1
|
Wallerstein J, Han X, Levkovets M, Lesovoy D, Malmodin D, Mirabello C, Wallner B, Sun R, Sandalova T, Agback P, Karlsson G, Achour A, Agback T, Orekhov V. Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses. Commun Biol 2024; 7:868. [PMID: 39014105 PMCID: PMC11252132 DOI: 10.1038/s42003-024-06558-y] [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: 02/16/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
Mucosa-associated lymphoid tissue lymphoma-translocation protein 1 (MALT1) is an attractive target for the development of modulatory compounds in the treatment of lymphoma and other cancers. While the three-dimensional structure of MALT1 has been previously determined through X-ray analysis, its dynamic behaviour in solution has remained unexplored. We present here dynamic analyses of the apo MALT1 form along with the E549A mutation. This investigation used NMR 15N relaxation and NOE measurements between side-chain methyl groups. Our findings confirm that MALT1 exists as a monomer in solution, and demonstrate that the domains display semi-independent movements in relation to each other. Our dynamic study, covering multiple time scales, along with the assessment of conformational populations by Molecular Dynamic simulations, Alpha Fold modelling and PCA analysis, put the side chain of residue W580 in an inward position, shedding light at potential mechanisms underlying the allosteric regulation of this enzyme.
Collapse
Affiliation(s)
- Johan Wallerstein
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, SE-17165, Solna, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Maria Levkovets
- Swedish NMR Centre, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden
| | - Dmitry Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia
| | - Daniel Malmodin
- Swedish NMR Centre, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden
| | - Claudio Mirabello
- Dept of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Björn Wallner
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, SE-17165, Solna, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, SE-17165, Solna, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
| | - Göran Karlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden
- Swedish NMR Centre, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, SE-17165, Solna, Sweden
- Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden.
- Swedish NMR Centre, University of Gothenburg, Box 465, SE-40530, Gothenburg, Sweden.
| |
Collapse
|
2
|
Dong Y, Bonin JP, Devant P, Liang Z, Sever AIM, Mintseris J, Aramini JM, Du G, Gygi SP, Kagan JC, Kay LE, Wu H. Structural transitions enable interleukin-18 maturation and signaling. Immunity 2024; 57:1533-1548.e10. [PMID: 38733997 PMCID: PMC11236505 DOI: 10.1016/j.immuni.2024.04.015] [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: 10/26/2023] [Revised: 02/28/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron microscopy (cryo-EM), two major conformations of the complex between caspase-1 and pro-IL-18. One conformation is similar to the complex of caspase-4 and pro-IL-18, with interactions at both the active site and an exosite (closed conformation), and the other only contains interactions at the active site (open conformation). Thus, pro-IL-18 recruitment and processing by caspase-1 is less dependent on the exosite than the active site, unlike caspase-4. Structure determination by nuclear magnetic resonance uncovers a compact fold of apo pro-IL-18, which is similar to caspase-1-bound pro-IL-18 but distinct from cleaved IL-18. Binding sites for IL-18 receptor and IL-18 binding protein are only formed upon conformational changes after pro-IL-18 cleavage. These studies show how pro-IL-18 is selected as a caspase-1 substrate, and why cleavage is necessary for its inflammatory activity.
Collapse
Affiliation(s)
- Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jeffrey P Bonin
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Pascal Devant
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhuoyi Liang
- Bioscience and Biomedical Engineering Thrust, Brain and Intelligence Research Institute, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Alexander I M Sever
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - James M Aramini
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Stephen P Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lewis E Kay
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
3
|
Huang X, Zhao Z, Zhu C, Chai L, Yan Y, Yuan Y, Wu L, Li M, Jiang X, Wang H, Liu Z, Li P, Li X. Species-specific IL-1β is an inflammatory sensor of Seneca Valley Virus 3C Protease. PLoS Pathog 2024; 20:e1012398. [PMID: 39038050 PMCID: PMC11293702 DOI: 10.1371/journal.ppat.1012398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 08/01/2024] [Accepted: 07/05/2024] [Indexed: 07/24/2024] Open
Abstract
Inflammasomes play pivotal roles in inflammation by processing and promoting the secretion of IL-1β. Caspase-1 is involved in the maturation of IL-1β and IL-18, while human caspase-4 specifically processes IL-18. Recent structural studies of caspase-4 bound to Pro-IL-18 reveal the molecular basis of Pro-IL-18 activation by caspase-4. However, the mechanism of caspase-1 processing of pro-IL-1β and other IL-1β-converting enzymes remains elusive. Here, we observed that swine Pro-IL-1β (sPro-IL-1β) exists as an oligomeric precursor unlike monomeric human Pro-IL-1β (hPro-IL-1β). Interestingly, Seneca Valley Virus (SVV) 3C protease cleaves sPro-IL-1β to produce mature IL-1β, while it cleaves hPro-IL-1β but does not produce mature IL-1β in a specific manner. When the inflammasome is blocked, SVV 3C continues to activate IL-1β through direct cleavage in porcine alveolar macrophages (PAMs). Through molecular modeling and mutagenesis studies, we discovered that the pro-domain of sPro-IL-1β serves as an 'exosite' with its hydrophobic residues docking into a positively charged 3C protease pocket, thereby directing the substrate to the active site. The cleavage of sPro-IL-1β generates a monomeric and active form of IL-1β, initiating the downstream signaling. Thus, these studies provide IL-1β is an inflammatory sensor that directly detects viral protease through an independent pathway operating in parallel with host inflammasomes.
Collapse
Affiliation(s)
- Xiangyu Huang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhenchao Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lvye Chai
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ya Yan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ye Yuan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lei Wu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Minjie Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaohan Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haiwei Wang
- State Key Laboratory of Animal Disease Control, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zheng Liu
- Koblika Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Xin Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| |
Collapse
|
4
|
Du G, Healy LB, David L, Walker C, El-Baba TJ, Lutomski CA, Goh B, Gu B, Pi X, Devant P, Fontana P, Dong Y, Ma X, Miao R, Balasubramanian A, Puthenveetil R, Banerjee A, Luo HR, Kagan JC, Oh SF, Robinson CV, Lieberman J, Wu H. ROS-dependent S-palmitoylation activates cleaved and intact gasdermin D. Nature 2024; 630:437-446. [PMID: 38599239 PMCID: PMC11283288 DOI: 10.1038/s41586-024-07373-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation and was previously shown to form large transmembrane pores after cleavage by inflammatory caspases to generate the GSDMD N-terminal domain (GSDMD-NT)1-10. Here we report that GSDMD Cys191 is S-palmitoylated and that palmitoylation is required for pore formation. S-palmitoylation, which does not affect GSDMD cleavage, is augmented by mitochondria-generated reactive oxygen species (ROS). Cleavage-deficient GSDMD (D275A) is also palmitoylated after inflammasome stimulation or treatment with ROS activators and causes pyroptosis, although less efficiently than palmitoylated GSDMD-NT. Palmitoylated, but not unpalmitoylated, full-length GSDMD induces liposome leakage and forms a pore similar in structure to GSDMD-NT pores shown by cryogenic electron microscopy. ZDHHC5 and ZDHHC9 are the major palmitoyltransferases that mediate GSDMD palmitoylation, and their expression is upregulated by inflammasome activation and ROS. The other human gasdermins are also palmitoylated at their N termini. These data challenge the concept that cleavage is the only trigger for GSDMD activation. They suggest that reversible palmitoylation is a checkpoint for pore formation by both GSDMD-NT and intact GSDMD that functions as a general switch for the activation of this pore-forming family.
Collapse
Affiliation(s)
- Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| | - Liam B Healy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Seqirus, Cambridge, MA, USA.
| | - Caitlin Walker
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Tarick J El-Baba
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
| | - Corinne A Lutomski
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
| | - Byoungsook Goh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Bowen Gu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Pascal Devant
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Xiyu Ma
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Rui Miao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Arumugam Balasubramanian
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Robbins Puthenveetil
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Hongbo R Luo
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan C Kagan
- Harvard Medical School and Division of Gastroenterology, Boston Children's Hospital, Boston, MA, USA
| | - Sungwhan F Oh
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for NanoScience Discovery, University of Oxford, Oxford, UK
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| |
Collapse
|
5
|
Devant P, Dong Y, Mintseris J, Ma W, Gygi SP, Wu H, Kagan JC. Structural insights into cytokine cleavage by inflammatory caspase-4. Nature 2023; 624:451-459. [PMID: 37993712 PMCID: PMC10807405 DOI: 10.1038/s41586-023-06751-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023]
Abstract
Inflammatory caspases are key enzymes in mammalian innate immunity that control the processing and release of interleukin-1 (IL-1)-family cytokines1,2. Despite the biological importance, the structural basis for inflammatory caspase-mediated cytokine processing has remained unclear. To date, catalytic cleavage of IL-1-family members, including pro-IL-1β and pro-IL-18, has been attributed primarily to caspase-1 activities within canonical inflammasomes3. Here we demonstrate that the lipopolysaccharide receptor caspase-4 from humans and other mammalian species (except rodents) can cleave pro-IL-18 with an efficiency similar to pro-IL-1β and pro-IL-18 cleavage by the prototypical IL-1-converting enzyme caspase-1. This ability of caspase-4 to cleave pro-IL-18, combined with its previously defined ability to cleave and activate the lytic pore-forming protein gasdermin D (GSDMD)4,5, enables human cells to bypass the need for canonical inflammasomes and caspase-1 for IL-18 release. The structure of the caspase-4-pro-IL-18 complex determined using cryogenic electron microscopy reveals that pro-lL-18 interacts with caspase-4 through two distinct interfaces: a protease exosite and an interface at the caspase-4 active site involving residues in the pro-domain of pro-IL-18, including the tetrapeptide caspase-recognition sequence6. The mechanisms revealed for cytokine substrate capture and cleavage differ from those observed for the caspase substrate GSDMD7,8. These findings provide a structural framework for the discussion of caspase activities in health and disease.
Collapse
Affiliation(s)
- Pascal Devant
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Weiyi Ma
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
6
|
Lloyd J, Biasutto A, Dürr KL, Jazayeri A, Hopper JT, Oldham NJ. Mapping the Binding Interactions between Human Gasdermin D and Human Caspase-1 Using Carbene Footprinting. JACS AU 2023; 3:2025-2035. [PMID: 37502151 PMCID: PMC10369405 DOI: 10.1021/jacsau.3c00236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
Carbene footprinting is a recently developed mass spectrometry-based chemical labeling technique that probes protein interactions and conformation. Here, we use the methodology to investigate binding interactions between the protease human Caspase-1 (C285A) and full-length human Gasdermin D (hGSDMD), which are important in inflammatory cell death. GSDMD is cleaved by Caspase-1, releasing its N-terminal domain which oligomerizes in the membrane to form large pores, resulting in lytic cell death. Regions of reduced carbene labeling (masking), caused by protein binding, were observed for each partner in the presence of the other and were consistent with hCaspase-1 exosite and active-site interactions. Most notably, the results showed direct occupancy of hCaspase-1 (C285A) active-site by hGSDMD for the first time. Differential carbene labeling of full-length hGSDMD and the pore-forming N-terminal domain assembled in liposomes showed masking of the latter, consistent with oligomeric assembly and insertion into the lipid bilayer. Interactions between Caspase-1 and the specific inhibitor VRT-043198 were also studied by this approach. In wild-type hCaspase-1, VRT-043198 modifies the active-site Cys285 through the formation of a S,O-hemiacetal. Here, we showed by carbene labeling that this inhibitor can noncovalently occupy the active site of a C285A mutant. These findings add considerably to our knowledge of the hCaspase-1-hGSDMD system.
Collapse
Affiliation(s)
- James
R. Lloyd
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Antonio Biasutto
- OMass
Therapeutics, Schrodinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Katharina L. Dürr
- OMass
Therapeutics, Schrodinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Ali Jazayeri
- OMass
Therapeutics, Schrodinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Jonathan T.S. Hopper
- OMass
Therapeutics, Schrodinger Building, Oxford Science Park, Oxford OX4 4GE, U.K.
| | - Neil J. Oldham
- School
of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| |
Collapse
|
7
|
Du G, Healy LB, David L, Walker C, Fontana P, Dong Y, Devant P, Puthenveetil R, Ficarro SB, Banerjee A, Kagan JC, Lieberman J, Wu H. ROS-dependent palmitoylation is an obligate licensing modification for GSDMD pore formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531538. [PMID: 36945424 PMCID: PMC10028872 DOI: 10.1101/2023.03.07.531538] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Gasdermin D (GSDMD) is the common effector for cytokine secretion and pyroptosis downstream of inflammasome activation by forming large transmembrane pores upon cleavage by inflammatory caspases. Here we report the surprising finding that GSDMD cleavage is not sufficient for its pore formation. Instead, GSDMD is lipidated by S-palmitoylation at Cys191 upon inflammasome activation, and only palmitoylated GSDMD N-terminal domain (GSDMD-NT) is capable of membrane translocation and pore formation, suggesting that palmitoylation licenses GSDMD activation. Treatment by the palmitoylation inhibitor 2-bromopalmitate and alanine mutation of Cys191 abrogate GSDMD membrane localization, cytokine secretion, and cell death, without affecting GSDMD cleavage. Because palmitoylation is formed by a reversible thioester bond sensitive to free thiols, we tested if GSDMD palmitoylation is regulated by cellular redox state. Lipopolysaccharide (LPS) mildly and LPS plus the NLRP3 inflammasome activator nigericin markedly elevate reactive oxygen species (ROS) and GSDMD palmitoylation, suggesting that these two processes are coupled. Manipulation of cellular ROS by its activators and quenchers augment and abolish, respectively, GSDMD palmitoylation, GSDMD pore formation and cell death. We discover that zDHHC5 and zDHHC9 are the major palmitoyl transferases that mediate GSDMD palmitoylation, and when cleaved, recombinant and partly palmitoylated GSDMD is 10-fold more active in pore formation than bacterially expressed, unpalmitoylated GSDMD, evidenced by liposome leakage assay. Finally, other GSDM family members are also palmitoylated, suggesting that ROS stress and palmitoylation may be a general switch for the activation of this pore-forming family. One-Sentence Summary GSDMD palmitoylation is induced by ROS and required for pore formation.
Collapse
|
8
|
Wei S, Feng M, Zhang S. Molecular Characteristics of Cell Pyroptosis and Its Inhibitors: A Review of Activation, Regulation, and Inhibitors. Int J Mol Sci 2022; 23:ijms232416115. [PMID: 36555757 PMCID: PMC9783510 DOI: 10.3390/ijms232416115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Pyroptosis is an active and ordered form of programmed cell death. The signaling pathways of pyroptosis are mainly divided into canonical pathways mediated by caspase-1 and noncanonical pathways mediated by caspase-11. Cell pyroptosis is characterized by the activation of inflammatory caspases (mainly caspase-1, 4, 5, 11) and cleavage of various members of the Gasdermin family to form membrane perforation components, leading to cell membrane rupture, inflammatory mediators release, and cell death. Moderate pyroptosis is an innate immune response that fights against infection and plays an important role in the occurrence and development of the normal function of the immune system. However, excessive pyroptosis occurs and leads to immune disorders in many pathological conditions. Based on canonical pathways, research on pyroptosis regulation has demonstrated several pyroptotic inhibitors, including small-molecule drugs, natural products, and formulations of traditional Chinese medicines. In this paper, we review the characteristics and molecular mechanisms of pyroptosis, summarize inhibitors of pyroptosis, and propound that herbal medicines should be a focus on the research and development for pyroptosis blockers.
Collapse
Affiliation(s)
| | | | - Shidong Zhang
- Correspondence: ; Tel.: +86-931-211-5256; Fax: +86-931-211-5191
| |
Collapse
|
9
|
Song Y, Song J, Wang M, Wang J, Ma B, Zhang W. Porcine Gasdermin D Is a Substrate of Caspase-1 and an Executioner of Pyroptosis. Front Immunol 2022; 13:828911. [PMID: 35359964 PMCID: PMC8964005 DOI: 10.3389/fimmu.2022.828911] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Gasdermin (GSDM) family proteins were recently identified as the executioner of pyroptosis. The mechanism of pyroptosis mediated by gasdermin D (GSDMD) (a member of GSDM family) in humans and mice is well understood. In pyroptosis, mouse and human GSDMDs are cleaved by activated proinflammatory caspases (caspase-1, 4, 5, or 11) to produce anamino-terminal domain (GSDMD-NT) and a carboxyl-terminal domain (GSDMD-CT). The GSDMD-NT drives cell membrane rupture, which leads to the pyroptotic death of the cells. The expression of porcine GSDMD (pGSDMD) has recently been determined, but the activation and regulation mechanism of pGSDMD and its ability to mediate pyroptosis are largely unknown. In the present study, the activation of porcine caspase-1 (pcaspase-1) and cleavage of pGSDMD occurred in the duodenum and jejunum of a piglet challenged with enterotoxigenic Escherichia coli were first determined. Then the capability of pcaspase-1 to cleave pGSDMD was determined in a cell-free system and in human embryonic kidney cells. The pGSDMD cleavage by pcaspase-1 occurred after the pGSDMD molecule’s 276Phenylalanine-Glutamine-Serine-Aspartic acid279 motif. The pGSDMD-NT generated from the pGSDMD cleavage by pcaspase-1 showed the ability to drive cell membrane rupture in eukaryotic cells. When expressed in E. coli competent cells, pGSDMD-NT showed bactericidal activity. These results suggest that pGSDMD is a substate of pcaspase-1 and an executioner of pyroptosis. Our work sheds light on pGSDMD’s activation mechanisms and functions.
Collapse
Affiliation(s)
- Yueyang Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Jiameng Song
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Meng Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Junwei Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Bo Ma
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| | - Wenlong Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, China
| |
Collapse
|
10
|
Shrestha S, Clark AC. Evolution of the folding landscape of effector caspases. J Biol Chem 2021; 297:101249. [PMID: 34592312 PMCID: PMC8628267 DOI: 10.1016/j.jbc.2021.101249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/07/2022] Open
Abstract
Caspases are a family of cysteinyl proteases that control programmed cell death and maintain homeostasis in multicellular organisms. The caspase family is an excellent model to study protein evolution because all caspases are produced as zymogens (procaspases [PCPs]) that must be activated to gain full activity; the protein structures are conserved through hundreds of millions of years of evolution; and some allosteric features arose with the early ancestor, whereas others are more recent evolutionary events. The apoptotic caspases evolved from a common ancestor (CA) into two distinct subfamilies: monomers (initiator caspases) or dimers (effector caspases). Differences in activation mechanisms of the two subfamilies, and their oligomeric forms, play a central role in the regulation of apoptosis. Here, we examine changes in the folding landscape by characterizing human effector caspases and their CA. The results show that the effector caspases unfold by a minimum three-state equilibrium model at pH 7.5, where the native dimer is in equilibrium with a partially folded monomeric (PCP-7, CA) or dimeric (PCP-6) intermediate. In comparison, the unfolding pathway of PCP-3 contains both oligomeric forms of the intermediate. Overall, the data show that the folding landscape was first established with the CA and was retained for >650 million years. Partially folded monomeric or dimeric intermediates in the ancestral ensemble provide mechanisms for evolutionary changes that affect stability of extant caspases. The conserved folding landscape allows for the fine-tuning of enzyme stability in a species-dependent manner while retaining the overall caspase–hemoglobinase fold.
Collapse
Affiliation(s)
- Suman Shrestha
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - A Clay Clark
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.
| |
Collapse
|
11
|
Soni IV, Hardy JA. Caspase-9 Activation of Procaspase-3 but Not Procaspase-6 Is Based on the Local Context of Cleavage Site Motifs and on Sequence. Biochemistry 2021; 60:2824-2835. [PMID: 34472839 DOI: 10.1021/acs.biochem.1c00459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Studying the interactions between a protease and its protein substrates at a molecular level is crucial for identifying the factors facilitating selection of particular proteolytic substrates and not others. These selection criteria include both the sequence and the local context of the substrate cleavage site where the active site of the protease initially binds and then performs proteolytic cleavage. Caspase-9, an initiator of the intrinsic apoptotic pathway, mediates activation of executioner procaspase-3 by cleavage of the intersubunit linker (ISL) at site 172IETD↓S. Although procaspase-6, another executioner, possesses two ISL cleavage sites (site 1, 176DVVD↓N; site 2, 190TEVD↓A), neither is directly cut by caspase-9. Thus, caspase-9 directly activates procaspase-3 but not procaspase-6. To elucidate this selectivity of caspase-9, we engineered constructs of procaspase-3 (e.g., swapping the ISL site, 172IETD↓S, with DVVDN and TEVDA) and procaspase-6 (e.g., swapping site 1, 176DVVD↓N, and site 2, 190TEVD↓A, with IETDS). Using the substrate digestion data of these constructs, we show here that the P4-P1' sequence of procaspase-6 ISL site 1 (DVVDN) can be accessed but not cleaved by caspase-9. We also found that caspase-9 can recognize the P4-P1' sequence of procaspase-6 ISL site 2 (TEVDA); however, the local context of this cleavage site is the critical factor that prevents proteolytic cleavage. Overall, our data have demonstrated that both the sequence and the local context of the ISL cleavage sites play a vital role in preventing the activation of procaspase-6 directly by caspase-9.
Collapse
Affiliation(s)
- Ishankumar V Soni
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States.,Models to Medicine Center, Institute of Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| |
Collapse
|
12
|
Makoni NJ, Nichols MR. The intricate biophysical puzzle of caspase-1 activation. Arch Biochem Biophys 2021; 699:108753. [PMID: 33453207 DOI: 10.1016/j.abb.2021.108753] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 12/13/2022]
Abstract
This review takes a closer look at the structural components of the molecules involved in the processes leading to caspase-1 activation. Interleukins 1β and 18 (IL-1β, IL-18) are well-known proinflammatory cytokines that are produced following cleavage of their respective precursor proteins by the cysteine protease caspase-1. Active caspase-1 is the final step of the NLRP3 inflammasome, a three-protein intracellular complex involved in inflammation and induction of pyroptosis (a proinflammatory cell-death process). NLRP3 activators facilitate assembly of the inflammasome complex and subsequent activation of caspase-1 by autoproteolysis. However, the definitive structural components of active caspase-1 are still unclear and new data add to the complexity of this process. This review outlines the historical and recent findings that provide supporting evidence for the structural aspects of caspase-1 autoproteolysis and activation.
Collapse
Affiliation(s)
- Nyasha J Makoni
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA
| | - Michael R Nichols
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
| |
Collapse
|
13
|
Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity. Biochem J 2020; 476:3475-3492. [PMID: 31675069 PMCID: PMC6874516 DOI: 10.1042/bcj20190625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/18/2022]
Abstract
Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
Collapse
|
14
|
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: 107] [Impact Index Per Article: 26.8] [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.
Collapse
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.
| |
Collapse
|
15
|
Wang K, Sun Q, Zhong X, Zeng M, Zeng H, Shi X, Li Z, Wang Y, Zhao Q, Shao F, Ding J. Structural Mechanism for GSDMD Targeting by Autoprocessed Caspases in Pyroptosis. Cell 2020; 180:941-955.e20. [PMID: 32109412 DOI: 10.1016/j.cell.2020.02.002] [Citation(s) in RCA: 366] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/16/2019] [Accepted: 01/31/2020] [Indexed: 01/05/2023]
Abstract
The pyroptosis execution protein GSDMD is cleaved by inflammasome-activated caspase-1 and LPS-activated caspase-11/4/5. The cleavage unmasks the pore-forming domain from GSDMD-C-terminal domain. How the caspases recognize GSDMD and its connection with caspase activation are unknown. Here, we show site-specific caspase-4/11 autoprocessing, generating a p10 product, is required and sufficient for cleaving GSDMD and inducing pyroptosis. The p10-form autoprocessed caspase-4/11 binds the GSDMD-C domain with a high affinity. Structural comparison of autoprocessed and unprocessed capase-11 identifies a β sheet induced by the autoprocessing. In caspase-4/11-GSDMD-C complex crystal structures, the β sheet organizes a hydrophobic GSDMD-binding interface that is only possible for p10-form caspase-4/11. The binding promotes dimerization-mediated caspase activation, rendering a cleavage independently of the cleavage-site tetrapeptide sequence. Crystal structure of caspase-1-GSDMD-C complex shows a similar GSDMD-recognition mode. Our study reveals an unprecedented substrate-targeting mechanism for caspases. The hydrophobic interface suggests an additional space for developing inhibitors specific for pyroptotic caspases.
Collapse
Affiliation(s)
- Kun Wang
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Qi Sun
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences 2019RU076, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Xiu Zhong
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Mengxue Zeng
- National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Huan Zeng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Xuyan Shi
- National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Zilin Li
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences 2019RU076, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Yupeng Wang
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences 2019RU076, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China
| | - Qiang Zhao
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, 510080 Guangzhou, China
| | - Feng Shao
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, National Institute of Biological Sciences, 102206 Beijing, China; Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences 2019RU076, 102206 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China.
| | - Jingjin Ding
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; National Institute of Biological Sciences, Beijing, 102206 Beijing, China.
| |
Collapse
|
16
|
Božič J, Bidovec K, Vizovišek M, Dolenc I, Stoka V. Menadione-induced apoptosis in U937 cells involves Bid cleavage and stefin B degradation. J Cell Biochem 2019; 120:10662-10669. [PMID: 30652348 DOI: 10.1002/jcb.28356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023]
Abstract
Earlier studies showed that the oxidant menadione (MD) induces apoptosis in certain cells and also has anticancer effects. Most of these studies emphasized the role of the mitochondria in this process. However, the engagement of other organelles is less known. Particularly, the role of lysosomes and their proteolytic system, which participates in apoptotic cell death, is still unclear. The aim of this study was to investigate the role of lysosomal cathepsins on molecular signaling in MD-induced apoptosis in U937 cells. MD treatment induced translocation of cysteine cathepsins B, C, and S, and aspartic cathepsin D. Once in the cytosol, some cathepsins cleaved the proapoptotic molecule, Bid, in a process that was completely prevented by E64d, a general inhibitor of cysteine cathepsins, and partially prevented by the pancaspase inhibitor, z-VAD-fmk. Upon loss of the mitochondrial membrane potential, apoptosome activation led to caspase-9 processing, activation of caspase-3-like caspases, and poly (ADP-ribose) polymerase cleavage. Notably, the endogenous protein inhibitor, stefin B, was degraded by cathepsin D and caspases. This process was prevented by z-VAD-fmk, and partially by pepstatin A-penetratin. These findings suggest that the cleaved Bid protein acts as an amplifier of apoptotic signaling through mitochondria, thus enhancing the activity of cysteine cathepsins following stefin B degradation.
Collapse
Affiliation(s)
- Janja Božič
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Katja Bidovec
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Iztok Dolenc
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Veronika Stoka
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| |
Collapse
|
17
|
Mokhtar-Ahmadabadi R, Madadi Z, Akbari-Birgani S, Grillon C, Hasani L, Hosseinkhani S, Zareian S. Developing a circularly permuted variant of Renilla luciferase as a bioluminescent sensor for measuring Caspase-9 activity in the cell-free and cell-based systems. Biochem Biophys Res Commun 2018; 506:1032-1039. [PMID: 30409426 DOI: 10.1016/j.bbrc.2018.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/03/2018] [Indexed: 11/29/2022]
Abstract
Biosensors and whole cell biosensors consisting of biological molecules and living cells can sense a special stimulus on a living system and convert it to a measurable signal. A major group of them are the bioluminescent sensors derived from luciferases. This type of biosensors has a broad application in molecular biology and imaging systems. In this project, a luciferase-based biosensor for detecting and measuring caspase-9 activity is designed and constructed using the circular permutation strategy. The spectroscopic method results reveal changes in the biosensor structure. Additionally, its activity is examined in a cell-free coupled assay system. Afterward, the biosensor is utilized for measuring the cellular caspase-9 activity upon apoptosis induction in a cancer cell line. In following the gene of biosensor is sub-cloned into a eukaryotic vector and transfected to HEK293T cell line and then its activity is measured upon apoptosis induction in the presence and absence of a caspase-9 inhibitor. The obtained results show that the designed biosensor detects the caspase-9 activity in the cell-free and cell-based systems.
Collapse
Affiliation(s)
- Roya Mokhtar-Ahmadabadi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Zahra Madadi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Shiva Akbari-Birgani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran; Research Center for Basic Sciences and Modern Technologies (RBST), Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran.
| | - Catherine Grillon
- Centre de Biophysique Moléculaire, UPR CNRS 4301, 45071, Orléans, France
| | - Leila Hasani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shekufeh Zareian
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, 45137-66731, Iran; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| |
Collapse
|
18
|
Kalabova D, Smidova A, Petrvalska O, Alblova M, Kosek D, Man P, Obsil T, Obsilova V. Human procaspase-2 phosphorylation at both S139 and S164 is required for 14-3-3 binding. Biochem Biophys Res Commun 2017; 493:940-945. [PMID: 28943433 DOI: 10.1016/j.bbrc.2017.09.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 09/20/2017] [Indexed: 11/29/2022]
Abstract
Procaspase-2 phosphorylation at several residues prevents its activation and blocks apoptosis. This process involves procaspase-2 phosphorylation at S164 and its binding to the scaffolding protein 14-3-3. However, bioinformatics analysis has suggested that a second phosphoserine-containing motif may also be required for 14-3-3 binding. In this study, we show that human procaspase-2 interaction with 14-3-3 is governed by phosphorylation at both S139 and S164. Using biochemical and biophysical approaches, we show that doubly phosphorylated procaspase-2 and 14-3-3 form an equimolar complex with a dissociation constant in the nanomolar range. Furthermore, our data indicate that other regions of procaspase-2, in addition to phosphorylation motifs, may be involved in the interaction with 14-3-3.
Collapse
Affiliation(s)
- Dana Kalabova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic; 2nd Faculty of Medicine, Charles University, V Uvalu 84, 15006 Prague, Czech Republic
| | - Aneta Smidova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Olivia Petrvalska
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Miroslava Alblova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Dalibor Kosek
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Petr Man
- BIOCEV-Institute of Microbiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Tomas Obsil
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic; Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 12843 Prague, Czech Republic
| | - Veronika Obsilova
- Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Prumyslova 595, 252 50 Vestec, Czech Republic.
| |
Collapse
|
19
|
Adriaenssens Y, Jiménez Fernández D, Vande Walle L, Elvas F, Joossens J, Lambeir A, Augustyns K, Lamkanfi M, Van der Veken P. Carboxylate isosteres for caspase inhibitors: the acylsulfonamide case revisited. Org Biomol Chem 2017; 15:7456-7473. [PMID: 28837200 DOI: 10.1039/c7ob01403a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As part of an ongoing effort to discover inhibitors of caspase-1 with an optimized selectivity and biopharmaceutical profile, acylsulfonamides were explored as carboxylate isosteres for caspase inhibitors. Acylsulfonamide analogues of the clinically investigated caspase-1 inhibitor VRT-043198 and of the pan-caspase inhibitor Z-VAD-CHO were synthesized. The isostere-containing analogues with an aldehyde warhead had inhibitory potencies comparable to the carboxylate references. In addition, the conformational and tautomeric characteristics of these molecules were determined using 1H- and 13C-based NMR. The propensity of acylsulfonamides with an aldehyde warhead to occur in a ring-closed conformation at physiological pH significantly increases the sensitivity to hydrolysis of the acylsulfonamide moiety, yielding the parent carboxylate containing inhibitors. These results indicate that the acylsulfonamide analogues of the aldehyde-based inhibitor VRT-043198 might have potential as a novel type of prodrug for the latter. Finally, inhibition of caspase 1 and 11 mediated inflammation in mouse macrophages was found to correlate with the potencies of the compounds in enzymatic assays.
Collapse
Affiliation(s)
- Y Adriaenssens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Smith CE, Soti S, Jones TA, Nakagawa A, Xue D, Yin H. Non-steroidal Anti-inflammatory Drugs Are Caspase Inhibitors. Cell Chem Biol 2017; 24:281-292. [PMID: 28238723 PMCID: PMC5357154 DOI: 10.1016/j.chembiol.2017.02.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/07/2017] [Accepted: 01/31/2017] [Indexed: 01/07/2023]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most commonly used drugs in the world. While the role of NSAIDs as cyclooxygenase (COX) inhibitors is well established, other targets may contribute to anti-inflammation. Here we report caspases as a new pharmacological target for NSAID family drugs such as ibuprofen, naproxen, and ketorolac at physiologic concentrations both in vitro and in vivo. We characterize caspase activity in both in vitro and in cell culture, and combine computational modeling and biophysical analysis to determine the mechanism of action. We observe that inhibition of caspase catalysis reduces cell death and the generation of pro-inflammatory cytokines. Further, NSAID inhibition of caspases is COX independent, representing a new anti-inflammatory mechanism. This finding expands upon existing NSAID anti-inflammatory behaviors, with implications for patient safety and next-generation drug design.
Collapse
Affiliation(s)
- Christina E Smith
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Subada Soti
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Torey A Jones
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Akihisa Nakagawa
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ding Xue
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Hang Yin
- Department of Chemistry & Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.
| |
Collapse
|
21
|
Hwang D, Kim SA, Yang EG, Song HK, Chung HS. A facile method to prepare large quantities of active caspase-3 overexpressed by auto-induction in the C41(DE3) strain. Protein Expr Purif 2016; 126:104-108. [DOI: 10.1016/j.pep.2016.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/17/2016] [Accepted: 06/13/2016] [Indexed: 10/21/2022]
|
22
|
Abstract
Caspases are proteases that are essential components of apoptotic cell death pathways. There are approximately one dozen apoptotic caspases found in organisms where cells die via apoptosis. These caspases are responsible for initiation or execution of apoptosis through the proteolytic cleavage of specific substrates. These substrates contain specific motifs that are recognized and cleaved by caspases that result in alterations of substrate function that promotes the apoptotic phenotype. Analysis of caspase involvement, much like any other protease, can be followed using peptides corresponding to cleavage motifs of these substrates, which can be used as substrates, inhibitors, or affinity-based probes.Different caspases have different substrates and therefore different motifs are recognized by each different caspase. However, these different caspases have a common amino acid recognition pattern containing an aspartic acid residue at the amino-side of the cleavage site. Therefore, caspase substrates have a certain overlap in the cleavage motif as this aspartic acid is found in almost every one. This means that certain peptide motifs are not exclusively cleaved by one single caspase. This lack of exclusive cleavage has brought the use of these motif-based probes into question and spurred the development of truly caspase-specific motifs. This chapter describes the use of peptide-based probes to measure caspase activity while highlighting the limitations of these reagents.
Collapse
Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, 432 Theobald Science Center, Northern Boulevard, Old Westbury, NY, 11568, USA.
| |
Collapse
|
23
|
Combined inhibition of caspase 3 and caspase 7 by two highly selective DARPins slows down cellular demise. Biochem J 2014; 461:279-90. [PMID: 24779913 DOI: 10.1042/bj20131456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Caspases play important roles during apoptosis, inflammation and proliferation. The high homology among family members makes selective targeting of individual caspases difficult, which is necessary to precisely define the role of these enzymes. We have selected caspase-7-specific binders from a library of DARPins (designed ankyrin repeat proteins). The DARPins D7.18 and D7.43 bind specifically to procaspase 7 and active caspase 7, but not to other members of the family. Binding of the DARPins does not affect the active enzyme, but interferes with its activation by other caspases. The crystal structure of the caspase 7-D7.18 complex elucidates the high selectivity and the mode of inhibition. Combining these caspase-7-specific DARPins with the previously reported caspase-3-inhibitory DARPin D3.4S76R reduces the activity of caspase 3 and 7 in double-transfected HeLa cells during apoptosis. In addition, these cells showed less susceptibility to TRAIL (tumour-necrosis-factor-related apoptosis-inducing ligand)-induced apoptosis in living cell experiments. D7.18 and D7.43 are therefore novel tools for in vitro studies on procaspase 7 activation as well as for clarifying the role of its activation in different cellular processes. If applied in combination with D3.4S76R, they represent an excellent instrument to increase our understanding of these enzymes during various cellular processes.
Collapse
|
24
|
McStay GP, Green DR. Preparation of cytosolic extracts and activation of caspases by cytochrome c. Cold Spring Harb Protoc 2014; 2014:778-82. [PMID: 24987139 DOI: 10.1101/pdb.prot080275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
It can be useful to explore the caspase activation process in an in vitro setting. In this protocol, cytosolic extracts prepared from cell culture are incubated with cytochrome c and adenosine triphosphate (dATP), leading to the oligomerization of apoptotic protease activating factor-1 (APAF-1) and the formation of the apoptosome. The apoptosome serves as an activation platform for caspase-9, which binds to the apoptosome through heterodimeric caspase recruitment domain (CARD) interactions and then dimerizes. This leads to cleavage of the executioner, caspase-3. These extracts contain highly active caspases that can be analyzed using a variety of biochemical assays.
Collapse
Affiliation(s)
- Gavin P McStay
- Department of Life Sciences, New York Institute of Technology, Old Westbury, New York 11568
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| |
Collapse
|
25
|
Abstract
The paracaspase MALT1 is a Cys-dependent, Arg-specific protease that plays an essential role in the activation and proliferation of lymphocytes during the immune response. Oncogenic activation of MALT1 is associated with the development of specific forms of B-cell lymphomas. Through specific cleavage of its substrates, MALT1 controls various aspects of lymphocyte activation, including the activation of transcriptional pathways, the stabilization of mRNAs, and an increase in cellular adhesion. In lymphocytes, the activity of MALT1 is tightly controlled by its inducible monoubiquitination, which promotes the dimerization of MALT1. Here, we describe both in vitro and in vivo assays that have been developed to assess MALT1 activity.
Collapse
Affiliation(s)
- Stephan Hailfinger
- Department of Biochemistry, University of Lausanne, Lausanne, Switzerland
| | | | | |
Collapse
|
26
|
Cabalzar K, Pelzer C, Wolf A, Lenz G, Iwaszkiewicz J, Zoete V, Hailfinger S, Thome M. Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface. PLoS One 2013; 8:e72051. [PMID: 23977204 PMCID: PMC3747146 DOI: 10.1371/journal.pone.0072051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/06/2013] [Indexed: 12/17/2022] Open
Abstract
The mucosa-associated lymphoid tissue protein-1 (MALT1, also known as paracaspase) is a protease whose activity is essential for the activation of lymphocytes and the growth of cells derived from human diffuse large B-cell lymphomas of the activated B-cell subtype (ABC DLBCL). Crystallographic approaches have shown that MALT1 can form dimers via its protease domain, but why dimerization is relevant for the biological activity of MALT1 remains largely unknown. Using a molecular modeling approach, we predicted Glu 549 (E549) to be localized within the MALT1 dimer interface and thus potentially relevant. Experimental mutation of this residue into alanine (E549A) led to a complete impairment of MALT1 proteolytic activity. This correlated with an impaired capacity of the mutant to form dimers of the protease domain in vitro, and a reduced capacity to promote NF-κB activation and transcription of the growth-promoting cytokine interleukin-2 in antigen receptor-stimulated lymphocytes. Moreover, this mutant could not rescue the growth of ABC DLBCL cell lines upon MALT1 silencing. Interestingly, the MALT1 mutant E549A was unable to undergo monoubiquitination, which we identified previously as a critical step in MALT1 activation. Collectively, these findings suggest a model in which E549 at the dimerization interface is required for the formation of the enzymatically active, monoubiquitinated form of MALT1.
Collapse
Affiliation(s)
- Katrin Cabalzar
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Christiane Pelzer
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Annette Wolf
- Department of Hematology, Oncology and Tumor Immunology, Molecular Cancer Research Center, Charité - Universitätsmedizin Berlin, Germany
| | - Georg Lenz
- Department of Hematology, Oncology and Tumor Immunology, Molecular Cancer Research Center, Charité - Universitätsmedizin Berlin, Germany
| | | | - Vincent Zoete
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephan Hailfinger
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- * E-mail:
| |
Collapse
|
27
|
Seeger MA, Zbinden R, Flütsch A, Gutte PGM, Engeler S, Roschitzki-Voser H, Grütter MG. Design, construction, and characterization of a second-generation DARP in library with reduced hydrophobicity. Protein Sci 2013; 22:1239-57. [PMID: 23868333 DOI: 10.1002/pro.2312] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 12/18/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) are well-established binding molecules based on a highly stable nonantibody scaffold. Building on 13 crystal structures of DARPin-target complexes and stability measurements of DARPin mutants, we have generated a new DARPin library containing an extended randomized surface. To counteract the enrichment of unspecific hydrophobic binders during selections against difficult targets containing hydrophobic surfaces such as membrane proteins, the frequency of apolar residues at diversified positions was drastically reduced and substituted by an increased number of tyrosines. Ribosome display selections against two human caspases and membrane transporter AcrB yielded highly enriched pools of unique and strong DARPin binders which were mainly monomeric. We noted a prominent enrichment of tryptophan residues during binder selections. A crystal structure of a representative of this library in complex with caspase-7 visualizes the key roles of both tryptophans and tyrosines in providing target contacts. These aromatic and polar side chains thus substitute the apolar residues valine, leucine, isoleucine, methionine, and phenylalanine of the original DARPins. Our work describes biophysical and structural analyses required to extend existing binder scaffolds and simplifies an existing protocol for the assembly of highly diverse synthetic binder libraries.
Collapse
Affiliation(s)
- Markus A Seeger
- Department of Biochemistry, University of Zurich, 8057, Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
28
|
Hata S, Kitamura F, Sorimachi H. Efficient expression and purification of recombinant human μ-calpain using an Escherichia coli expression system. Genes Cells 2013; 18:753-63. [PMID: 23786391 DOI: 10.1111/gtc.12071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022]
Abstract
Calpains comprise a superfamily of Ca(2+) -regulated cysteine proteases that are indispensable for the regulation of various cellular functions. Of these, the mammalian μ- and m-calpains are the best characterized isoforms. They are ubiquitously expressed and form heterodimers consisting of a distinct 80-kDa catalytic subunit (CAPN1 for μ-calpain and CAPN2 for m-calpain) and a common 30-kDa regulatory subunit (CAPNS1). To date, various expression systems have been developed for producing recombinant calpains for structural and functional studies; however, no low-cost, simple and efficient bacterial expression system for μ-calpain has been available, because the protein forms aggregates. Here, we established an efficient method for producing active recombinant human μ-calpain using an Escherichia coli expression system. This was achieved by co-expressing CAPN1 and CAPNS1 lacking the N-terminal Gly-rich domain (CAPNS1ΔGR) in the SoluBL21 strain. From 1 L of E. coli culture, over 2 and 6 mg, respectively, of μ-calpain and its active-site mutant μ-calpain:C115S (CAPN1:C115S+CAPNS1ΔGR) were purified by two successive column chromatographies. Compared to the native enzyme, the purified μ-calpain showed almost identical properties, demonstrating its suitability for use in structural and functional studies. This is the first report of the bacterial expression and the simple and efficient purification of active recombinant μ-calpain.
Collapse
Affiliation(s)
- Shoji Hata
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kami-kitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | | | | |
Collapse
|
29
|
Schroeder T, Barandun J, Flütsch A, Briand C, Mittl PRE, Grütter MG. Specific inhibition of caspase-3 by a competitive DARPin: molecular mimicry between native and designed inhibitors. Structure 2013; 21:277-89. [PMID: 23333429 DOI: 10.1016/j.str.2012.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/03/2012] [Accepted: 12/14/2012] [Indexed: 11/28/2022]
Abstract
Dysregulation of apoptosis is associated with several human diseases. The main apoptotic mediators are caspases, which propagate death signals to downstream targets. Executioner caspase-3 is responsible for the majority of cleavage events and its therapeutic potential is of high interest with to date several available active site peptide inhibitors. These molecules inhibit caspase-3, but also homologous caspases. Here, we describe caspase-3 specific inhibitors D3.4 and D3.8, which have been selected from a library of designed ankyrin repeat proteins (DARPins). The crystal structures of D3.4 and mutants thereof show how high specificity and inhibition is achieved. They also show similarities in the binding mode with that of the natural caspase inhibitor XIAP (X-linked inhibitor of apoptosis). The kinetic data reveal a competitive inhibition mechanism. D3.4 is specific for caspase-3 and does not bind the highly homologous caspase-7. D3.4 therefore is an excellent tool to define the precise role of caspase-3 in the various apoptotic pathways.
Collapse
Affiliation(s)
- Thilo Schroeder
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | | | | | | | | | | |
Collapse
|