1
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Detomasi TC, Batka AE, Valastyan JS, Hydorn MA, Craik CS, Bassler BL, Marletta MA. Proteases influence colony aggregation behavior in Vibrio cholerae. J Biol Chem 2023; 299:105386. [PMID: 37898401 PMCID: PMC10709122 DOI: 10.1016/j.jbc.2023.105386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Aggregation behavior provides bacteria protection from harsh environments and threats to survival. Two uncharacterized proteases, LapX and Lap, are important for Vibrio cholerae liquid-based aggregation. Here, we determined that LapX is a serine protease with a preference for cleavage after glutamate and glutamine residues in the P1 position, which processes a physiologically based peptide substrate with a catalytic efficiency of 180 ± 80 M-1s-1. The activity with a LapX substrate identified by a multiplex substrate profiling by mass spectrometry screen was 590 ± 20 M-1s-1. Lap shares high sequence identity with an aminopeptidase (termed VpAP) from Vibrio proteolyticus and contains an inhibitory bacterial prepeptidase C-terminal domain that, when eliminated, increases catalytic efficiency on leucine p-nitroanilide nearly four-fold from 5.4 ± 4.1 × 104 M-1s-1 to 20.3 ± 4.3 × 104 M-1s-1. We demonstrate that LapX processes Lap to its mature form and thus amplifies Lap activity. The increase is approximately eighteen-fold for full-length Lap (95.7 ± 5.6 × 104 M-1s-1) and six-fold for Lap lacking the prepeptidase C-terminal domain (11.3 ± 1.9 × 105 M-1s-1). In addition, substrate profiling reveals preferences for these two proteases that could inform in vivo function. Furthermore, purified LapX and Lap restore the timing of the V. cholerae aggregation program to a mutant lacking the lapX and lap genes. Both proteases must be present to restore WT timing, and thus they appear to act sequentially: LapX acts on Lap, and Lap acts on the substrate involved in aggregation.
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Affiliation(s)
- Tyler C Detomasi
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Allison E Batka
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Julie S Valastyan
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Molly A Hydorn
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Bonnie L Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA; The Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Michael A Marletta
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
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2
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Liu Z, Busscher BM, Storl-Desmond M, Xiao TS. Mechanisms of Gasdermin Recognition by Proteases. J Mol Biol 2022; 434:167274. [PMID: 34599940 PMCID: PMC8844061 DOI: 10.1016/j.jmb.2021.167274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 10/20/2022]
Abstract
Members of the gasdermin family contain positively charged N-terminal domains (NTDs) capable of binding phospholipids and assembling membrane pores, and C-terminal domains (CTDs) that bind the NTDs to prevent pore formation in the resting states. The flexible NTD-CTD linker regions of gasdermins are highly variable in length and sequences, which may be attributable to gasdermin recognition by diverse proteases. In addition, protease cleavage within the NTDs is known to inactivate several gasdermin family members. Recognition and cleavage of the gasdermin family members by different proteases share common and distinct features at the protease active sites, as well as exosites recently identified for the inflammatory caspases. Utilization of exosites may strengthen enzyme-substrate interaction, improve efficiency of proteolysis, and enhance substrate selectivity. It remains to be determined if the dual site recognition of gasdermin D (GSDMD) by the inflammatory caspases is employed by other GSDMD-targeting proteases, or is involved in proteolytic processing of other gasdermins. Biochemical and structural approaches will be instrumental in revealing how potential exosites in diverse proteases engage different gasdermin substrates. Different features of gasdermin sequence, structure, expression characteristics, and post-translational modifications may dictate distinct mechanisms of protease-dependent activation or inactivation. Such diverse mechanisms may underlie the divergent physiological and pathological functions of gasdermins, and furnish opportunities for therapeutic targeting of gasdermins in infectious diseases and inflammatory disorders.
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Affiliation(s)
| | | | | | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, United States.
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3
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Liu Z, Wang C, Yang J, Chen Y, Zhou B, Abbott DW, Xiao TS. Caspase-1 Engages Full-Length Gasdermin D through Two Distinct Interfaces That Mediate Caspase Recruitment and Substrate Cleavage. Immunity 2020; 53:106-114.e5. [PMID: 32553275 PMCID: PMC7382298 DOI: 10.1016/j.immuni.2020.06.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/11/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
The recognition and cleavage of gasdermin D (GSDMD) by inflammatory caspases-1, 4, 5, and 11 are essential steps in initiating pyroptosis after inflammasome activation. Previous work has identified cleavage site signatures in substrates such as GSDMD, but it is unclear whether these are the sole determinants for caspase engagement. Here we report the crystal structure of a complex between human caspase-1 and the full-length murine GSDMD. In addition to engagement of the GSDMD N- and C-domain linker by the caspase-1 active site, an anti-parallel β sheet at the caspase-1 L2 and L2' loops bound a hydrophobic pocket within the GSDMD C-terminal domain distal to its N-terminal domain. This "exosite" interface endows an additional function for the GSDMD C-terminal domain as a caspase-recruitment module besides its role in autoinhibition. Our study thus reveals dual-interface engagement of GSDMD by caspase-1, which may be applicable to other physiological substrates of caspases.
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Affiliation(s)
- Zhonghua Liu
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chuanping Wang
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jie Yang
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd, TRY-21, La Jolla, CA 92037, USA
| | - Yinghua Chen
- Protein Expression Purification Crystallization and Molecular Biophysics Core, Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bowen Zhou
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Derek W Abbott
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tsan Sam Xiao
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA.
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4
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Rosen LE, Klebba JE, Asfaha JB, Ghent CM, Campbell MG, Cheng Y, Morgan DO. Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site. Nat Commun 2019; 10:5189. [PMID: 31729382 PMCID: PMC6858450 DOI: 10.1038/s41467-019-13209-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
Chromosome segregation begins when the cysteine protease, separase, cleaves the Scc1 subunit of cohesin at the metaphase-to-anaphase transition. Separase is inhibited prior to metaphase by the tightly bound securin protein, which contains a pseudosubstrate motif that blocks the separase active site. To investigate separase substrate specificity and regulation, here we develop a system for producing recombinant, securin-free human separase. Using this enzyme, we identify an LPE motif on the Scc1 substrate that is distinct from the cleavage site and is required for rapid and specific substrate cleavage. Securin also contains a conserved LPE motif, and we provide evidence that this sequence blocks separase engagement of the Scc1 LPE motif. Our results suggest that rapid cohesin cleavage by separase requires a substrate docking interaction outside the active site. This interaction is blocked by securin, providing a second mechanism by which securin inhibits cohesin cleavage.
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Affiliation(s)
- Laura E Rosen
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - Joseph E Klebba
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - Jonathan B Asfaha
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - Chloe M Ghent
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - Melody G Campbell
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94143, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, 94143, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, CA, 94143, USA.
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5
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MacPherson DJ, Mills CL, Ondrechen MJ, Hardy JA. Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis. J Biol Chem 2018; 294:71-88. [PMID: 30420425 DOI: 10.1074/jbc.ra118.005914] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/07/2018] [Indexed: 12/15/2022] Open
Abstract
Caspases are cysteine-aspartic proteases involved in the regulation of programmed cell death (apoptosis) and a number of other biological processes. Despite overall similarities in structure and active-site composition, caspases show striking selectivity for particular protein substrates. Exosites are emerging as one of the mechanisms by which caspases can recruit, engage, and orient these substrates for proper hydrolysis. Following computational analyses and database searches for candidate exosites, we utilized site-directed mutagenesis to identify a new exosite in caspase-6 at the hinge between the disordered N-terminal domain (NTD), residues 23-45, and core of the caspase-6 structure. We observed that substitutions of the tri-arginine patch Arg-42-Arg-44 or the R44K cancer-associated mutation in caspase-6 markedly alter its rates of protein substrate hydrolysis. Notably, turnover of protein substrates but not of short peptide substrates was affected by these exosite alterations, underscoring the importance of this region for protein substrate recruitment. Hydrogen-deuterium exchange MS-mediated interrogation of the intrinsic dynamics of these enzymes suggested the presence of a substrate-binding platform encompassed by the NTD and the 240's region (containing residues 236-246), which serves as a general exosite for caspase-6-specific substrate recruitment. In summary, we have identified an exosite on caspase-6 that is critical for protein substrate recognition and turnover and therefore highly relevant for diseases such as cancer in which caspase-6-mediated apoptosis is often disrupted, and in neurodegeneration in which caspase-6 plays a central role.
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Affiliation(s)
- Derek J MacPherson
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Amherst, Massachusetts 01003.
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6
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Jeen T, Algar WR. Mimicking Cell Surface Enhancement of Protease Activity on the Surface of a Quantum Dot Nanoparticle. Bioconjug Chem 2018; 29:3783-3792. [DOI: 10.1021/acs.bioconjchem.8b00647] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Tiffany Jeen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - W. Russ Algar
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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7
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Dong H, Sarkes DA, Rice JJ, Hurley MM, Fu AJ, Stratis-Cullum DN. Living Bacteria-Nanoparticle Hybrids Mediated through Surface-Displayed Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:5837-5848. [PMID: 29692178 DOI: 10.1021/acs.langmuir.8b00114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this study, we investigated the preparation of living bacteria-nanoparticle hybrids mediated by surface-displayed peptides. The assembly of metallic nanoparticles on living bacteria has been achieved under mild conditions utilizing metal-peptide interactions, whereas the viability of the bacterial cells was greatly preserved. Escherichia coli was engineered with inducible gene circuits to control the display of peptides with desired sequences. Several designed peptide sequences as well as known gold-binding peptides were expressed on the cell surface using enhanced circularly permuted outer membrane protein X (eCPX) scaffolds. Driven by metal-peptide affinity, "biofriendly" citrate-stabilized gold nanoparticles were self-assembled onto the surface of bacteria with displayed peptides, which required overcoming the repulsive force between negatively charged nanoparticles and negatively charged cells. The bacteria/Au nanoparticle hybrids were highly viable and maintained the ability to grow and divide, which is a crucial step toward the creation of living material systems. Further activity and preservation of the bacterial hybrid assembly was demonstrated. The method described herein enables the conjugation of bacterial surfaces with diverse metal-rich nanoparticles in an inducible, and therefore easily controlled, manner. The expressed peptide sequences can be easily modified to alter the binding affinity and specificity for a wide variety of materials to form on-demand, high-density living biohybrids.
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Affiliation(s)
- Hong Dong
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- General Technical Services , 1451 Route 34 South , Wall Township , New Jersey 07727 , United States
| | - Deborah A Sarkes
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Jeffrey J Rice
- Department of Chemical Engineering , Auburn University , 212 Ross Hall , Auburn , Alabama 36849 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Margaret M Hurley
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
| | - Adele J Fu
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
- Oak Ridge Associated Universities , 4692 Millennium Drive, Suite 101 , Belcamp , Maryland 21017 , United States
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch , US Army Research Laboratory , 2800 Powder Mill Road , Adelphi , Maryland 20783 , United States
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8
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Ziemann S, van der Linde K, Lahrmann U, Acar B, Kaschani F, Colby T, Kaiser M, Ding Y, Schmelz E, Huffaker A, Holton N, Zipfel C, Doehlemann G. An apoplastic peptide activates salicylic acid signalling in maize. NATURE PLANTS 2018; 4:172-180. [PMID: 29483684 DOI: 10.1038/s41477-018-0116-y] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/26/2018] [Indexed: 05/06/2023]
Abstract
Localized control of cell death is crucial for the resistance of plants to pathogens. Papain-like cysteine proteases (PLCPs) regulate plant defence to drive cell death and protection against biotrophic pathogens. In maize (Zea mays), PLCPs are crucial in the orchestration of salicylic acid (SA)-dependent defence signalling. Despite this central role in immunity, it remains unknown how PLCPs are activated, and which downstream signals they induce to trigger plant immunity. Here, we discover an immune signalling peptide, Z. mays immune signalling peptide 1 (Zip1), which is produced after salicylic acid (SA) treatment. In vitro studies demonstrate that PLCPs are required to release bioactive Zip1 from its propeptide precursor. Conversely, Zip1 treatment strongly elicits SA accumulation in leaves. Moreover, transcriptome analyses revealed that Zip1 and SA induce highly overlapping transcriptional changes. Consequently, Zip1 promotes the infection of the necrotrophic fungus Botrytis cinerea, while it reduces virulence of the biotrophic fungus Ustilago maydis. Thus, Zip1 represents the previously missing signal that is released by PLCPs to activate SA defence signalling.
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Affiliation(s)
- Sebastian Ziemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
| | - Karina van der Linde
- Department of Biology, Stanford University, Stanford, CA, USA
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg, Germany
| | - Urs Lahrmann
- Fraunhofer Institute for Toxicology and Experimental Medicine ITEM, Division of Personalized Tumor Therapy, Regensburg, Germany
| | - Beyda Acar
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany
| | - Farnusch Kaschani
- Centre for Medical Biotechnology, Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Tom Colby
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Markus Kaiser
- Centre for Medical Biotechnology, Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Yezhang Ding
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Eric Schmelz
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Alisa Huffaker
- Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA, USA
| | - Nicholas Holton
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, BioCenter, Cologne, Germany.
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9
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Discovery of an enzyme and substrate selective inhibitor of ADAM10 using an exosite-binding glycosylated substrate. Sci Rep 2016; 6:11. [PMID: 28442704 PMCID: PMC5431342 DOI: 10.1038/s41598-016-0013-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/12/2016] [Indexed: 02/01/2023] Open
Abstract
ADAM10 and ADAM17 have been shown to contribute to the acquired drug resistance of HER2-positive breast cancer in response to trastuzumab. The majority of ADAM10 and ADAM17 inhibitor development has been focused on the discovery of compounds that bind the active site zinc, however, in recent years, there has been a shift from active site to secondary substrate binding site (exosite) inhibitor discovery in order to identify non-zinc-binding molecules. In the present work a glycosylated, exosite-binding substrate of ADAM10 and ADAM17 was utilized to screen 370,276 compounds from the MLPCN collection. As a result of this uHTS effort, a selective, time-dependent, non-zinc-binding inhibitor of ADAM10 with Ki = 883 nM was discovered. This compound exhibited low cell toxicity and was able to selectively inhibit shedding of known ADAM10 substrates in several cell-based models. We hypothesize that differential glycosylation of these cognate substrates is the source of selectivity of our novel inhibitor. The data indicate that this novel inhibitor can be used as an in vitro and, potentially, in vivo, probe of ADAM10 activity. Additionally, results of the present and prior studies strongly suggest that glycosylated substrate are applicable as screening agents for discovery of selective ADAM probes and therapeutics.
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10
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Siow HL, Choi SB, Gan CY. Structure–activity studies of protease activating, lipase inhibiting, bile acid binding and cholesterol-lowering effects of pre-screened cumin seed bioactive peptides. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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11
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Goldberg AB, Cho E, Miller CJ, Lou HJ, Turk BE. Identification of a Substrate-selective Exosite within the Metalloproteinase Anthrax Lethal Factor. J Biol Chem 2016; 292:814-825. [PMID: 27909054 DOI: 10.1074/jbc.m116.761734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/23/2016] [Indexed: 01/02/2023] Open
Abstract
The metalloproteinase anthrax lethal factor (LF) is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. LF is a highly specific protease, exclusively cleaving mitogen-activated protein kinase kinases (MKKs) and rodent NLRP1B (NACHT leucine-rich repeat and pyrin domain-containing protein 1B). How LF achieves such restricted substrate specificity is not understood. Previous studies have suggested the existence of an exosite interaction between LF and MKKs that promotes cleavage efficiency and specificity. Through a combination of in silico prediction and site-directed mutagenesis, we have mapped an exosite to a non-catalytic region of LF. Mutations within this site selectively impair proteolysis of full-length MKKs yet have no impact on cleavage of short peptide substrates. Although this region appears important for cleaving all LF protein substrates, we found that mutation of specific residues within the exosite differentially affects MKK and NLRP1B cleavage in vitro and in cultured cells. One residue in particular, Trp-271, is essential for cleavage of MKK3, MKK4, and MKK6 but dispensable for targeting of MEK1, MEK2, and NLRP1B. Analysis of chimeric substrates suggests that this residue interacts with the MKK catalytic domain. We found that LF-W271A blocked ERK phosphorylation and growth in a melanoma cell line, suggesting that it may provide a highly selective inhibitor of MEK1/2 for use as a cancer therapeutic. These findings provide insight into how a bacterial toxin functions to specifically impair host signaling pathways and suggest a general strategy for mapping protease exosite interactions.
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Affiliation(s)
- Allison B Goldberg
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Eunice Cho
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Chad J Miller
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Hua Jane Lou
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Benjamin E Turk
- From the Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut 06520
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12
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Wysocka M, Gruba N, Grzywa R, Giełdoń A, Bąchor R, Brzozowski K, Sieńczyk M, Dieter J, Szewczuk Z, Rolka K, Lesner A. PEGylated substrates of NSP4 protease: A tool to study protease specificity. Sci Rep 2016; 6:22856. [PMID: 26955973 PMCID: PMC4783772 DOI: 10.1038/srep22856] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/23/2016] [Indexed: 12/19/2022] Open
Abstract
Herein we present the synthesis of a novel type of peptidomimetics composed of repeating diaminopropionic acid residues modified with structurally diverse heterobifunctional polyethylene glycol chains (abbreviated as DAPEG). Based on the developed compounds, a library of fluorogenic substrates was synthesized. Further library deconvolution towards human neutrophil serine protease 4 (NSP4) yielded highly sensitive and selective internally quenched peptidomimetic substrates. In silico analysis of the obtained peptidomimetics revealed the presence of an interaction network with distant subsites located on the enzyme surface.
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Affiliation(s)
| | - Natalia Gruba
- Faculty of Chemistry, University of Gdansk, Gdansk Poland
| | - Renata Grzywa
- Faculty of Chemistry, Wroclaw Technical University, Wroclaw, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdansk, Gdansk Poland
| | | | | | - Marcin Sieńczyk
- Faculty of Chemistry, Wroclaw Technical University, Wroclaw, Poland
| | - Jenne Dieter
- Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, Munich, Germany
| | | | | | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk Poland
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13
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Page MJ, Lourenço AL, David T, LeBeau AM, Cattaruzza F, Castro HC, VanBrocklin HF, Coughlin SR, Craik CS. Non-invasive imaging and cellular tracking of pulmonary emboli by near-infrared fluorescence and positron-emission tomography. Nat Commun 2015; 6:8448. [PMID: 26423607 PMCID: PMC4593073 DOI: 10.1038/ncomms9448] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/21/2015] [Indexed: 12/22/2022] Open
Abstract
Functional imaging of proteolytic activity is an emerging strategy to quantify disease and response to therapy at the molecular level. We present a new peptide-based imaging probe technology that advances these goals by exploiting enzymatic activity to deposit probes labelled with near-infrared (NIR) fluorophores or radioisotopes in cell membranes of disease-associated proteolysis. This strategy allows for non-invasive detection of protease activity in vivo and ex vivo by tracking deposited probes in tissues. We demonstrate non-invasive detection of thrombin generation in a murine model of pulmonary embolism using our protease-activated peptide probes in microscopic clots within the lungs with NIR fluorescence optical imaging and positron-emission tomography. Thrombin activity is imaged deep in tissue and tracked predominantly to platelets within the lumen of blood vessels. The modular design of our probes allows for facile investigation of other proteases, and their contributions to disease by tailoring the protease activation and cell-binding elements. Functional imaging of proteolytic activity is an emerging strategy to guide patient diagnosis and monitor clinical outcome. Here the authors present a peptide-based probe to detect and localize thrombin activity ex vivo and non-invasively in mouse models of wounding and pulmonary thrombosis.
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Affiliation(s)
- Michael J Page
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - André L Lourenço
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA.,CAPES Foundation, Ministry of Education of Brazil, Brasília DF 70040-020, Brazil.,LABiEMol, Postgraduate Program in Pathology, Universidade Federal Fluminense, Niterói, Rio de Janeiro RJ 23230-060, Brazil
| | - Tovo David
- Cardiovascular Research Institute, University of California, San Francisco, California 94158-9001, USA
| | - Aaron M LeBeau
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - Fiore Cattaruzza
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
| | - Helena C Castro
- LABiEMol, Postgraduate Program in Pathology, Universidade Federal Fluminense, Niterói, Rio de Janeiro RJ 23230-060, Brazil
| | - Henry F VanBrocklin
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California 94107, USA
| | - Shaun R Coughlin
- Cardiovascular Research Institute, University of California, San Francisco, California 94158-9001, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-2517, USA
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Sankaran S, Kiren MC, Jonkheijm P. Incorporating Bacteria as a Living Component in Supramolecular Self-Assembled Monolayers through Dynamic Nanoscale Interactions. ACS NANO 2015; 9:3579-86. [PMID: 25738514 DOI: 10.1021/acsnano.5b00694] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Supramolecular assemblies, formed through noncovalent interactions, has become particularly attractive to develop dynamic and responsive architectures to address living systems at the nanoscale. Cucurbit[8]uril (CB[8]), a pumpkin shaped macrocylic host molecule, has been successfully used to construct various self-assembled architectures for biomedical applications since it can simultaneously bind two aromatic guest molecules within its cavity. Such architectures can also be designed to respond to external stimuli. Integrating living organisms as an active component into such supramolecular architectures would add a new dimension to the capabilities of such systems. To achieve this, we have incorporated supramolecular functionality at the bacterial surface by genetically modifying a transmembrane protein to display a CB[8]-binding motif as part of a cystine-stabilized miniprotein. We were able to confirm that this supramolecular motif on the bacterial surface specifically binds CB[8] and forms multiple intercellular ternary complexes leading to aggregation of the bacterial solution. We performed various aggregation experiments to understand how CB[8] interacts with this bacterial strain and also demonstrate that it can be chemically reversed using a competitor. To confirm that this strain can be incorporated with a CB[8] based architecture, we show that the bacterial cells were able to adhere to CB[8] self-assembled monolayers (SAMs) on gold and still retain considerable motility for several hours, indicating that the system can potentially be used to develop supramolecular bacterial biomotors. The bacterial strain also has the potential to be combined with other CB[8] based architectures like nanoparticles, vesicles and hydrogels.
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Affiliation(s)
- Shrikrishnan Sankaran
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
| | - Mustafa Can Kiren
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
| | - Pascal Jonkheijm
- Laboratory group of Bioinspired Molecular Engineering, Molecular Nanofabrication Group, Faculty of Science and Technology and MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, Enschede 7500AE, The Netherlands
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Small JL, O'Donoghue AJ, Boritsch EC, Tsodikov OV, Knudsen GM, Vandal O, Craik CS, Ehrt S. Substrate specificity of MarP, a periplasmic protease required for resistance to acid and oxidative stress in Mycobacterium tuberculosis. J Biol Chem 2013; 288:12489-99. [PMID: 23504313 DOI: 10.1074/jbc.m113.456541] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The transmembrane serine protease MarP is important for pH homeostasis in Mycobacterium tuberculosis (Mtb). Previous structural studies revealed that MarP contains a chymotrypsin fold and a disulfide bond that stabilizes the protease active site in the substrate-bound conformation. Here, we determined that MarP is located in the Mtb periplasm and showed that this localization is essential for function. Using the recombinant protease domain of MarP, we identified its substrate specificity using two independent assays: positional-scanning synthetic combinatorial library profiling and multiplex substrate profiling by mass spectrometry. These methods revealed that MarP prefers bulky residues at P4, tryptophan or leucine at P2, arginine or hydrophobic residues at P1, and alanine or asparagine at P1'. Guided by these data, we designed fluorogenic peptide substrates and characterized the kinetic properties of MarP. Finally, we tested the impact of mutating MarP cysteine residues on the peptidolytic activity of recombinant MarP and its ability to complement phenotypes of Mtb ΔMarP. Taken together, our studies provide insight into the enzymatic properties of MarP, its substrate preference, and the importance of its transmembrane helices and disulfide bond.
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Affiliation(s)
- Jennifer L Small
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA
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