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Ruiz-Blázquez P, Fernández-Fernández M, Pistorio V, Martinez-Sanchez C, Costanzo M, Iruzubieta P, Zhuravleva E, Cacho-Pujol J, Ariño S, Del Castillo-Cruz A, Núñez S, Andersen JB, Ruoppolo M, Crespo J, García-Ruiz C, Pavone LM, Reinheckel T, Sancho-Bru P, Coll M, Fernández-Checa JC, Moles A. Cathepsin D is essential for the degradomic shift of macrophages required to resolve liver fibrosis. Mol Metab 2024; 87:101989. [PMID: 39019115 PMCID: PMC11327474 DOI: 10.1016/j.molmet.2024.101989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Fibrosis contributes to 45% of deaths in industrialized nations and is characterized by an abnormal accumulation of extracellular matrix (ECM). There are no specific anti-fibrotic treatments for liver fibrosis, and previous unsuccessful attempts at drug development have focused on preventing ECM deposition. Because liver fibrosis is largely acknowledged to be reversible, regulating fibrosis resolution could offer novel therapeutical options. However, little is known about the mechanisms controlling ECM remodeling during resolution. Changes in proteolytic activity are essential for ECM homeostasis and macrophages are an important source of proteases. Herein, in this study we evaluate the role of macrophage-derived cathepsin D (CtsD) during liver fibrosis. METHODS CtsD expression and associated pathways were characterized in single-cell RNA sequencing and transcriptomic datasets in human cirrhosis. Liver fibrosis progression, reversion and functional characterization were assessed in novel myeloid-CtsD and hepatocyte-CtsD knock-out mice. RESULTS Analysis of single-cell RNA sequencing datasets demonstrated CtsD was expressed in macrophages and hepatocytes in human cirrhosis. Liver fibrosis progression, reversion and functional characterization were assessed in novel myeloid-CtsD (CtsDΔMyel) and hepatocyte-CtsD knock-out mice. CtsD deletion in macrophages, but not in hepatocytes, resulted in enhanced liver fibrosis. Both inflammatory and matrisome proteomic signatures were enriched in fibrotic CtsDΔMyel livers. Besides, CtsDΔMyel liver macrophages displayed functional, phenotypical and secretomic changes, which resulted in a degradomic phenotypical shift, responsible for the defective proteolytic processing of collagen I in vitro and impaired collagen remodeling during fibrosis resolution in vivo. Finally, CtsD-expressing mononuclear phagocytes of cirrhotic human livers were enriched in lysosomal and ECM degradative signaling pathways. CONCLUSIONS Our work describes for the first-time CtsD-driven lysosomal activity as a central hub for restorative macrophage function during fibrosis resolution and opens new avenues to explore their degradome landscape to inform drug development.
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Affiliation(s)
- Paloma Ruiz-Blázquez
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; CiberEHD, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - María Fernández-Fernández
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; CiberEHD, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - Valeria Pistorio
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | | | - Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Naples, Italy
| | - Paula Iruzubieta
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Research Institute Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Ekaterina Zhuravleva
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; LEO Foundation Skin Immunology Research Center (SIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Júlia Cacho-Pujol
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - Silvia Ariño
- CiberEHD, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | | | | | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Margherita Ruoppolo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy; CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Naples, Italy
| | - Javier Crespo
- Department of Gastroenterology and Hepatology, Marqués de Valdecilla University Hospital, Research Institute Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Carmen García-Ruiz
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; CiberEHD, Spain; IDIBAPS, Barcelona, Spain; USC Research Center for ALPD, Los Angeles, United States; Associated Unit IIBB-IMIM, Barcelona, Spain
| | - Luigi Michele Pavone
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, Albert-Ludwigs-University, Freiburg, Germany; German Cancer Consortium (DKTK), DKFZ Partner Site Freiburg, Germany; Center for Biological Signaling Studies BIOSS, University of Freiburg, Germany
| | - Pau Sancho-Bru
- CiberEHD, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - Mar Coll
- CiberEHD, Spain; University of Barcelona, Barcelona, Spain; IDIBAPS, Barcelona, Spain; Medicine Department, Faculty of Medicine, University of Barcelona, Spain
| | - José C Fernández-Checa
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; CiberEHD, Spain; IDIBAPS, Barcelona, Spain; USC Research Center for ALPD, Los Angeles, United States; Associated Unit IIBB-IMIM, Barcelona, Spain
| | - Anna Moles
- Institute of Biomedical Research of Barcelona, Spanish National Research Council, Barcelona, Spain; CiberEHD, Spain; IDIBAPS, Barcelona, Spain; Associated Unit IIBB-IMIM, Barcelona, Spain.
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Cao WJ, Liu R, Zhao WX, Li J, Wang Y, Yuan XJ, Wang HL, Zhang YZ, Chen XL, Zhang YQ. Potential of Marine Bacterial Metalloprotease A69 in the Preparation of Peanut Peptides with Angiotensin-Converting Enzyme (ACE)-Inhibitory and Antioxidant Properties. Mar Drugs 2024; 22:305. [PMID: 39057414 PMCID: PMC11277839 DOI: 10.3390/md22070305] [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: 06/09/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Marine bacterial proteases have rarely been used to produce bioactive peptides, although many have been reported. This study aims to evaluate the potential of the marine bacterial metalloprotease A69 from recombinant Bacillus subtilis in the preparation of peanut peptides (PPs) with antioxidant activity and angiotensin-converting enzyme (ACE)-inhibitory activity. Based on the optimization of the hydrolysis parameters of protease A69, a process for PPs preparation was set up in which the peanut protein was hydrolyzed by A69 at 3000 U g-1 and 60 °C, pH 7.0 for 4 h. The prepared PPs exhibited a high content of peptides with molecular weights lower than 1000 Da (>80%) and 3000 Da (>95%) and contained 17 kinds of amino acids. Moreover, the PPs displayed elevated scavenging of hydroxyl radical and 1,1-diphenyl-2-picryl-hydrazyl radical, with IC50 values of 1.50 mg mL-1 and 1.66 mg mL-1, respectively, indicating the good antioxidant activity of the PPs. The PPs also showed remarkable ACE-inhibitory activity, with an IC50 value of 0.71 mg mL-1. By liquid chromatography mass spectrometry analysis, the sequences of 19 ACE inhibitory peptides and 15 antioxidant peptides were identified from the PPs. These results indicate that the prepared PPs have a good nutritional value, as well as good antioxidant and antihypertensive effects, and that the marine bacterial metalloprotease A69 has promising potential in relation to the preparation of bioactive peptides from peanut protein.
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Affiliation(s)
- Wen-Jie Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Rui Liu
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Wen-Xiao Zhao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Jian Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Yan Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Xiao-Jie Yuan
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Hui-Lin Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Joint Research Center for Marine Microbial Science and Technology of Shandong University and Ocean University of China, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
- Joint Research Center for Marine Microbial Science and Technology of Shandong University and Ocean University of China, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yu-Qiang Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao 266237, China; (W.-J.C.); (R.L.); (W.-X.Z.); (J.L.); (Y.W.); (X.-J.Y.); (H.-L.W.); (Y.-Z.Z.)
- Joint Research Center for Marine Microbial Science and Technology of Shandong University and Ocean University of China, Qingdao 266237, China
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Jamal GA, Jahangirian E, Hamblin MR, Mirzaei H, Tarrahimofrad H, Alikowsarzadeh N. Proteases, a powerful biochemical tool in the service of medicine, clinical and pharmaceutical. Prep Biochem Biotechnol 2024:1-25. [PMID: 38909284 DOI: 10.1080/10826068.2024.2364234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Proteases, enzymes that hydrolyze peptide bonds, have various applications in medicine, clinical applications, and pharmaceutical development. They are used in cancer treatment, wound debridement, contact lens cleaning, prion degradation, biofilm removal, and fibrinolytic agents. Proteases are also crucial in cardiovascular disease treatment, emphasizing the need for safe, affordable, and effective fibrinolytic drugs. Proteolytic enzymes and protease biosensors are increasingly used in diagnostic and therapeutic applications. Advanced technologies, such as nanomaterials-based sensors, are being developed to enhance the sensitivity, specificity, and versatility of protease biosensors. These biosensors are becoming effective tools for disease detection due to their precision and rapidity. They can detect extracellular and intracellular proteases, as well as fluorescence-based methods for real-time and label-free detection of virus-related proteases. The active utilization of proteolytic enzymatic biosensors is expected to expand significantly in biomedical research, in-vitro model systems, and drug development. We focused on journal articles and books published in English between 1982 and 2024 for this study.
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Affiliation(s)
- Ghadir A Jamal
- Faculty of Allied Health Sciences, Kuwait University, Kuwait City, Kuwait
| | - Ehsan Jahangirian
- Department of Molecular, Zist Tashkhis Farda Company (tBioDx), Tehran, Iran
| | - Michael R Hamblin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Health Science, Laser Research Center, University of Johannesburg, Doornfontein, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Neda Alikowsarzadeh
- Molecular and Life Science Department, Han University of Applied Science, Arnhem, Nederland
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4
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Gray ME, Zielinski KM, Xu F, Elder KK, McKay SJ, Ojo VT, Benjamin SR, Yaseen AA, Brooks TA, Tumey LN. A comparison of the activity, lysosomal stability, and efficacy of legumain-cleavable and cathepsin cleavable ADC linkers. Xenobiotica 2024:1-13. [PMID: 38738708 DOI: 10.1080/00498254.2024.2352051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/02/2024] [Indexed: 05/14/2024]
Abstract
1. Over the past two decades antibody-drug conjugates (ADCs) have emerged as a highly effective drug delivery technology. ADCs utilize a monoclonal antibody, a chemical linker, and a therapeutic payload to selectively deliver highly potent pharmaceutical agents to specific cell types.2. Challenges such as premature linker cleavage and clearance due to linker hydrophobicity have adversely impacted the stability and safety of ADCs. While there are various solutions to these challenges, our team has focused on replacement of hydrophobic ValCit linkers (cleaved by CatB) with Asn-containing linkers that are cleaved by lysosomal legumain.3. Legumain is abundantly present in lysosomes and is known to play a role in tumor microenvironment dynamics. Herein, we directly compare the lysosomal cleavage, cytotoxicity, plasma stability, and efficacy of a traditional cathepsin cleavable ADC to a matched Asn-containing legumain-cleavable ADC.4. We demonstrate that Asn-containing linker sequences are specifically cleaved by lysosomal legumain and that Asn-linked MMAE ADCs are broadly active against a variety of tumors, even those with low legumain expression. Finally, we show that AsnAsn-linked ADCs exhibit comparable or improved efficacy to traditional ValCit-linked ADCs. Our study paves the way for replacement of the traditional ValCit linker technology with more hydrophilic Asn-containing peptide linker sequences.
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Affiliation(s)
- Meghan E Gray
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Karina M Zielinski
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Fanny Xu
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Kayla K Elder
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Steven J McKay
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Victor T Ojo
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Samantha R Benjamin
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Aiman A Yaseen
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - Tracy A Brooks
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
| | - L Nathan Tumey
- Binghamton University, School of Pharmacy and Pharmaceutical Sciences, PO Box 6000, Binghamton NY 13902-6000, USA
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5
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Nemoto TK, Nishimata H, Shirakura K, Ohara-Nemoto Y. Potential elevation of exopeptidase activity of Glu-specific endopeptidase I/GluV8 mediated by hydrophobic P1'-position amino acid residue. Biochimie 2024; 220:99-106. [PMID: 38159715 DOI: 10.1016/j.biochi.2023.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/20/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
We recently reported that the activities of dipeptidyl-peptidase (DPP)7 and DPP11, S46-family exopeptidases were significantly elevated by the presence of prime-side amino acid residues of substrates caused by an increase in kcat [Ohara-Nemoto Y. et al., J Biol Chem 298(3):101585. doi: 10.1016/j.jbc.2022]. In the present study, the effects of prime-side residues on Glu-specific endopeptidase I/GluV8 from Staphylococcus aureus were investigated using a two-step cleavage method with tetrapeptidyl-methycoumaryl-7-amide (MCA) carrying P2- to P2'-position residues coupled with DPP11 as the second enzyme. GluV8 showed maximal activity toward benzyloxycarbonyl (Z)-LLE-MCA, while the effects of hydrolysis of substrates one residue shorter, such as acetyl (Ac)-Val-Glu- and Leu-Glu-MCA, were negligible. Nevertheless, activity towards Ac-VE-|-ID-MCA, a substrate carrying P1' and P2' residues, emerged and reached a level 44 % of that for Z-LLE-MCA. Among 11 Ac-HAXD-MCA (X is a varied amino acid), the highest level of activity enhancement was achieved with P1'-Leu and Ile, followed by Phe, Val, Ser, Tyr, and Ala, while Gly and Lys showed scant effects. This activation order was in parallel with the hydrophobicity indexes of these amino acids. The prime-side residues increased kcat/KM primarily through a maximum 500-fold elevation of kcat as well as S46-family exopeptidases. The MEROPS substrate database also indicates a close relationship between activity and hydrophobicity of the P1' residues in 93 N-terminal-truncated substrates, though no correlation was observed among all 4328 GluV8 entities examined. Taken together, these results are the first to demonstrate N-terminal exopeptidase activity of GluV8, considered to be prompted by hydrophobic P1' amino acid residues.
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Affiliation(s)
- Takayuki K Nemoto
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan; Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, 1-1-1 Idai-dori, Yahaba-cho, Iwate, 028-3694, Japan.
| | - Haruka Nishimata
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan.
| | - Kana Shirakura
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan.
| | - Yuko Ohara-Nemoto
- Department of Pediatric Dentistry, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki, 852-8588, Japan; Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University, 1-1-1 Idai-dori, Yahaba-cho, Iwate, 028-3694, Japan.
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6
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Grozdanić M, Sobotič B, Biasizzo M, Sever T, Vidmar R, Vizovišek M, Turk B, Fonović M. Cathepsin L-mediated EGFR cleavage affects intracellular signalling pathways in cancer. Biol Chem 2024; 405:283-296. [PMID: 37889671 DOI: 10.1515/hsz-2023-0213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
Proteolytic activity in the tumour microenvironment is an important factor in cancer development since it can also affect intracellular signalling pathways via positive feedback loops that result in either increased tumour growth or resistance to anticancer mechanisms. In this study, we demonstrated extracellular cathepsin L-mediated cleavage of epidermal growth factor receptor (EGFR) and identified the cleavage site in the extracellular domain after R224. To further evaluate the relevance of this cleavage, we cloned and expressed a truncated version of EGFR, starting at G225, in HeLa cells. We confirmed the constitutive activation of the truncated protein in the absence of ligand binding and determined possible changes in intracellular signalling. Furthermore, we determined the effect of truncated EGFR protein expression on HeLa cell viability and response to the EGFR inhibitors, tyrosine kinase inhibitor (TKI) erlotinib and monoclonal antibody (mAb) cetuximab. Our data reveal the nuclear localization and phosphorylation of EGFR and signal trancducer and activator of transcription 3 (STAT3) in cells that express the truncated EGFR protein and suggest that these phenomena cause resistance to EGFR inhibitors.
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Affiliation(s)
- Marija Grozdanić
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Barbara Sobotič
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Monika Biasizzo
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Tilen Sever
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Robert Vidmar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Matej Vizovišek
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
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Xu S, Xu X, Wang Z, Wu R. A Systematic Investigation of Proteoforms with N-Terminal Glycine and Their Dynamics Reveals Its Impacts on Protein Stability. Angew Chem Int Ed Engl 2024; 63:e202315286. [PMID: 38117010 PMCID: PMC10981938 DOI: 10.1002/anie.202315286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
The N-termini of proteins can regulate their degradation, and the same protein with different N-termini may have distinct dynamics. Recently, it was found that N-terminal glycine can serve as a degron recognized by two E3 ligases, but N-terminal glycine was also reported to stabilize proteins. Here we developed a chemoenzymatic method for selective enrichment of proteoforms with N-terminal glycine and integrated dual protease cleavage to further improve the enrichment specificity. Over 2000 unique peptides with protein N-terminal glycine were analyzed from >1000 proteins, and most of them are previously unknown, indicating the effectiveness of the current method to capture low-abundance proteoforms with N-terminal glycine. The degradation rates of proteoforms with N-terminal glycine were quantified along with those of proteins from the whole proteome. Bioinformatic analyses reveal that proteoforms with N-terminal glycine with the fastest and slowest degradation rates have different functions and localizations. Membrane proteins with N-terminal glycine and proteins with N-terminal glycine from the N-terminal methionine excision degrade more rapidly. Furthermore, the secondary structures, adjacent amino acid residues, and protease specificities for N-terminal glycine are also vital for protein degradation. The results advance our understanding of the effects of N-terminal glycine on protein properties and functions.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Ziegler AR, Dufour A, Scott NE, Edgington-Mitchell LE. Ion Mobility-Based Enrichment-Free N-Terminomics Analysis Reveals Novel Legumain Substrates in Murine Spleen. Mol Cell Proteomics 2024; 23:100714. [PMID: 38199506 PMCID: PMC10862022 DOI: 10.1016/j.mcpro.2024.100714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
Aberrant levels of the asparaginyl endopeptidase legumain have been linked to inflammation, neurodegeneration, and cancer, yet our understanding of this protease is incomplete. Systematic attempts to identify legumain substrates have been previously confined to in vitro studies, which fail to mirror physiological conditions and obscure biologically relevant cleavage events. Using high-field asymmetric waveform ion mobility spectrometry (FAIMS), we developed a streamlined approach for proteome and N-terminome analyses without the need for N-termini enrichment. Compared to unfractionated proteomic analysis, we demonstrate FAIMS fractionation improves N-termini identification by >2.5 fold, resulting in the identification of >2882 unique N-termini from limited sample amounts. In murine spleens, this approach identifies 6366 proteins and 2528 unique N-termini, with 235 cleavage events enriched in WT compared to legumain-deficient spleens. Among these, 119 neo-N-termini arose from asparaginyl endopeptidase activities, representing novel putative physiological legumain substrates. The direct cleavage of selected substrates by legumain was confirmed using in vitro assays, providing support for the existence of physiologically relevant extra-lysosomal legumain activity. Combined, these data shed critical light on the functions of legumain and demonstrate the utility of FAIMS as an accessible method to improve depth and quality of N-terminomics studies.
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Affiliation(s)
- Alexander R Ziegler
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, Alberta, Canada
| | - Nichollas E Scott
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Parkville, Victoria, Australia.
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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9
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Kollet O, Das A, Karamanos N, Auf dem Keller U, Sagi I. Redefining metalloproteases specificity through network proteolysis. Trends Mol Med 2024; 30:147-163. [PMID: 38036391 PMCID: PMC11004056 DOI: 10.1016/j.molmed.2023.11.001] [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: 09/09/2023] [Revised: 10/18/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Proteolytic processes on cell surfaces and extracellular matrix (ECM) sustain cell behavior and tissue integrity in health and disease. Matrix metalloproteases (MMPs) and a disintegrin and metalloproteases (ADAMs) remodel cell microenvironments through irreversible proteolysis of ECM proteins and cell surface bioactive molecules. Pan-MMP inhibitors in inflammation and cancer clinical trials have encountered challenges due to promiscuous activities of MMPs. Systems biology advances revealed that MMPs initiate multifactorial proteolytic cascades, creating new substrates, activating or suppressing other MMPs, and generating signaling molecules. This review highlights the intricate network that underscores the role of MMPs beyond individual substrate-enzyme activities. Gaining insight into MMP function and tissue specificity is crucial for developing effective drug discovery strategies and novel therapeutics. This requires considering the dynamic cellular processes and consequences of network proteolysis.
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Affiliation(s)
- Orit Kollet
- The Weizmann Institute of Science, Department of Immunology and Regenerative Biology, Rehovot, Israel
| | - Alakesh Das
- The Weizmann Institute of Science, Department of Immunology and Regenerative Biology, Rehovot, Israel
| | - Nikos Karamanos
- University of Patras, Biochemistry, Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, Patras, Greece
| | - Ulrich Auf dem Keller
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Lyngby, Denmark
| | - Irit Sagi
- The Weizmann Institute of Science, Department of Immunology and Regenerative Biology, Rehovot, Israel.
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10
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Li Q, Lenertz M, Armstrong Z, MacRae A, Feng L, Ugrinov A, Yang Z. A Protocol to Depict the Proteolytic Processes Using a Combination of Metal-Organic Materials (MOMs), Electron Paramagnetic Resonance (EPR), and Mass Spectrometry (MS). Bio Protoc 2024; 14:e4909. [PMID: 38213322 PMCID: PMC10777052 DOI: 10.21769/bioprotoc.4909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Proteolysis is a critical biochemical process yet a challenging field to study experimentally due to the self-degradation of a protease and the complex, dynamic degradation steps of a substrate. Mass spectrometry (MS) is the traditional way for proteolytic studies, yet it is challenging when time-resolved, step-by-step details of the degradation process are needed. We recently found a way to resolve the cleavage site, preference/selectivity of cleavage regions, and proteolytic kinetics by combining site-directed spin labeling (SDSL) of protein substrate, time-resolved two-dimensional (2D) electron paramagnetic resonance (EPR) spectroscopy, protease immobilization via metal-organic materials (MOMs), and MS. The method has been demonstrated on a model substrate and protease, yet there is a lack of details on the practical operations to carry out our strategy. Thus, this protocol summarizes the key steps and considerations when carrying out the EPR/MS study on proteolytic processes, which can be generalized to study other protein/polypeptide substrates in proteolysis. Details for the experimental operation and cautions of each step are reported with figures illustrating the concepts. This protocol provides an effective approach to understanding the proteolytic process with the advantages of offering time-resolved, residue-level resolution of structural basis underlying the process. Such information is important for revealing the cleavage site and proteolytic mechanisms of unknown proteases. The advantage of EPR, probing the target substrate regardless of the complexities caused by the proteases and their self-degradation, offers a practically effective, rapid, and easy-to-operate approach to studying proteolysis. Key features • Combining protease immobilization, EPR, spin labeling, and MS experimental methods allows for the analysis of proteolysis process in real time. • Reveals cleavage site, kinetics of product generation, and preference of cleavage regions via time-resolved SDSL-EPR. • MS confirms EPR findings and helps depict the sequences and populations of the cleaved segments in real time. • The demonstrated method can be generalized to other proteins or polypeptide substrates upon proteolysis by other proteases.
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Affiliation(s)
- Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Mary Lenertz
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
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11
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Tušar L, Loboda J, Impens F, Sosnowski P, Van Quickelberghe E, Vidmar R, Demol H, Sedeyn K, Saelens X, Vizovišek M, Mihelič M, Fonović M, Horvat J, Kosec G, Turk B, Gevaert K, Turk D. Proteomic data and structure analysis combined reveal interplay of structural rigidity and flexibility on selectivity of cysteine cathepsins. Commun Biol 2023; 6:450. [PMID: 37095140 PMCID: PMC10124925 DOI: 10.1038/s42003-023-04772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/28/2023] [Indexed: 04/26/2023] Open
Abstract
Addressing the elusive specificity of cysteine cathepsins, which in contrast to caspases and trypsin-like proteases lack strict specificity determining P1 pocket, calls for innovative approaches. Proteomic analysis of cell lysates with human cathepsins K, V, B, L, S, and F identified 30,000 cleavage sites, which we analyzed by software platform SAPS-ESI (Statistical Approach to Peptidyl Substrate-Enzyme Specific Interactions). SAPS-ESI is used to generate clusters and training sets for support vector machine learning. Cleavage site predictions on the SARS-CoV-2 S protein, confirmed experimentally, expose the most probable first cut under physiological conditions and suggested furin-like behavior of cathepsins. Crystal structure analysis of representative peptides in complex with cathepsin V reveals rigid and flexible sites consistent with analysis of proteomics data by SAPS-ESI that correspond to positions with heterogeneous and homogeneous distribution of residues. Thereby support for design of selective cleavable linkers of drug conjugates and drug discovery studies is provided.
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Affiliation(s)
- Livija Tušar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Jure Loboda
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- The Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Piotr Sosnowski
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Emmy Van Quickelberghe
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Robert Vidmar
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Hans Demol
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology and, Department for Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology and, Department for Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
| | - Matej Vizovišek
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Marko Mihelič
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Marko Fonović
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Jaka Horvat
- Acies Bio d.o.o., Tehnološki park 21, 1000, Ljubljana, Slovenia
| | - Gregor Kosec
- Acies Bio d.o.o., Tehnološki park 21, 1000, Ljubljana, Slovenia
| | - Boris Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, SI-1000, Ljubljana, Slovenia
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology and UGent Department of Biomolecular Medicine, Technologiepark-Zwijnaarde 75, 9052, Ghent, Belgium.
| | - Dušan Turk
- Jožef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova cesta 39, 1000, Ljubljana, Slovenia.
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000, Ljubljana, Slovenia.
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12
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Wang T, Zhou Y, Zhou Z, Zhang P, Yan R, Sun L, Ma W, Zhang T, Shen S, Liu H, Lu H, Ye L, Feng J, Chen Z, Zhong X, Wu G, Cai Y, Jia W, Gao P, Zhang H. Secreted protease PRSS35 suppresses hepatocellular carcinoma by disabling CXCL2-mediated neutrophil extracellular traps. Nat Commun 2023; 14:1513. [PMID: 36934105 PMCID: PMC10024721 DOI: 10.1038/s41467-023-37227-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 03/08/2023] [Indexed: 03/19/2023] Open
Abstract
Hepatocytes function largely through the secretion of proteins that regulate cell proliferation, metabolism, and intercellular communications. During the progression of hepatocellular carcinoma (HCC), the hepatocyte secretome changes dynamically as both a consequence and a causative factor in tumorigenesis, although the full scope of secreted protein function in this process remains unclear. Here, we show that the secreted pseudo serine protease PRSS35 functions as a tumor suppressor in HCC. Mechanistically, we demonstrate that active PRSS35 is processed via cleavage by proprotein convertases. Active PRSS35 then suppresses protein levels of CXCL2 through targeted cleavage of tandem lysine (KK) recognition motif. Consequently, CXCL2 degradation attenuates neutrophil recruitment to tumors and formation of neutrophil extracellular traps, ultimately suppressing HCC progression. These findings expand our understanding of the hepatocyte secretome's role in cancer development while providing a basis for the clinical translation of PRRS35 as a therapeutic target or diagnostic biomarker.
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Affiliation(s)
- Ting Wang
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yingli Zhou
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Zilong Zhou
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Pinggen Zhang
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Ronghui Yan
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Linchong Sun
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenhao Ma
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Tong Zhang
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shengqi Shen
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haiying Liu
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Hui Lu
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Ling Ye
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Junru Feng
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhaolin Chen
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiuying Zhong
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Gao Wu
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yongping Cai
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, China
| | - Weidong Jia
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Ping Gao
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Huafeng Zhang
- Anhui Key Laboratory of Hepatopancreatobiliary Surgery, Department of General Surgery, Anhui Provincial Hospital, the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
- Anhui Province Key Laboratory of Biomedical Aging Research, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China.
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13
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Sun B, Liu Z, Liu J, Zhao S, Wang L, Wang F. The utility of proteases in proteomics, from sequence profiling to structure and function analysis. Proteomics 2023; 23:e2200132. [PMID: 36382392 DOI: 10.1002/pmic.202200132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
In mass spectrometry (MS)-based bottom-up proteomics, protease digestion plays an essential role in profiling both proteome sequences and post-translational modifications (PTMs). Trypsin is the gold standard in digesting intact proteins into small-size peptides, which are more suitable for high-performance liquid chromatography (HPLC) separation and tandem MS (MS/MS) characterization. However, protein sequences lacking Lys and Arg cannot be cleaved by trypsin and may be missed in conventional proteomic analysis. Proteases with cleavage sites complementary to trypsin are widely applied in proteomic analysis to greatly improve the coverage of proteome sequences and PTM sites. In this review, we survey the common and newly emerging proteases used in proteomics analysis mainly in the last 5 years, focusing on their unique cleavage features and specific proteomics applications such as missing protein characterization, new PTM discovery, and de novo sequencing. In addition, we summarize the applications of proteases in structural proteomics and protein function analysis in recent years. Finally, we discuss the future development directions of new proteases and applications in proteomics.
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Affiliation(s)
- Binwen Sun
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
| | - Jin Liu
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Shan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
| | - Liming Wang
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Engineering Technology Research Center for Translational Medicine, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, Second Affiliated Hospital, Dalian Medical University, 467 Zhongshan Road, Dalian, 116027, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 463 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
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14
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Janiszewski T, Kołt S, Ciastoń I, Vizovisek M, Poręba M, Turk B, Drąg M, Kozieł J, Kasperkiewicz P. Investigation of osteoclast cathepsin K activity in osteoclastogenesis and bone loss using a set of chemical reagents. Cell Chem Biol 2023; 30:159-174.e8. [PMID: 36696904 DOI: 10.1016/j.chembiol.2023.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/28/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023]
Abstract
Cathepsin K (CatK) is a lysosomal cysteine protease whose highest expression is found in osteoclasts, which are the cells responsible for bone resorption. Investigations of the functions and physiological relevance of CatK have often relied on antibody-related techniques, which makes studying its activity patterns a challenging task. Hence, we developed a set of chemical tools for the investigation of CatK activity. We show that our probe is a valuable tool for monitoring the proteolytic activation of CatK during osteoclast formation. Moreover, we demonstrate that our inhibitor of CatK impedes osteoclastogenesis and bone resorption and that CatK is stored in its active form in osteoclasts within their lysosomal compartment and mainly in the ruffled borders of osteoclasts. Given that our probe recognizes active CatK within living cells without exhibiting any observed cytotoxicity in the several models tested, we expect that it would be well suited to theranostic applications in CatK-related diseases.
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Affiliation(s)
- Tomasz Janiszewski
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Sonia Kołt
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Izabela Ciastoń
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Matej Vizovisek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Ljubljana, Slovenia
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Kozieł
- Department of Microbiology, Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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15
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Li Q, Armstrong Z, MacRae A, Ugrinov A, Feng L, Chen B, Huang Y, Li H, Pan Y, Yang Z. Metal-Organic Materials (MOMs) Enhance Proteolytic Selectivity, Efficiency, and Reusability of Trypsin: A Time-Resolved Study on Proteolysis. ACS APPLIED MATERIALS & INTERFACES 2023; 15:8927-8936. [PMID: 36757369 DOI: 10.1021/acsami.2c19873] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Proteases are involved in essential biological functions in nature and have become drug targets recently. In spite of the promising progress, two challenges, (i) the intrinsic instability and (ii) the difficulty in monitoring the catalytic process in real time, still hinder the further understanding and engineering of protease functionalities. These challenges are caused by the lack of proper materials/approaches to stabilize proteases and monitor proteolytic products (truncated polypeptides) in real time in a highly heterogeneous reaction mixture. This work combines metal-organic materials (MOMs), site-directed spin labeling-electron paramagnetic resonance (SDSL-EPR) spectroscopy, and mass spectrometry (MS) to overcome both barriers. A model protease, trypsin, which cleaves the peptide bonds at lysine or arginine residues, was immobilized on a Ca-MOM via aqueous-phase, one-pot cocrystallization, which allows for trypsin protection and ease of separation from its proteolytic products. Time-resolved EPR and MS were employed to monitor the populations, rotational motion, and sequences of the cleaved peptide truncations of a model protein substrate as the reaction proceeded. Our data suggest a significant (at least 5-10 times) enhancement in the catalytic efficiency (kcat/km) of trypsin@Ca-MOM and excellent reusability as compared to free trypsin in solution. Surprisingly, entrapping trypsin in Ca-MOMs results in cleavage site/region selectivity against the protein substrate, as compared to the near nonselective cleavage of all lysine and arginine residues of the substrate in solution. Remarkably, immobilizing trypsin allows for the separation and, thus, MS study on the sequences of truncated peptides in real time, leading to a time-resolved "movie" of trypsin proteolysis. This work demonstrates the use of MOMs and cocrystallization to enhance the selectivity, catalytic efficiency, and stability of trypsin, suggesting the possibility of tuning the catalytic performance of a general protease using MOMs.
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Affiliation(s)
- Qiaobin Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Zoe Armstrong
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Austin MacRae
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Li Feng
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Ying Huang
- Department of Civil, Construction, and Environmental Engineering, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Hui Li
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Yanxiong Pan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Changchun 130022, China
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58102, United States
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16
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Biasizzo M, Javoršek U, Vidak E, Zarić M, Turk B. Cysteine cathepsins: A long and winding road towards clinics. Mol Aspects Med 2022; 88:101150. [PMID: 36283280 DOI: 10.1016/j.mam.2022.101150] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 12/03/2022]
Abstract
Biomedical research often focuses on properties that differentiate between diseased and healthy tissue; one of the current focuses is elevated expression and altered localisation of proteases. Among these proteases, dysregulation of cysteine cathepsins can frequently be observed in inflammation-associated diseases, which tips the functional balance from normal physiological to pathological manifestations. Their overexpression and secretion regularly exhibit a strong correlation with the development and progression of such diseases, making them attractive pharmacological targets. But beyond their mostly detrimental role in inflammation-associated diseases, cysteine cathepsins are physiologically highly important enzymes involved in various biological processes crucial for maintaining homeostasis and responding to different stimuli. Consequently, several challenges have emerged during the efforts made to translate basic research data into clinical applications. In this review, we present both physiological and pathological roles of cysteine cathepsins and discuss the clinical potential of cysteine cathepsin-targeting strategies for disease management and diagnosis.
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Affiliation(s)
- Monika Biasizzo
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Urban Javoršek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Eva Vidak
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Miki Zarić
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; International Postgraduate School Jozef Stefan, Jamova 39, SI-1000, Ljubljana, Slovenia
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000, Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000, Ljubljana, Slovenia.
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17
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Lecaille F, Chazeirat T, Saidi A, Lalmanach G. Cathepsin V: Molecular characteristics and significance in health and disease. Mol Aspects Med 2022; 88:101086. [PMID: 35305807 DOI: 10.1016/j.mam.2022.101086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 12/31/2022]
Abstract
Human cysteine cathepsins form a family of eleven proteases (B, C, F, H, K, L, O, S, V, W, X/Z) that play important roles in a considerable number of biological and pathophysiological processes. Among them, cathepsin V, also known as cathepsin L2, is a lysosomal enzyme, which is mainly expressed in cornea, thymus, heart, brain, and skin. Cathepsin V is a multifunctional endopeptidase that is involved in both the release of antigenic peptides and the maturation of MHC class II molecules and participates in the turnover of elastin fibrils as well in the cleavage of intra- and extra-cellular substrates. Moreover, there is increasing evidence that cathepsin V may contribute to the progression of diverse diseases, due to the dysregulation of its expression and/or its activity. For instance, increased expression of cathepsin V is closely correlated with malignancies (breast cancer, squamous cell carcinoma, or colorectal cancer) as well vascular disorders (atherosclerosis, aortic aneurysm, hypertension) being the most prominent examples. This review aims to shed light on current knowledge on molecular aspects of cathepsin V (genomic organization, protein structure, substrate specificity), its regulation by protein and non-protein inhibitors as well to summarize its expression (tissue and cellular distribution). Then the core biological and pathophysiological roles of cathepsin V will be depicted, raising the question of its interest as a valuable target that can open up pioneering therapeutic avenues.
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Affiliation(s)
- Fabien Lecaille
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France.
| | - Thibault Chazeirat
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France
| | - Ahlame Saidi
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France
| | - Gilles Lalmanach
- Université de Tours, Tours, France; INSERM, UMR 1100, Centre d'Etude des Pathologies Respiratoires (CEPR), Team "Mécanismes protéolytiques dans l'inflammation", Tours, France.
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18
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Ćwilichowska N, Świderska KW, Dobrzyń A, Drąg M, Poręba M. Diagnostic and therapeutic potential of protease inhibition. Mol Aspects Med 2022; 88:101144. [PMID: 36174281 DOI: 10.1016/j.mam.2022.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Proteases are enzymes that hydrolyze peptide bonds in proteins and peptides; thus, they control virtually all biological processes. Our understanding of protease function has advanced considerably from nonselective digestive enzymes to highly specialized molecular scissors that orchestrate complex signaling networks through a limited proteolysis. The catalytic activity of proteases is tightly regulated at several levels, ranging from gene expression through trafficking and maturation to posttranslational modifications. However, when this delicate balance is disturbed, many diseases develop, including cancer, inflammatory disorders, diabetes, and neurodegenerative diseases. This new understanding of the role of proteases in pathologic physiology indicates that these enzymes represent excellent molecular targets for the development of therapeutic inhibitors, as well as for the design of chemical probes to visualize their redundant activity. Recently, numerous platform technologies have been developed to identify and optimize protease substrates and inhibitors, which were further used as lead structures for the development of chemical probes and therapeutic drugs. Due to this considerable success, the clinical potential of proteases in therapeutics and diagnostics is rapidly growing and is still not completely explored. Therefore, small molecules that can selectively target aberrant protease activity are emerging in diseases cells. In this review, we describe modern trends in the design of protease drugs as well as small molecule activity-based probes to visualize selected proteases in clinical settings.
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Affiliation(s)
- Natalia Ćwilichowska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina W Świderska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Dobrzyń
- Nencki Institute of Experimental Biology, Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
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19
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Elamin T, Santos NP, Briza P, Brandstetter H, Dall E. Structural and functional studies of legumain-mycocypin complexes revealed a competitive, exosite-regulated mode of interaction. J Biol Chem 2022; 298:102502. [PMID: 36116553 PMCID: PMC9579014 DOI: 10.1016/j.jbc.2022.102502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 12/01/2022] Open
Abstract
Under pathophysiologic conditions such as Alzheimer's disease and cancer, the endolysosomal cysteine protease legumain was found to translocate to the cytosol, the nucleus, and the extracellular space. These noncanonical localizations demand for a tight regulation of legumain activity, which is in part conferred by protein inhibitors. While there is a significant body of knowledge on the interaction of human legumain with endogenous cystatins, only little is known on its regulation by fungal mycocypins. Mycocypins are characterized by (i) versatile, plastic surface loops allowing them to inhibit different classes of enzymes and (ii) a high resistance toward extremes of pH and temperature. These properties make mycocypins attractive starting points for biotechnological and medical applications. In this study, we show that mycocypins utilize an adaptable reactive center loop to target the active site of legumain in a substrate-like manner. The interaction was further stabilized by variable, isoform-specific exosites, converting the substrate recognition into inhibition. Additionally, we found that selected mycocypins were capable of covalent complex formation with legumain by forming a disulfide bond to the active site cysteine. Furthermore, our inhibition studies with other clan CD proteases suggested that mycocypins may serve as broad-spectrum inhibitors of clan CD proteases. Our studies uncovered the potential of mycocypins as a new scaffold for drug development, providing the basis for the design of specific legumain inhibitors.
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Affiliation(s)
- Tasneem Elamin
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Naiá P Santos
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Elfriede Dall
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria.
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20
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Clostridium novyi’s Alpha-Toxin Changes Proteome and Phosphoproteome of HEp-2 Cells. Int J Mol Sci 2022; 23:ijms23179939. [PMID: 36077344 PMCID: PMC9456407 DOI: 10.3390/ijms23179939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/17/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
C. novyi type A produces the alpha-toxin (TcnA) that belongs to the large clostridial glucosylating toxins (LCGTs) and is able to modify small GTPases by N-acetylglucosamination on conserved threonine residues. In contrast, other LCGTs including Clostridioides difficile toxin A and toxin B (TcdA; TcdB) modify small GTPases by mono-o-glucosylation. Both modifications inactivate the GTPases and cause strong effects on GTPase-dependent signal transduction pathways and the consequent reorganization of the actin cytoskeleton leading to cell rounding and finally cell death. However, the effect of TcnA on target cells is largely unexplored. Therefore, we performed a comprehensive screening approach of TcnA treated HEp-2 cells and analyzed their proteome and their phosphoproteome using LC-MS-based methods. With this data-dependent acquisition (DDA) approach, 5086 proteins and 9427 phosphosites could be identified and quantified. Of these, 35 proteins were found to be significantly altered after toxin treatment, and 1832 phosphosites were responsive to TcnA treatment. By analyzing the TcnA-induced proteomic effects of HEp-2 cells, 23 common signaling pathways were identified to be altered, including Actin Cytoskeleton Signaling, Epithelial Adherens Junction Signaling, and Signaling by Rho Family GTPases. All these pathways are also regulated after application of TcdA or TcdB of C. difficile. After TcnA treatment the regulation on phosphorylation level was much stronger compared to the proteome level, in terms of both strength of regulation and the number of regulated phosphosites. Interestingly, various signaling pathways such as Signaling by Rho Family GTPases or Integrin Signaling were activated on proteome level while being inhibited on phosphorylation level or vice versa as observed for the Role of BRCA1 in DNA Damage Response. ZIP kinase, as well as Calmodulin-dependent protein kinases IV & II, were observed as activated while Aurora-A kinase and CDK kinases tended to be inhibited in cells treated with TcnA based on their substrate regulation pattern.
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21
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Hopp TP, Spiewak K, Matthews MAH, Athanasiou Z, Blackmore RS, Gelbfish GA. Characterization of proteolytic degradation products of vaginally administered bovine lactoferrin. PLoS One 2022; 17:e0268537. [PMID: 35587943 PMCID: PMC9119511 DOI: 10.1371/journal.pone.0268537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/19/2022] [Indexed: 11/24/2022] Open
Abstract
When bovine lactoferrin (bLF) contacts human vaginal fluid (VF) it is subjected to proteolytic degradation. This report describes fragmentation patterns of bLF dosed vaginally in clinical trials or incubated ex vivo with VF. A consensus pattern of fragments was observed in samples from different women. The 80 kDa bLF molecule is initially cleaved between its homologous 40 kDa domains, the N-lobe and C-lobe, and then degraded into sub-fragments and mixtures of small peptides. We characterized this fragmentation process by polyacrylamide gel electrophoresis, western blotting, chromatographic separation, and mass spectral sequence analysis. Common to most VF fragmentation patterns were large amounts of an N-lobe 37 kDa fragment and a C-lobe 43 kDa fragment resulting from a single cleavage following tyrosine 324. Both fragments possessed full sets of iron-ligand amino acids and retained iron-binding ability. In some VF samples, alternative forms of large fragments were found, which like the 37+43 kDa pair, totaled 80 kDa. These included 58+22 kDa, 18+62 kDa, and 16+64 kDa forms. In general, the smaller component was from the N-lobe and the larger from the C-lobe. The 18+62 kDa pair was absent in some VF samples but highly abundant in others. This variability suggests multiple endopeptidases are involved, with the 18 kDa fragment’s presence dependent upon the balance of enzymes. Further action of VF endopeptidases produced smaller peptide fragments, and we found evidence that exopeptidases trimmed their N- and C-termini. The 3.1 kDa antimicrobial peptide lactoferricin B was not detected. These studies were facilitated by a novel technique we developed: tricolor western blots, which enabled simultaneous visualization of N- and C-terminal epitopes.
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Affiliation(s)
- Thomas P. Hopp
- Metrodora Therapeutics LLC, Brooklyn, New York, NY, United States of America
- * E-mail:
| | - Klaudyna Spiewak
- Metrodora Therapeutics LLC, Brooklyn, New York, NY, United States of America
| | | | - Zafeiria Athanasiou
- Metrodora Therapeutics LLC, Brooklyn, New York, NY, United States of America
| | | | - Gary A. Gelbfish
- Metrodora Therapeutics LLC, Brooklyn, New York, NY, United States of America
- Department of Surgery, Mount Sinai School of Medicine, New York, NY, United States of America
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22
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A New Role of Acute Phase Proteins: Local Production Is an Ancient, General Stress-Response System of Mammalian Cells. Int J Mol Sci 2022; 23:ijms23062972. [PMID: 35328392 PMCID: PMC8954921 DOI: 10.3390/ijms23062972] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/20/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023] Open
Abstract
The prevailing general view of acute-phase proteins (APPs) is that they are produced by the liver in response to the stress of the body as part of a systemic acute-phase response. We demonstrated a coordinated, local production of these proteins upon cell stress by the stressed cells. The local, stress-induced APP production has been demonstrated in different tissues (kidney, breast cancer) and with different stressors (hypoxia, fibrosis and electromagnetic heat). Thus, this local acute-phase response (APR) seems to be a universal mechanism. APP production is an ancient defense mechanism observed in nematodes and fruit flies as well. Local APP production at the tissue level is also supported by sporadic literature data for single proteins; however, the complex, coordinated, local appearance of this stress response has been first demonstrated only recently. Although a number of literature data are available for the local production of single acute-phase proteins, their interpretation as a local, coordinated stress response is new. A better understanding of the role of APPs in cellular stress response may also be of diagnostic/prognostic and therapeutic significance.
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23
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Dyer RP, Weiss GA. Making the cut with protease engineering. Cell Chem Biol 2022; 29:177-190. [PMID: 34921772 PMCID: PMC9127713 DOI: 10.1016/j.chembiol.2021.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 07/30/2021] [Accepted: 11/29/2021] [Indexed: 12/30/2022]
Abstract
Proteases cut with enviable precision and regulate diverse molecular events in biology. Such qualities drive a seemingly inexhaustible appetite for proteases with new activities and capabilities. Comprising 25% of the total industrial enzyme market, proteases appear in consumer goods, such as detergents, textile processing, and numerous foods; additionally, proteases include 25 US Food and Drug Administration-approved medicines and various research tools. Recent advances in protease engineering strategies address target specificity, catalytic efficiency, and stability. This guide to protease engineering surveys best practices and emerging strategies. We further highlight gaps and flexibilities inherent to each system that suggest opportunities for new technology development along with engineered proteases to solve challenges in proteomics, protein sequencing, and synthetic gene circuits.
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Affiliation(s)
- Rebekah P Dyer
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA
| | - Gregory A Weiss
- Department of Chemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA; Department of Pharmaceutical Sciences, University of California, Irvine, 1102 NS-2, Irvine, CA 92697-2025, USA.
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24
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Yang ZR. In silico prediction of Severe Acute Respiratory Syndrome Coronavirus 2 main protease cleavage sites. Proteins 2021; 90:791-801. [PMID: 34739145 PMCID: PMC8661936 DOI: 10.1002/prot.26274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
One of the emerging subjects to combat the SARS-CoV-2 virus is to design accurate and efficient drug such as inhibitors against the viral protease to stop the viral spread. In addition to laboratory investigation of the viral protease, which is fundamental, the in silico research of viral protease such as the protease cleavage site prediction is critically important and urgent. However, this problem has yet to be addressed. This article has, for the first time, investigated this problem using the pattern recognition approaches. The article has shown that the pattern recognition approaches incorporating a specially tailored kernel function for dealing with amino acids has the outstanding performance in the accuracy of cleavage site prediction and the discovery of the prototype cleavage peptides.
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25
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Dall E, Stanojlovic V, Demir F, Briza P, Dahms SO, Huesgen PF, Cabrele C, Brandstetter H. The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities. ACS Catal 2021; 11:11885-11896. [PMID: 34621593 PMCID: PMC8491156 DOI: 10.1021/acscatal.1c02057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Protein modification by enzymatic breaking and forming of peptide bonds significantly expands the repertoire of genetically encoded protein sequences. The dual protease-ligase legumain exerts the two opposing activities within a single protein scaffold. Primarily localized to the endolysosomal system, legumain represents a key enzyme in the generation of antigenic peptides for subsequent presentation on the MHCII complex. Here we show that human legumain catalyzes the ligation and cyclization of linear peptides at near-neutral pH conditions, where legumain is intrinsically unstable. Conformational stabilization significantly enhanced legumain's ligase activity, which further benefited from engineering the prime substrate recognition sites for improved affinity. Additionally, we provide evidence that specific legumain activation states allow for differential regulation of its activities. Together these results set the basis for engineering legumain proteases and ligases with applications in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Peter Briza
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Sven O. Dahms
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Pitter F. Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52428 Jülich, Germany
- CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
- Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, 50674 Cologne, Germany
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, 5020 Salzburg, Austria
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26
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Abstract
All living organisms depend on tightly regulated cellular networks to control biological functions. Proteolysis is an important irreversible post-translational modification that regulates most, if not all, cellular processes. Proteases are a large family of enzymes that perform hydrolysis of protein substrates, leading to protein activation or degradation. The 473 known and 90 putative human proteases are divided into 5 main mechanistic groups: metalloproteases, serine proteases, cysteine proteases, threonine proteases, and aspartic acid proteases. Proteases are fundamental to all biological systems, and when dysregulated they profoundly influence disease progression. Inhibiting proteases has led to effective therapies for viral infections, cardiovascular disorders, and blood coagulation just to name a few. Between 5 and 10% of all pharmaceutical targets are proteases, despite limited knowledge about their biological roles. More than 50% of all human proteases have no known substrates. We present here a comprehensive list of all current known human proteases. We also present current and novel biochemical tools to characterize protease functions in vitro, in vivo, and ex vivo. These tools make it achievable to define both beneficial and detrimental activities of proteases in health and disease.
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Affiliation(s)
- Longxiang Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kimberly Main
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Henry Wang
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Olivier Julien
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, AB T2N 1N4, Canada.,McCaig Institute for Bone & Joint Health, University of Calgary, Calgary, AB T2N 1N4, Canada.,Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
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27
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Jiang Z, Lietz CB, Podvin S, Yoon MC, Toneff T, Hook V, O’Donoghue AJ. Differential Neuropeptidomes of Dense Core Secretory Vesicles (DCSV) Produced at Intravesicular and Extracellular pH Conditions by Proteolytic Processing. ACS Chem Neurosci 2021; 12:2385-2398. [PMID: 34153188 PMCID: PMC8267839 DOI: 10.1021/acschemneuro.1c00133] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
![]()
Neuropeptides mediate
cell–cell signaling in the nervous
and endocrine systems. The neuropeptidome is the spectrum of peptides
generated from precursors by proteolysis within dense core secretory
vesicles (DCSV). DCSV neuropeptides and contents are released to the
extracellular environment where further processing for neuropeptide
formation may occur. To assess the DCSV proteolytic capacity for production
of neuropeptidomes at intravesicular pH 5.5 and extracellular pH 7.2,
neuropeptidomics, proteomics, and protease assays were conducted using
chromaffin granules (CG) purified from adrenal medulla. CG are an
established model of DCSV. The CG neuropeptidome consisted of 1239
unique peptides derived from 15 proneuropeptides that were colocalized
with 64 proteases. Distinct CG neuropeptidomes were generated at the
internal DCSV pH of 5.5 compared to the extracellular pH of 7.2. Class-specific
protease inhibitors differentially regulated neuropeptidome production
involving aspartic, cysteine, serine, and metallo proteases. The substrate
cleavage properties of CG proteases were assessed by multiplex substrate
profiling by mass spectrometry (MSP-MS) that uses a synthetic peptide
library containing diverse cleavage sites for endopeptidases and exopeptidases.
Parallel inhibitor-sensitive cleavages for neuropeptidome production
and peptide library proteolysis led to elucidation of six CG proteases
involved in neuropeptidome production, represented by cathepsins A,
B, C, D, and L and carboxypeptidase E (CPE). The MSP-MS profiles of
these six enzymes represented the majority of CG proteolytic cleavages
utilized for neuropeptidome production. These findings provide new
insight into the DCSV proteolytic system for production of distinct
neuropeptidomes at the internal CG pH of 5.5 and at the extracellular
pH of 7.2.
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Affiliation(s)
- Zhenze Jiang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Christopher B. Lietz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Sonia Podvin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Michael C. Yoon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Toneff
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Vivian Hook
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
- Department of Neuroscience and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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28
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Di Spiezio A, Marques ARA, Schmidt L, Thießen N, Gallwitz L, Fogh J, Bartsch U, Saftig P. Analysis of cathepsin B and cathepsin L treatment to clear toxic lysosomal protein aggregates in neuronal ceroid lipofuscinosis. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166205. [PMID: 34214607 DOI: 10.1016/j.bbadis.2021.166205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022]
Abstract
Proteolysis mediated by lysosomal cathepsin proteases maintains a physiological flow in autophagy, phagocytosis and endocytosis. Neuronal Ceroid Lipofuscinosis (NCL) is a childhood neurodegenerative disorder characterized by disturbed autophagic flow and pathological accumulation of proteins. We demonstrated a therapeutic clearance of protein aggregates after dosing NCL10 mice with recombinant human pro-cathepsin-D. Prompted by these results and speculating that cathepsins may act in a redundant and in an hierarchical manner we envisaged that a treatment with human recombinant cysteine proteases pro-cathepsin-L (proCTSL) and pro-cathepsin-B (proCTSB) could similarly be used to induce protein degradation. Both enzymes were taken up by mannose 6-phosphate receptor- and LRP-receptor-mediated endocytosis and processed to the lysosomal mature cathepsins. In murine NCL10 astrocytes an abnormal increase in LAMP1 and saposin expression was revealed. Although proCTSB application did not improve this phenotype, proCTSL treatment led to reduced saposin-C levels in this model as well as in an acute brain slice model. Intracerebral dosing in a NCL10 mouse model revealed cellular and lysosomal uptake of both enzymes. Only proCTSL mildly reduced saposin-C levels and attenuated reactive astrogliosis. Application of both proteases did not improve weight loss and mortality of mutant mice. Our data reveal that although recombinant lysosomal proteases can be efficiently delivered to neuronal lysosomes cysteine proteases are less efficient in protein aggregates clearance as compared to the cathepsin-D treatment. Our data including in vitro degradation assays support the idea that bulk proteolysis requires a hierarchical process in which both aspartyl and cysteine hydrolases play a role.
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Affiliation(s)
| | - André R A Marques
- Chronic Diseases Research Centre (CEDOC), Universidade NOVA de Lisboa, 1150-082 Lisbon, Portugal
| | - Lina Schmidt
- Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Niklas Thießen
- Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Lisa Gallwitz
- Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | | | - Udo Bartsch
- Department of Ophthalmology, Experimental Opthalmology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118 Kiel, Germany.
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29
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Miller JT, Vitro CN, Fang S, Benjamin SR, Tumey LN. Enzyme-Agnostic Lysosomal Screen Identifies New Legumain-Cleavable ADC Linkers. Bioconjug Chem 2021; 32:842-858. [PMID: 33788548 DOI: 10.1021/acs.bioconjchem.1c00124] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Over the past two decades, antibody drug conjugates (ADCs) and small molecule drug conjugates (SMDCs) have widely employed valine-citruline and related cathepsin-cleavable linkers due to their stability in plasma and their rapid cleavage by lysosomal cathepsins. However, a number of recent studies have illustrated that these linkers are subject to cleavage by exogenous enzymes such as Ces1C and neutrophil elastase, thus resulting in off-target release of drug. As such, there is a need to diversify the portfolio of ADC linkers in order to overcome nonspecific drug release. Rather than targeting cathepsins, we began with an "enzyme agnostic" screen in which a panel of 75 peptide FRET pairs were screened for cleavage in lysosomal extracts and in plasma. Unexpectedly, a series of Asn-containing peptides emerged from this screen as being cleaved far more quickly than traditional ValCit-type linkers while retaining excellent stability in plasma. Catabolism studies demonstrated that these linkers were cleaved by legumain, an asparaginyl endopeptidase that is overexpressed in a variety of cancers and is known to be present in the lysosome. MMAE-containing ADCs that incorporated these new linkers were shown to exhibit highly potent and selective cytotoxicity, comparable to analogous ValCit ADCs. Importantly, the Asn-containing linkers were shown to be completely stable to human neutrophil elastase, an enzyme thought to be responsible for the neutropenia and thrombocytopenia associated with ValCitPABC-MMAE ADCs. The legumain-cleavable ADCs were shown to have excellent stability in both mouse and human serum, retaining >85% of the drug after 1 week of incubation. Moreover, the corresponding small molecule FRET pairs exhibited <10% cleavage after 18 h in mouse and human serum. On the basis of these results, we believe that these new linkers (AsnAsn in particular) have significant potential in both ADC and SMDC drug delivery applications.
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Affiliation(s)
- Jared T Miller
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Caitlin N Vitro
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Siteng Fang
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, United States
| | - Samantha R Benjamin
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, United States
| | - L Nathan Tumey
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University, P.O. Box 6000, Binghamton, New York 13902, United States
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30
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Mapping specificity, cleavage entropy, allosteric changes and substrates of blood proteases in a high-throughput screen. Nat Commun 2021; 12:1693. [PMID: 33727531 PMCID: PMC7966775 DOI: 10.1038/s41467-021-21754-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/10/2021] [Indexed: 02/06/2023] Open
Abstract
Proteases are among the largest protein families and critical regulators of biochemical processes like apoptosis and blood coagulation. Knowledge of proteases has been expanded by the development of proteomic approaches, however, technology for multiplexed screening of proteases within native environments is currently lacking behind. Here we introduce a simple method to profile protease activity based on isolation of protease products from native lysates using a 96FASP filter, their analysis in a mass spectrometer and a custom data analysis pipeline. The method is significantly faster, cheaper, technically less demanding, easy to multiplex and produces accurate protease fingerprints. Using the blood cascade proteases as a case study, we obtain protease substrate profiles that can be used to map specificity, cleavage entropy and allosteric effects and to design protease probes. The data further show that protease substrate predictions enable the selection of potential physiological substrates for targeted validation in biochemical assays. Characterizing proteases in their native environment is still challenging. Here, the authors develop a proteomics workflow for analyzing protease-specific peptides from cell lysates in 96-well format, providing mechanistic insights into blood proteases and enabling the prediction of protease substrates.
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31
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Vizovisek M, Ristanovic D, Menghini S, Christiansen MG, Schuerle S. The Tumor Proteolytic Landscape: A Challenging Frontier in Cancer Diagnosis and Therapy. Int J Mol Sci 2021; 22:ijms22052514. [PMID: 33802262 PMCID: PMC7958950 DOI: 10.3390/ijms22052514] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, dysregulation of proteases and atypical proteolysis have become increasingly recognized as important hallmarks of cancer, driving community-wide efforts to explore the proteolytic landscape of oncologic disease. With more than 100 proteases currently associated with different aspects of cancer development and progression, there is a clear impetus to harness their potential in the context of oncology. Advances in the protease field have yielded technologies enabling sensitive protease detection in various settings, paving the way towards diagnostic profiling of disease-related protease activity patterns. Methods including activity-based probes and substrates, antibodies, and various nanosystems that generate reporter signals, i.e., for PET or MRI, after interaction with the target protease have shown potential for clinical translation. Nevertheless, these technologies are costly, not easily multiplexed, and require advanced imaging technologies. While the current clinical applications of protease-responsive technologies in oncologic settings are still limited, emerging technologies and protease sensors are poised to enable comprehensive exploration of the tumor proteolytic landscape as a diagnostic and therapeutic frontier. This review aims to give an overview of the most relevant classes of proteases as indicators for tumor diagnosis, current approaches to detect and monitor their activity in vivo, and associated therapeutic applications.
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32
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Babatz TD, Spear ED, Xu W, Sun OL, Nie L, Carpenter EP, Michaelis S. Site specificity determinants for prelamin A cleavage by the zinc metalloprotease ZMPSTE24. J Biol Chem 2020; 296:100165. [PMID: 33293369 PMCID: PMC7948416 DOI: 10.1074/jbc.ra120.015792] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/23/2020] [Accepted: 12/08/2020] [Indexed: 01/11/2023] Open
Abstract
The integral membrane zinc metalloprotease ZMPSTE24 is important for human health and longevity. ZMPSTE24 performs a key proteolytic step in maturation of prelamin A, the farnesylated precursor of the nuclear scaffold protein lamin A. Mutations in the genes encoding either prelamin A or ZMPSTE24 that prevent cleavage cause the premature aging disease Hutchinson–Gilford progeria syndrome (HGPS) and related progeroid disorders. ZMPSTE24 has a novel structure, with seven transmembrane spans that form a large water-filled membrane chamber whose catalytic site faces the chamber interior. Prelamin A is the only known mammalian substrate for ZMPSTE24; however, the basis of this specificity remains unclear. To define the sequence requirements for ZMPSTE24 cleavage, we mutagenized the eight residues flanking the prelamin A scissile bond (TRSY↓LLGN) to all other 19 amino acids, creating a library of 152 variants. We also replaced these eight residues with sequences derived from putative ZMPSTE24 cleavage sites from amphibian, bird, and fish prelamin A. Cleavage of prelamin A variants was assessed using an in vivo yeast assay that provides a sensitive measure of ZMPSTE24 processing efficiency. We found that residues on the C-terminal side of the cleavage site are most sensitive to changes. Consistent with other zinc metalloproteases, including thermolysin, ZMPSTE24 preferred hydrophobic residues at the P1’ position (Leu647), but in addition, showed a similar, albeit muted, pattern at P2’. Our findings begin to define a consensus sequence for ZMPSTE24 that helps to clarify how this physiologically important protease functions and may ultimately lead to identifying additional substrates.
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Affiliation(s)
- Timothy D Babatz
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Eric D Spear
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Wenxin Xu
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Olivia L Sun
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA
| | - Laiyin Nie
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Oxford, UK
| | - Susan Michaelis
- Department of Cell Biology, The Johns Hopkins School of Medicine, Baltimore Maryland, USA.
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33
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Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H. Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition. J Biol Chem 2020; 295:13047-13064. [PMID: 32719006 PMCID: PMC7489914 DOI: 10.1074/jbc.ra120.014478] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/14/2020] [Indexed: 01/19/2023] Open
Abstract
The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest, e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here, we present the crystal structure of Arabidopsis thaliana legumain isoform β (AtLEGβ) in its zymogen state. Combining structural and biochemical experiments, we show for the first time that plant legumains encode distinct, isoform-specific activation mechanisms. Whereas the autocatalytic activation of isoform γ (AtLEGγ) is controlled by the latency-conferring dimer state, the activation of the monomeric AtLEGβ is concentration independent. Additionally, in AtLEGβ the plant-characteristic two-chain intermediate state is stabilized by hydrophobic rather than ionic interactions, as in AtLEGγ, resulting in significantly different pH stability profiles. The crystal structure of AtLEGβ revealed unrestricted nonprime substrate binding pockets, consistent with the broad substrate specificity, as determined by degradomic assays. Further to its protease activity, we show that AtLEGβ exhibits a true peptide ligase activity. Whereas cleavage-dependent transpeptidase activity has been reported for other plant legumains, AtLEGβ is the first example of a plant legumain capable of linking free termini. The discovery of these isoform-specific differences will allow us to identify and rationally design efficient ligases with application in biotechnology and drug development.
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Affiliation(s)
- Elfriede Dall
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
| | - Florian B Zauner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Wai Tuck Soh
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany
| | - Sven O Dahms
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Jülich, Germany; CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany; Institute for Biochemistry, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Hans Brandstetter
- Department of Biosciences, University of Salzburg, Salzburg, Austria.
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34
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A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding. Sci Rep 2020; 10:10563. [PMID: 32601479 PMCID: PMC7324608 DOI: 10.1038/s41598-020-67578-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori (H. pylori) secretes the chaperone and serine protease high temperature requirement A (HtrA) that cleaves gastric epithelial cell surface proteins to disrupt the epithelial integrity and barrier function. First inhibitory lead structures have demonstrated the essential role of HtrA in H. pylori physiology and pathogenesis. Comprehensive drug discovery techniques allowing high-throughput screening are now required to develop effective compounds. Here, we designed a novel fluorescence resonance energy transfer (FRET) peptide derived from a gel-based label-free proteomic approach (direct in-gel profiling of protease specificity) as a valuable substrate for H. pylori HtrA. Since serine proteases are often sensitive to metal ions, we investigated the influence of different divalent ions on the activity of HtrA. We identified Zn++ and Cu++ ions as inhibitors of H. pylori HtrA activity, as monitored by in vitro cleavage experiments using casein or E-cadherin as substrates and in the FRET peptide assay. Putative binding sites for Zn++ and Cu++ were then analyzed in thermal shift and microscale thermophoresis assays. The findings of this study will contribute to the development of novel metal ion-dependent protease inhibitors, which might help to fight bacterial infections.
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35
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Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. Biomolecules 2020; 10:biom10040612. [PMID: 32326640 PMCID: PMC7225963 DOI: 10.3390/biom10040612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/27/2022] Open
Abstract
Caspases are proteases conserved throughout Metazoans and responsible for initiating and executing the apoptotic program. Currently, there are over 1800 known apoptotic caspase substrates, many of them known regulators of cell proliferation and death, which makes them attractive therapeutic targets. However, most caspase substrates are by-standers, and identifying novel apoptotic mediators amongst all caspase substrates remains an unmet need. Here, we conducted an in silico search for significant apoptotic caspase targets across different species within the Vertebrata subphylum, using different criteria of conservation combined with structural features of cleavage sites. We observed that P1 aspartate is highly conserved while the cleavage sites are extensively variable and found that cleavage sites are located primarily in coiled regions composed of hydrophilic amino acids. Using the combination of these criteria, we determined the final list of the 107 most relevant caspase substrates including 30 novel targets previously unknown for their role in apoptosis and cancer. These newly identified substrates can be potential regulators of apoptosis and candidates for anti-tumor therapy.
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36
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Poreba M. Recent advances in the development of legumain-selective chemical probes and peptide prodrugs. Biol Chem 2020; 400:1529-1550. [PMID: 31021817 DOI: 10.1515/hsz-2019-0135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/18/2019] [Indexed: 12/13/2022]
Abstract
Legumain, which is also known as vacuolar processing enzyme (VPE) or asparaginyl endopeptidase (AEP), is a cysteine protease that was first discovered and characterized in the leguminous seeds of the moth bean in the early 1990s. Later, this enzyme was also detected in higher organisms, including eukaryotes. This pH-dependent protease displays the highest activity in acidic endolysosomal compartments; however, legumain also displays nuclear, cytosolic and extracellular activity when stabilized by other proteins or intramolecular complexes. Based on the results from over 25 years of research, this protease is involved in multiple cellular events, including protein degradation and antigen presentation. Moreover, when dysregulated, this protease contributes to the progression of several diseases, with cancer being the well-studied example. Research on legumain biology was undoubtedly facilitated by the use of small molecule chemical tools. Therefore, in this review, I present the historical perspectives and most current strategies for the development of small molecule substrates, inhibitors and activity-based probes for legumain. These tools are of paramount importance in elucidating the roles of legumain in multiple biological processes. Finally, as this enzyme appears to be a promising molecular target for anticancer therapies, the development of legumain-activated prodrugs is also described.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370, Wroclaw, Poland
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37
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Vizovišek M, Vidak E, Javoršek U, Mikhaylov G, Bratovš A, Turk B. Cysteine cathepsins as therapeutic targets in inflammatory diseases. Expert Opin Ther Targets 2020; 24:573-588. [PMID: 32228244 DOI: 10.1080/14728222.2020.1746765] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cysteine cathepsins are involved in the development and progression of numerous inflammation-associated diseases such as cancer, arthritis, bone and immune disorders. Consequently, there is a drive to progress research efforts focused on cathepsin use in diagnostics and as therapeutic targets in disease.Areas covered: This review discusses the potential of cysteine cathepsins as therapeutic targets in inflammation-associated diseases and recent advances in preclinical and clinical research. We describe direct targeting of cathepsins for treatment purposes and their indirect use in diagnostics.Expert opinion: The targeting of cysteine cathepsins has not translated into the clinic; this failure is attributed to off- and on-target side effects and/or the lack of companion biomarkers. This field now embraces developments in diagnostic imaging, the activation of prodrugs and antibody-drug conjugates for targeted drug delivery. The future lies in improved molecular tools and therapeutic concepts that will find a wide spectrum of uses in diagnostic and therapeutic applications.
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Affiliation(s)
- Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Eva Vidak
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Urban Javoršek
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Georgy Mikhaylov
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Andreja Bratovš
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Ljubljana, Slovenia.,Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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38
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Shin S, Hong JH, Na Y, Lee M, Qian WJ, Kim VN, Kim JS. Development of Multiplexed Immuno-N-Terminomics to Reveal the Landscape of Proteolytic Processing in Early Embryogenesis of Drosophila melanogaster. Anal Chem 2020; 92:4926-4934. [DOI: 10.1021/acs.analchem.9b05035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sanghee Shin
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Ji Hye Hong
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Korea
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - V. Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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39
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Soh WT, Demir F, Dall E, Perrar A, Dahms SO, Kuppusamy M, Brandstetter H, Huesgen PF. ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease. Anal Chem 2020; 92:2961-2971. [PMID: 31951383 PMCID: PMC7075662 DOI: 10.1021/acs.analchem.9b03604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Bottom-up
mass spectrometry-based proteomics utilizes proteolytic
enzymes with well characterized specificities to generate peptides
amenable for identification by high-throughput tandem mass spectrometry.
Trypsin, which cuts specifically after the basic residues lysine and
arginine, is the predominant enzyme used for proteome digestion, although
proteases with alternative specificities are required to detect sequences
that are not accessible after tryptic digest. Here, we show that the
human cysteine protease legumain exhibits a strict substrate specificity
for cleavage after asparagine and aspartic acid residues during in-solution
digestions of proteomes extracted from Escherichia
coli, mouse embryonic fibroblast cell cultures, and Arabidopsis thaliana leaves. Generating peptides
highly complementary in sequence, yet similar in their biophysical
properties, legumain (as compared to trypsin or GluC) enabled complementary
proteome and protein sequence coverage. Importantly, legumain further
enabled the identification and enrichment of protein N-termini not
accessible in GluC- or trypsin-digested samples. Legumain cannot cleave
after glycosylated Asn residues, which enabled the robust identification
and orthogonal validation of N-glycosylation sites based on alternating
sequential sample treatments with legumain and PNGaseF and vice versa.
Taken together, we demonstrate that legumain is a practical, efficient
protease for extending the proteome and sequence coverage achieved
with trypsin, with unique possibilities for the characterization of
post-translational modification sites.
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Affiliation(s)
- Wai Tuck Soh
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Elfriede Dall
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Sven O Dahms
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Maithreyan Kuppusamy
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Hans Brandstetter
- Department of Biosciences , University of Salzburg , 5020 Salzburg , Austria
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3 , Forschungszentrum Jülich , 52428 Jülich , Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, Medical Faculty and University Hospital , University of Cologne , 50931 Cologne , Germany.,Institute for Biochemistry, Faculty of Mathematics and Natural Sciences , University of Cologne , 50674 Cologne , Germany
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40
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Róka B, Tod P, Kaucsár T, Vizovišek M, Vidmar R, Turk B, Fonović M, Szénási G, Hamar P. The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice. Int J Mol Sci 2019; 21:E200. [PMID: 31892161 PMCID: PMC6982205 DOI: 10.3390/ijms21010200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
(1) Background: Sepsis-induced acute kidney injury (AKI) is the most common form of acute kidney injury (AKI). We studied the temporal profile of the sepsis-induced renal proteome changes. (2) Methods: Male mice were injected intraperitoneally with bacterial lipopolysaccharide (LPS) or saline (control). Renal proteome was studied by LC-MS/MS (ProteomeXchange: PXD014664) at the early phase (EP, 1.5 and 6 h after 40 mg/kg LPS) and the late phase (LP, 24 and 48 h after 10 mg/kg LPS) of LPS-induced AKI. Renal mRNA expression of acute phase proteins (APP) was assessed by qPCR. (3) Results: Renal proteome change was milder in EP vs. LP. APPs dominated the proteome in LP (proteins upregulated at least 4-fold (APPs/all): EP, 1.5 h: 0/10, 6 h: 1/10; LP, 24 h: 22/47, 48 h: 17/44). Lipocalin-2, complement C3, fibrinogen, haptoglobin and hemopexin were the most upregulated APPs. Renal mRNA expression preceded the APP changes with peak effects at 24 h, and indicated renal production of the majority of APPs. (4) Conclusions: Gene expression analysis revealed local production of APPs that commenced a few hours post injection and peaked at 24 h. This is the first demonstration of a massive, complex and coordinated acute phase response of the kidney involving several proteins not identified previously.
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Affiliation(s)
- Beáta Róka
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (B.R.); (P.T.); (T.K.); (G.S.)
| | - Pál Tod
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (B.R.); (P.T.); (T.K.); (G.S.)
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
| | - Tamás Kaucsár
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (B.R.); (P.T.); (T.K.); (G.S.)
| | - Matej Vizovišek
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (M.V.); (R.V.); (B.T.); (M.F.)
| | - Robert Vidmar
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (M.V.); (R.V.); (B.T.); (M.F.)
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (M.V.); (R.V.); (B.T.); (M.F.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, 1000 Ljubljana, Slovenia
| | - Marko Fonović
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia; (M.V.); (R.V.); (B.T.); (M.F.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, 1000 Ljubljana, Slovenia
| | - Gábor Szénási
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (B.R.); (P.T.); (T.K.); (G.S.)
| | - Péter Hamar
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (B.R.); (P.T.); (T.K.); (G.S.)
- Institute for Translational Medicine, Medical School, University of Pécs, 7624 Pécs, Hungary
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41
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Anderson BM, de Almeida LGN, Sekhon H, Young D, Dufour A, Edgington-Mitchell LE. N-Terminomics/TAILS Profiling of Macrophages after Chemical Inhibition of Legumain. Biochemistry 2019; 59:329-340. [PMID: 31774660 DOI: 10.1021/acs.biochem.9b00821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Legumain (asparaginyl endopeptidase) is the only protease with a preference for cleavage after asparagine residues. Increased legumain activity is a hallmark of inflammation, neurodegenerative diseases, and cancer, and legumain inhibitors have exhibited therapeutic effects in mouse models of these pathologies. Improved knowledge of its substrates and cellular functions is a requisite to further validation of legumain as a drug target. We, therefore, aimed to investigate the effects of legumain inhibition in macrophages using an unbiased and systematic approach. By shotgun proteomics, we identified 16 094 unique peptides in RAW264.7 cells. Among these, 326 unique peptides were upregulated in response to legumain inhibition, while 241 were downregulated. Many of these proteins were associated with mitochondria and metabolism, especially iron metabolism, indicating that legumain may have a previously unknown impact on related processes. Furthermore, we used N-terminomics/TAILS (terminal amine isotopic labeling of substrates) to identify potential substrates of legumain. We identified three new proteins that are cleaved after asparagine residues, which may reflect legumain-dependent cleavage. We confirmed that frataxin, a mitochondrial protein associated with the formation of iron-sulfur clusters, can be cleaved by legumain. This further asserts a potential contribution of legumain to mitochondrial function and iron metabolism. Lastly, we also identified a potential new cleavage site within legumain itself that may give rise to a 25 kDa form of legumain that has previously been observed in multiple cell and tissue types. Collectively, these data shed new light on the potential functions of legumain and will be critical for understanding its contribution to disease.
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Affiliation(s)
- Bethany M Anderson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Victoria 3052 , Australia
| | - Luiz G N de Almeida
- Department of Physiology and Pharmacology , University of Calgary , Calgary , Alberta T2N 4N1 , Canada.,McCaig Institute for Bone and Joint Health , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Henna Sekhon
- Department of Physiology and Pharmacology , University of Calgary , Calgary , Alberta T2N 4N1 , Canada.,McCaig Institute for Bone and Joint Health , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Daniel Young
- Department of Physiology and Pharmacology , University of Calgary , Calgary , Alberta T2N 4N1 , Canada.,McCaig Institute for Bone and Joint Health , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Antoine Dufour
- Department of Physiology and Pharmacology , University of Calgary , Calgary , Alberta T2N 4N1 , Canada.,McCaig Institute for Bone and Joint Health , University of Calgary , Calgary , Alberta T2N 4N1 , Canada
| | - Laura E Edgington-Mitchell
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Victoria 3052 , Australia.,Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences , Monash University , Parkville , Victoria 3052 , Australia.,Department of Oral and Maxillofacial Surgery , New York University College of Dentistry, Bluestone Center for Clinical Research , New York , New York 10010 , United States
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42
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Pichlo C, Juetten L, Wojtalla F, Schacherl M, Diaz D, Baumann U. Molecular determinants of the mechanism and substrate specificity of Clostridium difficile proline-proline endopeptidase-1. J Biol Chem 2019; 294:11525-11535. [PMID: 31182482 DOI: 10.1074/jbc.ra119.009029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/27/2019] [Indexed: 11/06/2022] Open
Abstract
Pro-Pro endopeptidase-1 (PPEP-1) is a secreted metalloprotease from the bacterial pathogen Clostridium difficile that cleaves two endogenous adhesion proteins. PPEP-1 is therefore important for bacterial motility and hence for efficient gut colonization during infection. PPEP-1 exhibits a unique specificity for Pro-Pro peptide bonds within the consensus sequence VNP↓PVP. In this study, we combined information from crystal and NMR structures with mutagenesis and enzyme kinetics to investigate the mechanism and substrate specificity of PPEP-1. Our analyses revealed that the substrate-binding cleft of PPEP-1 is shaped complementarily to the major conformation of the substrate in solution. We found that it possesses features that accept a tertiary amide and help discriminate P1' residues by their amide hydrogen bond-donating potential. We also noted that residues Lys-101, Trp-103, and Glu-184 are crucial for proteolytic activity. Upon substrate binding, these residues position a flexible loop over the substrate-binding cleft and modulate the second coordination sphere of the catalytic zinc ion. On the basis of these findings, we propose an induced-fit model in which prestructured substrates are recognized followed by substrate positioning within the active-site cleft and a concomitant increase in the Lewis acidity of the catalytic Zn2+ ion. In conclusion, our findings provide detailed structural and mechanistic insights into the substrate recognition and specificity of PPEP-1 from the common gut pathogen C. difficile.
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Affiliation(s)
- Christian Pichlo
- Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Linda Juetten
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, 50939 Cologne, Germany
| | - Fabian Wojtalla
- Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Magdalena Schacherl
- Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
| | - Dolores Diaz
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, 50939 Cologne, Germany
| | - Ulrich Baumann
- Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
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43
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Wartenberg M, Saidi A, Galibert M, Joulin-Giet A, Burlaud-Gaillard J, Lecaille F, Scott CJ, Aucagne V, Delmas AF, Lalmanach G. Imaging of extracellular cathepsin S activity by a selective near infrared fluorescence substrate-based probe. Biochimie 2019; 166:84-93. [PMID: 30914255 DOI: 10.1016/j.biochi.2019.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/19/2019] [Indexed: 02/05/2023]
Abstract
We designed a near-infrared fluorescent substrate-based probe (SBP), termed MG101, for monitoring extracellular cathepsin S (CatS) activity. We conceived a fused peptide hairpin loop-structure, combining a CatS recognition domain, an electrostatic zipper (with complementary charges of a polyanionic (D-Glu)5 segment and a polycationic (D-Arg)5 motif, as well as a N and C terminal Förster resonance energy transfer pair (donor: AlexaFluor680; quencher: BHQ3) to facilitate activity-dependent imaging. MG101 showed excellent stability since no fluorescence release corresponding to a self-dequenching was observed in the presence of either 2 M NaCl or after incubation at a broad range of pH (2.2-8.2). Cathepsins B, D, G, H, and K, neutrophil elastase and proteinase 3 did not cleave MG101, while CatS, and to a lesser extent CatL, hydrolysed MG101 at pH 5.5. However MG101 was fully selective for CatS at pH 7.4 (kcat/Km = 140,000 M-1 s-1) and sensitive to low concentration of CatS (<1 nM). The selectivity of MG101 was successfully endorsed ex vivo, as it was hydrolysed in cell lysates derived from wild-type but not knockout CatS murine spleen. Furthermore, application of the SBP probe with confocal microscopy confirmed the secretion of active CatS from THP-1 macrophages, which could be abrogated by pharmacological CatS inhibitors. Taken together, present data highlight MG101 as a novel near-infrared fluorescent SBP for the visualization of extracellular active CatS from macrophages and other cell types.
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Affiliation(s)
- Mylène Wartenberg
- Université de Tours, Tours, France; INSERM, UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", Tours, France
| | - Ahlame Saidi
- Université de Tours, Tours, France; INSERM, UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", Tours, France
| | - Mathieu Galibert
- CNRS UPR 4301, Center for Molecular Biophysics (CBM), Team: "Molecular, Structural and Chemical Biology", Orléans, France
| | - Alix Joulin-Giet
- Université de Tours, Tours, France; INSERM, UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", Tours, France
| | - Julien Burlaud-Gaillard
- Université de Tours, Tours, France; Plateforme IBiSA de Microscopie Electronique, Université de Tours, Tours, France
| | - Fabien Lecaille
- Université de Tours, Tours, France; INSERM, UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", Tours, France
| | - Christopher J Scott
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Vincent Aucagne
- CNRS UPR 4301, Center for Molecular Biophysics (CBM), Team: "Molecular, Structural and Chemical Biology", Orléans, France
| | - Agnès F Delmas
- CNRS UPR 4301, Center for Molecular Biophysics (CBM), Team: "Molecular, Structural and Chemical Biology", Orléans, France
| | - Gilles Lalmanach
- Université de Tours, Tours, France; INSERM, UMR 1100, Research Center for Respiratory Diseases (CEPR), Team: "Proteolytic Mechanisms in Inflammation", Tours, France.
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44
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Vidak E, Javoršek U, Vizovišek M, Turk B. Cysteine Cathepsins and their Extracellular Roles: Shaping the Microenvironment. Cells 2019; 8:cells8030264. [PMID: 30897858 PMCID: PMC6468544 DOI: 10.3390/cells8030264] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/12/2019] [Accepted: 03/15/2019] [Indexed: 12/17/2022] Open
Abstract
For a long time, cysteine cathepsins were considered primarily as proteases crucial for nonspecific bulk proteolysis in the endolysosomal system. However, this view has dramatically changed, and cathepsins are now considered key players in many important physiological processes, including in diseases like cancer, rheumatoid arthritis, and various inflammatory diseases. Cathepsins are emerging as important players in the extracellular space, and the paradigm is shifting from the degrading enzymes to the enzymes that can also specifically modify extracellular proteins. In pathological conditions, the activity of cathepsins is often dysregulated, resulting in their overexpression and secretion into the extracellular space. This is typically observed in cancer and inflammation, and cathepsins are therefore considered valuable diagnostic and therapeutic targets. In particular, the investigation of limited proteolysis by cathepsins in the extracellular space is opening numerous possibilities for future break-through discoveries. In this review, we highlight the most important findings that establish cysteine cathepsins as important players in the extracellular space and discuss their roles that reach beyond processing and degradation of extracellular matrix (ECM) components. In addition, we discuss the recent developments in cathepsin research and the new possibilities that are opening in translational medicine.
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Affiliation(s)
- Eva Vidak
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia.
- International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Urban Javoršek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia.
- International Postgraduate School Jozef Stefan, Jamova 39, SI-1000 Ljubljana, Slovenia.
| | - Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia.
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich Otto-Stern-Weg 3, 8093 Zürich, Switzerland.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia.
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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45
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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46
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Vizovišek M, Fonović M, Turk B. Cysteine cathepsins in extracellular matrix remodeling: Extracellular matrix degradation and beyond. Matrix Biol 2019; 75-76:141-159. [DOI: 10.1016/j.matbio.2018.01.024] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/14/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022]
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47
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Vizovišek M, Vidmar R, Drag M, Fonović M, Salvesen GS, Turk B. Protease Specificity: Towards In Vivo Imaging Applications and Biomarker Discovery. Trends Biochem Sci 2018; 43:829-844. [PMID: 30097385 DOI: 10.1016/j.tibs.2018.07.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/05/2018] [Accepted: 07/12/2018] [Indexed: 02/06/2023]
Abstract
Proteases are considered of major importance in biomedical research because of their crucial roles in health and disease. Their ability to hydrolyze their protein and peptide substrates at single or multiple sites, depending on their specificity, makes them unique among the enzymes. Understanding protease specificity is therefore crucial to understand their biology as well as to develop tools and drugs. Recent advancements in the fields of proteomics and chemical biology have improved our understanding of protease biology through extensive specificity profiling and identification of physiological protease substrates. There are growing efforts to transfer this knowledge into clinical modalities, but their success is often limited because of overlapping protease features, protease redundancy, and chemical tools lacking specificity. Herein, we discuss the current trends and challenges in protease research and how to exploit the growing information on protease specificities for understanding protease biology, as well as for development of selective substrates, cleavable linkers, and activity-based probes and for biomarker discovery.
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Affiliation(s)
- Matej Vizovišek
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Robert Vidmar
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; These authors contributed equally to this work
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Marko Fonović
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Guy S Salvesen
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
| | - Boris Turk
- Jozef Stefan Institute, Department of Biochemistry and Molecular and Structural Biology, Jamova 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, SI-1000 Ljubljana, Slovenia.
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48
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Naimi S, Zirah S, Hammami R, Fernandez B, Rebuffat S, Fliss I. Fate and Biological Activity of the Antimicrobial Lasso Peptide Microcin J25 Under Gastrointestinal Tract Conditions. Front Microbiol 2018; 9:1764. [PMID: 30123205 PMCID: PMC6085462 DOI: 10.3389/fmicb.2018.01764] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/16/2018] [Indexed: 11/24/2022] Open
Abstract
The bacteriocin microcin J25 (MccJ25) inhibits the growth of Gram-negative pathogens including Salmonella and Shigella species, and Escherichia coli. This 21-amino acid peptide has remarkable stability to heat and extreme pH values and resistance to many proteases, thanks to a characteristic lasso structure. In this study, we used the dynamic simulator TIM-1 as gastro-intestinal tract model to evaluate the stability and antibacterial activity of MccJ25 during passage through the proximal portion of the human gastrointestinal tract. MccJ25 concentration was measured in the different simulator sections by HPLC, and inhibition of Salmonella enterica serotype Enteritidis was evaluated using qualitative and quantitative assays. LC-MS/MS analysis and subsequent molecular networking analysis on the Global Natural Product Social Molecular Networking platform (GNPS) and analysis of the peptide degradation in the presence of proteolytic enzymes mimicking the gastro-intestinal conditions permitted to delineate the fate of MccJ25 through identification of the main degradation products. MccJ25 was relatively stable under gastric conditions, but degraded rapidly in the compartment mimicking the duodenum, notably in the presence of pancreatin. Among pancreatin components, elastase I appeared primarily responsible for MccJ25 breakdown, while α-chymotrypsin was less efficient.
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Affiliation(s)
- Sabrine Naimi
- STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Universités, Paris, France
| | - Riadh Hammami
- STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Benoît Fernandez
- STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Universités, Paris, France
| | - Ismail Fliss
- STELA Dairy Research Center, Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
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49
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Dall E, Hollerweger JC, Dahms SO, Cui H, Häussermann K, Brandstetter H. Structural and functional analysis of cystatin E reveals enzymologically relevant dimer and amyloid fibril states. J Biol Chem 2018; 293:13151-13165. [PMID: 29967063 PMCID: PMC6109925 DOI: 10.1074/jbc.ra118.002154] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/26/2018] [Indexed: 12/26/2022] Open
Abstract
Protein activity is often regulated by altering the oligomerization state. One mechanism of multimerization involves domain swapping, wherein proteins exchange parts of their structures and thereby form long-lived dimers or multimers. Domain swapping has been specifically observed in amyloidogenic proteins, for example the cystatin superfamily of cysteine protease inhibitors. Cystatins are twin-headed inhibitors, simultaneously targeting the lysosomal cathepsins and legumain, with important roles in cancer progression and Alzheimer's disease. Although cystatin E is the most potent legumain inhibitor identified so far, nothing is known about its propensity to oligomerize. In this study, we show that conformational destabilization of cystatin E leads to the formation of a domain-swapped dimer with increased conformational stability. This dimer was active as a legumain inhibitor by forming a trimeric complex. By contrast, the binding sites toward papain-like proteases were buried within the cystatin E dimer. We also showed that the dimers could further convert to amyloid fibrils. Unexpectedly, cystatin E amyloid fibrils contained functional protein, which inhibited both legumain and papain-like enzymes. Fibril formation was further regulated by glycosylation. We speculate that cystatin amyloid fibrils might serve as a binding platform to stabilize the pH-sensitive legumain and cathepsins in the extracellular environment, contributing to their physiological and pathological functions.
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Affiliation(s)
- Elfriede Dall
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Julia C Hollerweger
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Sven O Dahms
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
| | - Haissi Cui
- the Center for Integrated Protein Science Munich, Technical University of Munich, D-85748 Munich, Germany
| | - Katharina Häussermann
- the Center for Integrated Protein Science Munich, Technical University of Munich, D-85748 Munich, Germany
| | - Hans Brandstetter
- From the Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria and
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50
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Nguyen MTN, Shema G, Zahedi RP, Verhelst SHL. Protease Specificity Profiling in a Pipet Tip Using "Charge-Synchronized" Proteome-Derived Peptide Libraries. J Proteome Res 2018; 17:1923-1933. [PMID: 29664642 DOI: 10.1021/acs.jproteome.8b00004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
About 2% of the genome of human and other organisms codes for proteases. An important step toward deciphering the biological function of a protease and designing inhibitors is the profiling of protease specificity. In this work we present a novel, label-free, proteomics-based protease specificity profiling method that only requires simple sample preparation steps. It uses proteome-derived peptide libraries and enriches the cleaved sequences using strong cation exchange chromatography (SCX) material in a pipet tip. As a demonstration of the method's versatility, we successfully determined the specificity of GluC, caspase-3, chymotrypsin, MMP-1 and cathepsin G from several hundreds to almost 2000 cleavage events per protease. Interestingly, we also found a novel intrinsic preference of cathepsin G for Asn at the P1 subsite, which we confirmed using synthetic peptides. Overall, this method is straightforward and requires so far the lowest investment in material and equipment for protease specificity profiling. Therefore, we think it will be applicable in any biochemistry laboratory and promote an increased understanding of protease specificity.
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Affiliation(s)
- Minh T N Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany
| | - Gerta Shema
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany.,Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,Segal Cancer Proteomics Centre , Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Steven H L Verhelst
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine , KU Leuven-University of Leuven , Herestraat 49 box 802, 3000 Leuven , Belgium
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