Proteases articles within Nature Communications

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  • Article
    | Open Access

    Pathogenic IgA1 metalloproteases block the initial host immune response by cleaving host IgA1. Using cryoEM, the authors here provide structural insights into the substrate recognition mechanism of Streptococcus pneumoniae IgA1 protease, and develop a protease-inhibiting antibody.

    • Zhiming Wang
    • , Jeremy Rahkola
    •  & Elan Eisenmesser

  • Article
    | Open Access

    The lysosomal aspartic protease Cathepsin D (CTSD) is associated with breast cancer progression. Here the authors show that selective inactivation of CTSD in mammary epithelium delays tumor onset due to impaired mTORC1 signaling, but resumes malignant growth due to compensatory oncogenic pathways

    • Stephanie Ketterer
    • , Julia Mitschke
    •  & Thomas Reinheckel

  • Article
    | Open Access

    The SARS-CoV-2 main protease is an important target for the development of COVID-19 therapeutics. Here, the authors combine X-ray crystallography and mass spectrometry and performed a large scale fragment screening campaign, which yielded 96 liganded structures of this essential viral protein that are of interest for further drug development efforts.

    • Alice Douangamath
    • , Daren Fearon
    •  & Martin A. Walsh

  • Article
    | Open Access

    OgpA is an O-glycopeptidase from Akkermansia muciniphila, a mucin-degrading bacterium commonly found in the human gut. A thorough characterization of OgpA, including crystal structures in complex with substrate or product, reveals molecular basis of O-glycan recognition and enzyme specificity.

    • Beatriz Trastoy
    • , Andreas Naegeli
    •  & Marcelo E. Guerin

  • Article
    | Open Access

    Coronavirus main protease is essential for viral polyprotein processing and replication. Here Vuong et al. report efficient inhibition of SARS-CoV-2 replication by the dipeptide-based protease inhibitor GC376 and its parent GC373, which were originally used to treat feline coronavirus infection.

    • Wayne Vuong
    • , Muhammad Bashir Khan
    •  & M. Joanne Lemieux

  • Article
    | Open Access

    Asparaginyl endopeptidases (AEPs) catalyze the cyclization step during the biosynthesis of cyclic peptides in plants. Here, the authors report a recombinantly produced AEP that catalyzes the backbone cyclization of a linear cyclotide precursor and an engineered analog with high efficiency and in a pH-dependent manner.

    • Junqiao Du
    • , Kuok Yap
    •  & David J. Craik

  • Article
    | Open Access

    The plasma metalloprotease ADAMTS13 regulates the platelet-tethering function of von Willebrand factor (VWF) in a shear-dependent manner. Here the authors present the ADAMTS13 crystal structure of the 70kDa N-terminal metalloprotease to spacer domains, and using kinetic measurements they identify a substrate binding induced allosteric mechanism for ADAMTS13, where VWF functions both as an activating cofactor and substrate.

    • Anastasis Petri
    • , Hyo Jung Kim
    •  & James T. B. Crawley

  • Article
    | Open Access

    Aβ34 is generated from degradation of Aβ40 and Aβ42 by β-secretase. Here, the authors show that Aβ34 is a marker for amyloid clearance and is elevated in the CSF of patients that go on to convert from mild cognitive impairment to Alzheimer’s disease, suggesting it may be a useful biomarker.

    • Filip Liebsch
    • , Luka Kulic
    •  & Gerhard Multhaup

  • Article
    | Open Access

    Hippo signaling leads to the phosphorylation of the key transcriptional effector, Yap/Yki, although how Yap/Yki stability is regulated has remained unclear. Here, Sun et al. identify HAUSP/Usp7 as a conserved and clinically relevant regulator of the Hippo pathway that increases Yap/Yki stability.

    • Xiaohan Sun
    • , Yan Ding
    •  & Zizhang Zhou

  • Article
    | Open Access

    How cells regulate their lysosomal proteolytic capacity is only partly understood. Here, the authors show that lysosomal protease deficiency or substrate overload induces lysosomal stress leading to activation of a STAT3-dependent, TFEB-independent pathway of lysosomal hydrolase expression.

    • Jonathan Martínez-Fábregas
    • , Alan Prescott
    •  & Colin Watts

  • Article
    | Open Access

    Characterizing the binding selectivity landscape of interacting proteins is crucial in protein engineering. Here the authors use multi-target selective library screening and in silico next-generation sequencing to map the binding landscape of proteins and produce improved proteases inhibitors.

    • Si Naftaly
    • , Itay Cohen
    •  & Niv Papo

  • Article
    | Open Access

    Trypsin is a serine protease. Here the authors present the high resolution X-ray and neutron diffraction structures of uncomplexed and inhibitor bound trypsin that provide insights into the geometry of H-bonds in the active site of the enzyme and molecular dynamics simulations reveal the kinetics of ligand binding induced desolvation.

    • Johannes Schiebel
    • , Roberto Gaspari
    •  & Gerhard Klebe

  • Article
    | Open Access

    IFN-γ is central in inflammatory pathogenesis, response to infection and autoimmune diseases. Here the authors show that MMP12 expression is reduced in patients with SLE and that MMP12 post-translationally truncates IFN-y, inhibiting its function and affecting pathogenesis of mouse models of peritonitis, SLE and rheumatoid arthritis.

    • Antoine Dufour
    • , Caroline L. Bellac
    •  & Christopher M. Overall

  • Article
    | Open Access

    The 26S proteasome consists of a core particle that is capped at each side by a regulatory particle. Here the authors present cryo-EM structures of the activated human 26S proteasome holoenzyme in three alternative open-gate states, which provides mechanistic insights into gate opening and dynamic remodeling of the substrate–translocation pathway.

    • Yanan Zhu
    • , Wei Li Wang
    •  & Youdong Mao

  • Article
    | Open Access

    A soluble form of insulin receptor in human plasma has been previously reported. Here the authors demonstrate that insulin receptor is cleaved by BACE1 that can regulate biological active insulin receptor levels in a glucose concentration-dependent manner, both in physiological and diabetic conditions.

    • Paul J. Meakin
    • , Anna Mezzapesa
    •  & Franck Peiretti

  • Article
    | Open Access

    Deubiquitinases are proteases that cleave after the C-terminus of ubiquitin to hydrolyze ubiquitin chains and cleave ubiquitin from substrates. Here the authors describe a reactive-site-centric chemoproteomics approach to studying deubiquitinase activity, and expand the repertoire of known deubiquitinases.

    • David S. Hewings
    • , Johanna Heideker
    •  & Ingrid E. Wertz

  • Article
    | Open Access

    Disruption of the ubiquitin proteasome system (UPS) is often associated with neurodegenerative diseases. Here the authors demonstrate the existence of a general mechanism of proteasomal impairment triggered by a specific protein oligomer structure, irrespective of its protein constituent.

    • Tiffany A. Thibaudeau
    • , Raymond T. Anderson
    •  & David M. Smith

  • Article
    | Open Access

    The bacterial protease GtgE is involved in the establishment of Salmonellosis. Here the authors provide a structural and biochemical analysis of GtgE that sheds light on the molecular mechanisms of reprogramming infected host cells via site-specific proteolytic cleavage of the vesicular trafficking regulator Rab32.

    • Rudolf Wachtel
    • , Bastian Bräuning
    •  & Aymelt Itzen

  • Article
    | Open Access

    The proteases of flaviviruses are promising targets for development of specific antiviral drugs. Here, the authors report a high resolution crystal structure of the NS2B-NS3 protease of Zika virus that provides insight into substrate and inhibitor binding.

    • Wint Wint Phoo
    • , Yan Li
    •  & Dahai Luo

  • Article
    | Open Access

    Human YME1L is a membrane-anchored AAA+ protease that maintains proteostasis in the mitochondrial inner membrane and intermembrane space. Here the authors probe the substrate-binding and degradation activities of YME1L and suggest the existence of sequence-specific degradation signals in mitochondrial proteostasis.

    • Hui Shi
    • , Anthony J. Rampello
    •  & Steven E. Glynn

  • Article
    | Open Access

    Molecular fragments are useful tools in drug-discovery but they might be hard to identify due to their weak affinity to the targets. Here, the authors use a protein-templated assembly to design high affinity inhibitors of Coxsackie virus 3C protease, a pharmacological target against enteroviral infections.

    • Daniel Becker
    • , Zuzanna Kaczmarska
    •  & Jörg Rademann

  • Article
    | Open Access

    ADAM17 is a member of the ‘Disintegrin and Metalloproteinase’ family of proteases, that cleaves transmembrane substrates from the surfaces of cells. Here the authors show that surface exposure of phosphatidylserine is required for ADAM17 sheddase activity, possibly by directing the protease to its substrates.

    • Anselm Sommer
    • , Felix Kordowski
    •  & Karina Reiss

  • Article
    | Open Access

    In addition to their role in apoptosis, caspases are also involved in mediating non-apoptotic events. Here the authors show that the Drosophilamyosin family member CRINKLED and its mammalian counterpart act as substrate adaptor that facilitate caspase-mediated cleavage and localised kinase activity.

    • Mariam H. Orme
    • , Gianmaria Liccardi
    •  & Pascal Meier

  • Article
    | Open Access

    Drosophila telomeres are elongated by transposition of specialized retroelements rather than telomerase activity. Here, the authors show that Separase is enriched at Drosophila telomeres and loss of Sse, the gene encoding Separase, leads to telomere defects, suggesting a role for Separase in telomere protection.

    • Francesca Cipressa
    • , Patrizia Morciano
    •  & Giovanni Cenci

  • Article
    | Open Access

    Yersinia pestis, which evolved from a gastrointestinal pathogen, causes pneumonic and bubonic plague. Here Zimbler et al. show that the gain of a single protein enabled Y. pestisto first cause pneumonic plague, and one amino-acid change in the same protein then allowed the bacteria to efficiently cause bubonic plague.

    • Daniel L. Zimbler
    • , Jay A. Schroeder
    •  & Wyndham W. Lathem

  • Article
    | Open Access

    Tryptic digestion of SUMOylated proteins generates large peptides, rendering proteomic characterisation of this post-translational modification particularly challenging unless mutant SUMO is used. Hendriks et al.present a method that allows the quantitative identification of wild-type SUMO sites.

    • Ivo A. Hendriks
    • , Rochelle C. D’Souza
    •  & Alfred C. O. Vertegaal

  • Article
    | Open Access

    B-cell maturation antigen (BCMA) regulates the survival of B cells and is essential for the maintenance of long-lived plasma cells. Here, the authors show that γ-secretase directly sheds BCMA from the cell surface and therefore regulates the number of plasma cells.

    • Sarah A. Laurent
    • , Franziska S. Hoffmann
    •  & Edgar Meinl

  • Article |

    Elastase secreted by immune cells contributes to various lung diseases; however, elastase inhibitors have mostly failed in the clinic. Here, the authors discover a second, truncated form of elastase, which is the result of autocatalytic cleavage and is not well targeted by current synthetic elastase inhibitors.

    • T. Dau
    • , R. S. J. Sarker
    •  & D. E. Jenne

  • Article
    | Open Access

    The mitochondrial protease CLPP is found in most eukaryotic organisms but its biological role has been unclear. Here Osiewacz and colleagues show that deletion of CLPP extends lifespan of the filamentous fungus Podospora anserina, and that human and fungal CLPP are functionally conserved.

    • Fabian Fischer
    • , Andrea Weil
    •  & Heinz D. Osiewacz

  • Article
    | Open Access

    γ-Secretase modulators have promise in the treatment of Alzheimer's disease, but their molecular target is uncertain. Here, fluorescence resonance energy transfer is used to determine that the γ-secretase allosteric site is within the γ-secretase complex and that substrate docking is required for modulators to access the site.

    • Kengo Uemura
    • , Katherine C. Farner
    •  & Oksana Berezovska

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