Featured
-
-
Article
| Open AccessMotility of an autonomous protein-based artificial motor that operates via a burnt-bridge principle
Inspired by biology, great progress has been made in creating artificial molecular motors. Here the authors report the synthesis and characterization of the Lawnmower, an autonomous, protein-based artificial molecular motor and show their design is capable of track-guided motion.
- Chapin S. Korosec
- , Ivan N. Unksov
- & Nancy R. Forde
-
Article
| Open AccessMultiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design
Here the authors demonstrate that the SARS-CoV-2 main protease (Mpro) is subject to redox regulation in vitro, reversibly switching between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues.
- Lisa-Marie Funk
- , Gereon Poschmann
- & Kai Tittmann
-
Article
| Open AccessA DARPin promotes faster onset of botulinum neurotoxin A1 action
Botulinum neurotoxins (BoNTs), the causative agents of the disease botulism, are potent biological toxins. Here the authors use Designed Ankyrin Repeat Proteins (DARPins) to probe BoNT structure and function: DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro was identified.
- Oneda Leka
- , Yufan Wu
- & Richard A. Kammerer
-
Article
| Open AccessIdentification of PCPE-2 as the endogenous specific inhibitor of human BMP-1/tolloid-like proteinases
Most proteases have their own endogenous, specific inhibitors which protect living organisms from the deleterious effects of excessive proteolytic activity. Here, authors identify PCPE-2 as a potent and specific inhibitor of BMP-1/tolloid-like proteases.
- Sandrine Vadon-Le Goff
- , Agnès Tessier
- & Catherine Moali
-
Article
| Open AccessStructure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry
TMPRSS2 and CTSL/CTSB, host proteases that facilitate SARS-CoV-2 entry, are promising drug targets. Here the authors simultaneously inhibit these host proteases and see synergistic antiviral effects, offering a broad-spectrum intervention against SARS-CoV-2 variants.
- Haofeng Wang
- , Qi Yang
- & Haitao Yang
-
Article
| Open AccessA 5+1 assemble-to-activate mechanism of the Lon proteolytic machine
Many AAA+ (ATPases associated with diverse cellular activities) proteins function as a hexamer to remodel protein substrates. Here, the authors report the discovery of a pentameric form of the Lon AAA+ protease and show that it plays a role in the substrate-dependent activation of the AAA+ protein.
- Shanshan Li
- , Kan-Yen Hsieh
- & Chung-I Chang
-
Article
| Open AccessFunctional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis
Intracellular bacteria use deubiquitinase effectors to avoid being targeted for autophagic clearance. The authors show that the Chlamydia-like bacterium Simkania negevensis encodes an unusually broad range of these enzymes, including members that specifically target linear and K6-linked ubiquitin chains.
- Vanessa Boll
- , Thomas Hermanns
- & Kay Hofmann
-
Article
| Open AccessSelective activator of human ClpP triggers cell cycle arrest to inhibit lung squamous cell carcinoma
Chemo-activation of mitochondrial ClpP exhibits promising anticancer properties. Here, the authors develop a potent activator ZK53 that is highly selective on human ClpP but inactive toward bacterial ClpP proteins, and show that ZK53 causes cell cycle arrest via ClpP on lung squamous cell carcinoma cells and exhibits therapeutic effects in animal models.
- Lin-Lin Zhou
- , Tao Zhang
- & Cai-Guang Yang
-
Article
| Open AccessThe H163A mutation unravels an oxidized conformation of the SARS-CoV-2 main protease
SARS-CoV-2 main protease adapts a disulfide bonded inactive state to escape oxidative stress. Here, the authors report a crystal structure of an inactive conformation of the enzyme achieved through a H163A mutation, and the mechanistic details of conformational changes using atomistic simulations.
- Norman Tran
- , Sathish Dasari
- & Aravindhan Ganesan
-
Article
| Open AccessDeSUMOylation of a Verticillium dahliae enolase facilitates virulence by derepressing the expression of the effector VdSCP8
Verticillium dahliae, a soil-borne fungal pathogen, causes vascular wilt in a wide variety of economically important crops. This study reveals a sophisticated pathogenic mechanism of VdUlpB-deSUMOylated enolase to facilate fungal virulence by derepressing the expression of the effector VdSCP8.
- Xue-Ming Wu
- , Bo-Sen Zhang
- & Hui-Shan Guo
-
Article
| Open AccessXCP1 cleaves Pathogenesis-related protein 1 into CAPE9 for systemic immunity in Arabidopsis
The protein PR1 is crucial for plant immunity but has unclear bioactivity. Here PR1 is shown to release a phytocytokine CAPE and trigger systemic acquired resistance (SAR) via a caspase-like enzyme specific for CAPE production (ESCAPE).
- Ying-Lan Chen
- , Fan-Wei Lin
- & Yet-Ran Chen
-
Article
| Open AccessDual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
Understanding mechanisms of PLpro substrate selectivity offers new ways to decouple substrate activities and will inform new therapeutic strategies. Here, the authors use multi-disciplinary approaches to uncover how PLpro from SARS-CoV-2 can discriminate between different substrates.
- Pawel M. Wydorski
- , Jerzy Osipiuk
- & Lukasz A. Joachimiak
-
Article
| Open AccessTryptase β regulation of joint lubrication and inflammation via proteoglycan-4 in osteoarthritis
Altered expression and function of the extracellular matrix protein PRG4 have been associated with osteoarthritis. Here, the authors show that mast cell tryptase β cleaves PRG4, resulting in a reduction of lubrication and activation of inflammation in this context.
- Nabangshu Das
- , Luiz G. N. de Almeida
- & Antoine Dufour
-
Article
| Open AccessNeutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes
Most insights into deubiquitinase (DUB) substrate specificity originate from studies with isolated di-ubiquitins (diUb), but in cells diUbs with different linkage types coexist. Here, the authors develop a mass spectrometric DUB activity assay that can probe all diUbs simultaneously under substrate competition conditions.
- Bianca D. M. van Tol
- , Bjorn R. van Doodewaerd
- & Paul P. Geurink
-
Article
| Open AccessAn in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition
The Main protease of SARS-CoV-2 is key for viral replication, but its maturation process is still not completely understood. Here, the authors not only reveal unique details from the first step of maturation, but also demonstrate how different classes of inhibitor can block this step.
- Gabriela Dias Noske
- , Yun Song
- & Andre Schutzer Godoy
-
Article
| Open AccessIdentification of SARS-CoV-2 Mpro inhibitors containing P1’ 4-fluorobenzothiazole moiety highly active against SARS-CoV-2
Effective antivirals are critical for combatting SARS-CoV-2 infections. Here, the authors develop two orally available small molecules, which specifically inhibit the activity of the SARS-CoV-2 main protease and potently block the infectivity and replication of various SARS-CoV-2 strains in cells and mice.
- Nobuyo Higashi-Kuwata
- , Kohei Tsuji
- & Hiroaki Mitsuya
-
Article
| Open AccessEvolution of protease activation and specificity via alpha-2-macroglobulin-mediated covalent capture
Custom proteases find applications as therapeutics, in research and in biotechnological applications. Here, the authors establish a protease selection system based on bacterial alpha-2-macroglobulin protease inhibitors and evolve staphylococcal proteases for increased activity and altered specificity.
- Philipp Knyphausen
- , Mariana Rangel Pereira
- & Florian Hollfelder
-
Article
| Open AccessA widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins
The authors describe the VTD-deubiquitinases, a new eukaryotic enzyme family that is distantly related to herpesviral large tegument proteins. Structures of two family members with different linkage preferences allow insights into the mechanism and chain-specificity of this unusual deubiquitinase class.
- Ilka Erven
- , Elena Abraham
- & Kay Hofmann
-
Article
| Open AccessAnti-infective therapy using species-specific activators of Staphylococcus aureus ClpP
The development of selective ClpP activators targeting only the MRSA isolates without interfering with the human variant is currently challenging. Here, the authors report on the structure-based design of enantiomers of ZG197 and identify the discriminator factor between the proteins.
- Bingyan Wei
- , Tao Zhang
- & Cai-Guang Yang
-
Article
| Open AccessCryo-EM structures reveal the activation and substrate recognition mechanism of human enteropeptidase
Dysfunction of enteropeptidase (EP) can result in pancreatitis, a life-threatening disease. Yang et al. report a series of EP structures representing the EP catalytic cycle and propose a mechanistic model of enzyme function.
- Xiaoli Yang
- , Zhanyu Ding
- & Haojie Huang
-
Article
| Open AccessLipid-mediated activation of plasma membrane-localized deubiquitylating enzymes modulate endosomal trafficking
The endocytic degradation of plasma membrane proteins can be modulated by deubiquitylating enzymes (DUBs). Here, the authors describe two plasma membrane localized Arabidopsis DUBs that can be activated by binding to anionic lipids and influence the endocytic transport of plasma membrane proteins.
- Karin Vogel
- , Tobias Bläske
- & Erika Isono
-
Article
| Open AccessMolecular basis for isoform-selective inhibition of presenilin-1 by MRK-560
Presenilin isoforms (PS1 and PS2) containing γ-secretase show contrasting sensitivity to MRK-560. Here, the authors determined cryo-EM structures of PS1/PS2-complexes treated with MRK-560 and identified key residues responsible for the isoform-dependent selectivity.
- Xuefei Guo
- , Yumeng Wang
- & Yigong Shi
-
Article
| Open AccessHelical ultrastructure of the metalloprotease meprin α in complex with a small molecule inhibitor
Meprin α is a proteolytic regulator of the extracellular matrix that forms enormous oligomeric filaments of unknown purpose. Here, the authors determine by cryo-EM the structural basis of the meprin supercoiled filament and further characterise a small molecule inhibitor bound to its active site.
- Charles Bayly-Jones
- , Christopher J. Lupton
- & James C. Whisstock
-
Article
| Open AccessStructure of the proteolytic enzyme PAPP-A with the endogenous inhibitor stanniocalcin-2 reveals its inhibitory mechanism
The metalloproteinase PAPP-A promotes insulin-like growth factor (IGF) signaling by cleavage of inhibitory IGF binding proteins. Here, the authors report the 3D structure of PAPP-A in complex with its endogenous inhibitor, stanniocalcin-2.
- Sara Dam Kobberø
- , Michael Gajhede
- & Claus Oxvig
-
Article
| Open AccessStructural basis for specific inhibition of the deubiquitinase UCHL1
The deubiquitinase UCHL1 has been linked to cancer invasiveness and neurodegeneration yet its molecular roles have remained poorly defined. Here the authors reveal the structural basis for how UCHL1 can be specifically inhibited and how chemogenomic probes can be used to dissect its functions in living cells.
- Christian Grethe
- , Mirko Schmidt
- & Malte Gersch
-
Article
| Open AccessMultiscale profiling of protease activity in cancer
The activity of multiple enzymes is dysregulated in cancer, but this cannot always be measured through enzyme expression. Here, the authors develop methods to measure protease activity across the organism, tissue, and single cell scales, and identify protease dysregulation in lung cancer and its response to targeted therapy.
- Ava P. Amini
- , Jesse D. Kirkpatrick
- & Sangeeta N. Bhatia
-
Article
| Open AccessAllosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration
The protease HTRA1 is a genetic risk factor for geographic atrophy. Here, Gerhardy et al. describe its inhibition by a clinical Fab, whose binding locks it in an inactive state. The mechanism identifies an essential function of LoopA with this protease family.
- Stefan Gerhardy
- , Mark Ultsch
- & Daniel Kirchhofer
-
Article
| Open AccessDirect control of lysosomal catabolic activity by mTORC1 through regulation of V-ATPase assembly
mTORC1 blocks lysosomal nutrient generation. Here, the authors show that mTORC1 inactivation triggers V-ATPase assembly, which rapidly initiates lysosomal acidification and degradation of protein contents throughout the lysosomal population.
- Edoardo Ratto
- , S. Roy Chowdhury
- & Wilhelm Palm
-
Article
| Open AccessNative metabolomics identifies the rivulariapeptolide family of protease inhibitors
Bioactivity-guided isolation of specialized metabolites is an iterative process. Here, the authors demonstrate a native metabolomics approach that allows for fast screening of complex metabolite extracts against a protein of interest and simultaneous structure annotation.
- Raphael Reher
- , Allegra T. Aron
- & Daniel Petras
-
Article
| Open AccessRegulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli
Synthesis of lipopolysaccharides, essential components for most gram-negative bacteria, is under tight control. Here, authors use in vitro reconstitution and structural approaches to elucidate some of these regulatory mechanisms involving essential membrane proteins LapB and YejM.
- Sheng Shu
- & Wei Mi
-
Article
| Open AccessMolecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy
Celiac disease is characterized by intolerance to gluten, a cereal protein. Here, the authors show that neprosin, a glutamate peptidase from the pitcher plant, efficiently cleaves gluten components under physiological conditions in vitro and in the gut of mice.
- Laura del Amo-Maestro
- , Soraia R. Mendes
- & F. Xavier Gomis-Rüth
-
Article
| Open AccessNeprilysins regulate muscle contraction and heart function via cleavage of SERCA-inhibitory micropeptides
Muscle contraction depends on strictly controlled calcium transients within myocytes. Here, the authors show that the endopeptidase Neprilysin 4 represents an essential regulator of these transients and, consequently, of proper heart function.
- Ronja Schiemann
- , Annika Buhr
- & Heiko Meyer
-
Article
| Open AccessDefining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance
The authors determined crystal structures of the main protease (Mpro) of SARS-CoV-2 bound to substrate peptides. These structures define the substrate envelope and enable identification of sites that may be susceptible to drug resistance.
- Ala M. Shaqra
- , Sarah N. Zvornicanin
- & Celia A. Schiffer
-
Article
| Open AccessCryo-EM structures of human A2ML1 elucidate the protease-inhibitory mechanism of the A2M family
A2ML1 is a human protease inhibitor belonging to the A2M protein family. In this study, the authors determine structures of A2ML1 before and after protease inhibition and investigate its mechanism of action.
- Nadia Sukusu Nielsen
- , Alessandra Zarantonello
- & Jan J. Enghild
-
Article
| Open AccessMolecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins
GPI-T catalyzes the committed step in GPI anchor protein biogenesis. Here, Xu et al. report the cryo-EM structure of the human GPI-T, revealing critical elements within an elongated, shared active site which is topologically arranged for substrate specificity.
- Yidan Xu
- , Guowen Jia
- & Dianfan Li
-
Article
| Open AccessDevelopment of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19
Small molecule drugs promise to remain a valuable tool in controlling the ongoing COVID-19 pandemic. Here the authors describe optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for potential treatment of COVID-19.
- Hengrui Liu
- , Sho Iketani
- & Brent R. Stockwell
-
Article
| Open AccessStructural basis for the SUMO protease activity of the atypical ubiquitin-specific protease USPL1
USPL1 is a non-canonical member of the ubiquitin-specific protease (USP) family with activity toward SUMO instead of ubiquitin. Here, the authors present a crystal structure of USPL1 bound to SUMO2, revealing how this enzyme has evolved to bind SUMO as an example of divergent evolution in the USP family.
- Ying Li
- , Nathalia Varejão
- & David Reverter
-
Article
| Open AccessProtease-controlled secretion and display of intercellular signals
To program intercellular communication for biomedicine, it is crucial to regulate the secretion and surface display of signaling proteins. Here the authors develop RELEASE, a modular approach to control intercellular signals using protein-based circuits.
- Alexander E. Vlahos
- , Jeewoo Kang
- & Xiaojing J. Gao
-
Article
| Open AccessStructure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis
The collagenolytic mechanism of Vibrio collagenase, a virulence factor, remains unclear. Here, the authors report the structure of Vibrio collagenase VhaC and propose the mechanism for collagen recognition and degradation, providing new insight into bacterial collagenolysis.
- Yan Wang
- , Peng Wang
- & Yu-Zhong Zhang
-
Article
| Open AccessA structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family
ZUFSP-type enzymes cleave ubiquitin chains in a linkage-specific fashion, but members from different organisms have different specificities. Using an inter-kingdom comparison of activities and structures, the authors identify the domains responsible for this discrepancy.
- Thomas Hermanns
- , Christian Pichlo
- & Kay Hofmann
-
Article
| Open AccessCharacterising proteolysis during SARS-CoV-2 infection identifies viral cleavage sites and cellular targets with therapeutic potential
During SARS-CoV-2 replication, viral and cellular proteases play crucial roles and have been shown to be promising anti-viral targets. Here, Meyer et al. apply mass spectrometry to characterize the proteolytic cleavage profile of viral and cellular proteins in vitro.
- Bjoern Meyer
- , Jeanne Chiaravalli
- & Edward Emmott
-
Article
| Open AccessMapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen
Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
- Federico Uliana
- , Matej Vizovišek
- & Ruedi Aebersold
-
Article
| Open AccessCryo-EM structural analysis of FADD:Caspase-8 complexes defines the catalytic dimer architecture for co-ordinated control of cell fate
The core FADD:Caspase-8 complex and its regulatory partners, such as the cell death inhibitor c-FLIP, coordinate cell fate. Here authors present the structure of full-length procaspase-8 in a complex with FADD and reveal how recruitment of c-FLIPS into this complex inhibits Caspase-8 activity.
- Joanna L. Fox
- , Michelle A. Hughes
- & Marion MacFarlane
-
Article
| Open AccessStructure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors
The SARS-CoV-2 papain-like protease (PLpro) is of interest as an antiviral drug target. Here, the authors synthesize and characterise naphthalene-based inhibitors for PLpro and present the crystal structures of PLpro in its apo state and with the bound inhibitors, which is of interest for further structure-based drug design efforts.
- Jerzy Osipiuk
- , Saara-Anne Azizi
- & Andrzej Joachimiak
-
Article
| Open AccessGranzyme B inhibition reduces disease severity in autoimmune blistering diseases
Pemphigoid diseases involve autoimmune mediated blistering and immunopathology of the upper dermis. Here, the authors implicate granzyme B in the immunopathology in multiple in vivo models of pemphigoid diseases and utilise a topical granzyme B inhibitor that attenuates disease phenotypes in vivo.
- Sho Hiroyasu
- , Matthew R. Zeglinski
- & David J. Granville
-
Article
| Open AccessBivalent antibody pliers inhibit β-tryptase by an allosteric mechanism dependent on the IgG hinge
β-tryptases are responsible for most of the proteolytic activity during mast cell activation. Here, the authors develop β-tryptase-inhibiting antibodies and provide structural and biochemical evidence that the bivalency of the antibodies is a prerequisite for their inhibitory activity.
- Henry R. Maun
- , Rajesh Vij
- & James T. Koerber
-
Article
| Open AccessMechanism and inhibition of Streptococcus pneumoniae IgA1 protease
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 AccessCathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling
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 AccessCrystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease
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