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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Engelberg, Yizhaq; Landau, Meytal;

    Here we demonstrate self-assembly of the human LL-37 active core (residues 17-29) into a hexameric fibrillar architecture of densely packed helices, which formed alternating hydrophobic and positively charged zigzagged belts on its surface. These, in turn, likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. Correspondingly, LL-37 17-29 formed wide, ribbon-like, thermostable fibrils in solution, which co-localized with bacterial cells. Structure-guided mutagenesis analyses demonstrated that the self-assembly is essential for LL-37 17-29 antibacterial activity via direct interactions with the bacteria. LL-37 17-29 resembled, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This similarity may point to structural mimicry mechanisms used by the bacteria to hijack LL-37 functions in the immune system. One Sentence Summary The antibacterial activity of human and primate LL-37(17-29) is controlled by self-assembly into densely packed helical fibrils

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
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    Authors: Shimshoni, Elee; Ghini, Veronica; Solomonov, Inna; Luchinat, Claudio; +2 Authors

    AbstractTwo murine models for colitis were used to study multi-level changes and derive molecular signatures of colitis onset and development. By combining metabolomics data on tissues and fecal extracts with proteomics data on tissues, we provide a comprehensive picture of the metabolic profile of acute and chronic states of the disease, and most importantly, of two early pre-symptomatic states. We show that, increased anaerobic glycolysis, accompanied by altered TCA cycle and oxidative phosphorylation, associates with inflammation-induced hypoxia taking place in colon tissues. We also demonstrate significant changes in the metabolomic profiles of fecal extracts in different colitis states, most likely associated with the dysbiosis characteristic of colitis, as well as the dysregulated tissue metabolism. Most remarkably, strong and distinctive tissue and fecal metabolomic signatures can be detected before onset of symptoms. These results highlight the diagnostic potential of global metabolomics for inflammatory diseases.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
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    Authors: Galilee, Meytal; Alian, Akram;

    ABSTRACTNew anti-AIDS treatments must be continually developed in order to overcome resistance mutations including those emerging in the newest therapeutic target, the viral integrase (IN). Multimerization of IN is functionally imperative and provides a forthcoming therapeutic target. Allosteric inhibitors of IN bind to non-catalytic sites and prevent correct multimerization not only restricting viral integration but also the assembly and maturation of viral particles. Here, we report an allosteric inhibitor peptide targeting an unexploited SH3-docking platform of retroviral IN. The crystal structure of the peptide in complex with the HIV-1 IN core domain reveals a steric interference that would inhibit conserved docking of SH3-containing domain with the core domain vital for IN multimerization, providing a template for the development of novel anti-IN allosteric inhibitors.

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    Authors: Shir Marciano; Debabrata Dey; Dina Listov; Sarel J Fleishman; +7 Authors

    Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures. Experimentally determined structures are often considered in determining a protein's oligomeric state, but static structures miss the dynamic equilibrium between different quaternary forms. The problem is exacerbated in homo-oligomers, where the oligomeric states are challenging to characterize. Here, we re-evaluated the oligomeric state of 17 different bacterial proteins across a broad range of protein concentrations and solutions by native mass spectrometry (MS), mass photometry (MP), size exclusion chromatography (SEC), and small-angle X-ray scattering (SAXS), finding that most exhibit several oligomeric states. Surprisingly, some proteins did not show mass-action driven equilibrium between the oligomeric states. For approximately half the proteins, the predicted oligomeric forms described in publicly available databases underestimated the complexity of protein quaternary structures in solution. Conversely, AlphaFold multimer provided an accurate description of the potential multimeric states for most proteins, suggesting that it could help resolve uncertainties on the solution state of many proteins. Chemical science 13(39), 11680 - 11695 (2022). doi:10.1039/D2SC02794A Published by RSC, Cambridge

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    Chemical Science
    Article . 2022 . Peer-reviewed
    License: CC BY
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Chemical Sciencearrow_drop_down
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      Chemical Science
      Article . 2022 . Peer-reviewed
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    Authors: Boveia, Antonio; Doglioni, Caterina; Gao, Boyu; Greaves, Josh; +18 Authors

    Comparisons of the coverage of current and proposed dark matter searches can help us to understand the context in which a discovery of particle dark matter would be made. In some scenarios, a discovery could be reinforced by information from multiple, complementary types of experiments; in others, only one experiment would see a signal, giving only a partial, more ambiguous picture; in still others, no experiment would be sensitive and new approaches would be needed. In this whitepaper, we present an update to a similar study performed for the European Strategy Briefing Book performed within the dark matter at the Energy Frontier (EF10) Snowmass Topical Group We take as a starting point a set of projections for future collider facilities and a method of graphical comparisons routinely performed for LHC DM searches using simplified models recommended by the LHC Dark Matter Working Group and also used for the BSM and dark matter chapters of the European Strategy Briefing Book. These comparisons can also serve as launching point for cross-frontier discussions about dark matter complementarity. Comment: Submitted to the Proceedings of the US Community Study on the Future of Particle Physics (Snowmass 2021)

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    CERN Document Server
    Other literature type . 2022
    https://doi.org/10.48550/arxiv...
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      CERN Document Server
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    Authors: Gil Koren; Sagi Meir; Lennard Holschuh; Haydyn D. T. Mertens; +8 Authors

    Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins’ structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs’ amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments’ structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP’s sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function. Proceedings of the National Academy of Sciences of the United States of America 120(30), e2220180120 (2023). doi:10.1073/pnas.2220180120 Published by National Acad. of Sciences, Washington, DC

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    Proceedings of the National Academy of Sciences
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      Proceedings of the National Academy of Sciences
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Engelberg, Yizhaq; Landau, Meytal;

    Here we demonstrate self-assembly of the human LL-37 active core (residues 17-29) into a hexameric fibrillar architecture of densely packed helices, which formed alternating hydrophobic and positively charged zigzagged belts on its surface. These, in turn, likely underlie interactions with and subsequent disruption of negatively charged lipid bilayers, such as bacterial membranes. Correspondingly, LL-37 17-29 formed wide, ribbon-like, thermostable fibrils in solution, which co-localized with bacterial cells. Structure-guided mutagenesis analyses demonstrated that the self-assembly is essential for LL-37 17-29 antibacterial activity via direct interactions with the bacteria. LL-37 17-29 resembled, in sequence and in the ability to form amphipathic helical fibrils, the bacterial cytotoxic PSMα3 peptide that assembles into cross-α amyloid fibrils. This similarity may point to structural mimicry mechanisms used by the bacteria to hijack LL-37 functions in the immune system. One Sentence Summary The antibacterial activity of human and primate LL-37(17-29) is controlled by self-assembly into densely packed helical fibrils

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    Authors: Shimshoni, Elee; Ghini, Veronica; Solomonov, Inna; Luchinat, Claudio; +2 Authors

    AbstractTwo murine models for colitis were used to study multi-level changes and derive molecular signatures of colitis onset and development. By combining metabolomics data on tissues and fecal extracts with proteomics data on tissues, we provide a comprehensive picture of the metabolic profile of acute and chronic states of the disease, and most importantly, of two early pre-symptomatic states. We show that, increased anaerobic glycolysis, accompanied by altered TCA cycle and oxidative phosphorylation, associates with inflammation-induced hypoxia taking place in colon tissues. We also demonstrate significant changes in the metabolomic profiles of fecal extracts in different colitis states, most likely associated with the dysbiosis characteristic of colitis, as well as the dysregulated tissue metabolism. Most remarkably, strong and distinctive tissue and fecal metabolomic signatures can be detected before onset of symptoms. These results highlight the diagnostic potential of global metabolomics for inflammatory diseases.

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    Authors: Galilee, Meytal; Alian, Akram;

    ABSTRACTNew anti-AIDS treatments must be continually developed in order to overcome resistance mutations including those emerging in the newest therapeutic target, the viral integrase (IN). Multimerization of IN is functionally imperative and provides a forthcoming therapeutic target. Allosteric inhibitors of IN bind to non-catalytic sites and prevent correct multimerization not only restricting viral integration but also the assembly and maturation of viral particles. Here, we report an allosteric inhibitor peptide targeting an unexploited SH3-docking platform of retroviral IN. The crystal structure of the peptide in complex with the HIV-1 IN core domain reveals a steric interference that would inhibit conserved docking of SH3-containing domain with the core domain vital for IN multimerization, providing a template for the development of novel anti-IN allosteric inhibitors.

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    Authors: Shir Marciano; Debabrata Dey; Dina Listov; Sarel J Fleishman; +7 Authors

    Over half the proteins in the E. coli cytoplasm form homo or hetero-oligomeric structures. Experimentally determined structures are often considered in determining a protein's oligomeric state, but static structures miss the dynamic equilibrium between different quaternary forms. The problem is exacerbated in homo-oligomers, where the oligomeric states are challenging to characterize. Here, we re-evaluated the oligomeric state of 17 different bacterial proteins across a broad range of protein concentrations and solutions by native mass spectrometry (MS), mass photometry (MP), size exclusion chromatography (SEC), and small-angle X-ray scattering (SAXS), finding that most exhibit several oligomeric states. Surprisingly, some proteins did not show mass-action driven equilibrium between the oligomeric states. For approximately half the proteins, the predicted oligomeric forms described in publicly available databases underestimated the complexity of protein quaternary structures in solution. Conversely, AlphaFold multimer provided an accurate description of the potential multimeric states for most proteins, suggesting that it could help resolve uncertainties on the solution state of many proteins. Chemical science 13(39), 11680 - 11695 (2022). doi:10.1039/D2SC02794A Published by RSC, Cambridge

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    Chemical Science
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      Chemical Science
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    Authors: Boveia, Antonio; Doglioni, Caterina; Gao, Boyu; Greaves, Josh; +18 Authors

    Comparisons of the coverage of current and proposed dark matter searches can help us to understand the context in which a discovery of particle dark matter would be made. In some scenarios, a discovery could be reinforced by information from multiple, complementary types of experiments; in others, only one experiment would see a signal, giving only a partial, more ambiguous picture; in still others, no experiment would be sensitive and new approaches would be needed. In this whitepaper, we present an update to a similar study performed for the European Strategy Briefing Book performed within the dark matter at the Energy Frontier (EF10) Snowmass Topical Group We take as a starting point a set of projections for future collider facilities and a method of graphical comparisons routinely performed for LHC DM searches using simplified models recommended by the LHC Dark Matter Working Group and also used for the BSM and dark matter chapters of the European Strategy Briefing Book. These comparisons can also serve as launching point for cross-frontier discussions about dark matter complementarity. Comment: Submitted to the Proceedings of the US Community Study on the Future of Particle Physics (Snowmass 2021)

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    CERN Document Server
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    Authors: Gil Koren; Sagi Meir; Lennard Holschuh; Haydyn D. T. Mertens; +8 Authors

    Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins’ structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Therefore, to understand their biological function, it is critical to depict how the structural ensemble statistics correlate to the IDPs’ amino acid sequence. Here, using small-angle X-ray scattering and time-resolved Förster resonance energy transfer (trFRET), we study the intramolecular structural heterogeneity of the neurofilament low intrinsically disordered tail domain (NFLt). Using theoretical results of polymer physics, we find that the Flory scaling exponent of NFLt subsegments correlates linearly with their net charge, ranging from statistics of ideal to self-avoiding chains. Surprisingly, measuring the same segments in the context of the whole NFLt protein, we find that regardless of the peptide sequence, the segments’ structural statistics are more expanded than when measured independently. Our findings show that while polymer physics can, to some level, relate the IDP’s sequence to its ensemble conformations, long-range contacts between distant amino acids play a crucial role in determining intramolecular structures. This emphasizes the necessity of advanced polymer theories to fully describe IDPs ensembles with the hope that it will allow us to model their biological function. Proceedings of the National Academy of Sciences of the United States of America 120(30), e2220180120 (2023). doi:10.1073/pnas.2220180120 Published by National Acad. of Sciences, Washington, DC

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    Proceedings of the National Academy of Sciences
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