Communications, Vol 7, Iss 1, Pp 1-

    2016  Volume 13

    Abstract: Neutrophil elastase cleaves thrombin generating anti-inflammatory peptides. Here the authors show that cleavage of thrombin by Pseudomonas aeruginosaelastase generates a peptide that prevents TLR dimerization and signaling, interfering with the ... ...

    Abstract Neutrophil elastase cleaves thrombin generating anti-inflammatory peptides. Here the authors show that cleavage of thrombin by Pseudomonas aeruginosaelastase generates a peptide that prevents TLR dimerization and signaling, interfering with the inflammatory response to avoid host defense.
    Keywords Science ; Q
    Language English
    Publishing date 2016-05-01T00:00:00Z
    Publisher Nature Portfolio
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