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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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Tanco S, Aviles FX, Gevaert K, Lorenzo J, Van Damme P. Identification of Carboxypeptidase Substrates by C-Terminal COFRADIC. Methods Mol Biol 2017; 1574:115-133. [PMID: 28315247 DOI: 10.1007/978-1-4939-6850-3_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We here present a detailed procedure for studying protein C-termini and their posttranslational modifications by C-terminal COFRADIC. In fact, this procedure can enrich for both C-terminal and N-terminal peptides through a combination of a strong cation exchange fractionation step at low pH, which removes the majority of nonterminal peptides in whole-proteome digests, while the actual COFRADIC step segregates C-terminal peptides from N-terminal peptides. When used in a differential mode, C-terminal COFRADIC allows for the identification of neo-C-termini generated by the action of proteases, which in turn leads to the identification of protease substrates. More specifically, this technology can be applied to determine the natural substrate repertoire of carboxypeptidases on a proteome-wide scale.
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Affiliation(s)
- Sebastian Tanco
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Francesc Xavier Aviles
- Institut de Biotecnologia i Biomedicina (IBB), Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, IBB-Campus de la UAB, Bellaterra, 08193, Barcelona, Spain
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium
| | - Julia Lorenzo
- Institut de Biotecnologia i Biomedicina (IBB), Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, IBB-Campus de la UAB, Bellaterra, 08193, Barcelona, Spain.
| | - Petra Van Damme
- VIB-UGent Center for Medical Biotechnology, B-9000, Ghent, Belgium.
- Department of Biochemistry, Ghent University, B-9000, Ghent, Belgium.
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Huesgen PF, Overall CM. N- and C-terminal degradomics: new approaches to reveal biological roles for plant proteases from substrate identification. PHYSIOLOGIA PLANTARUM 2012; 145:5-17. [PMID: 22023699 DOI: 10.1111/j.1399-3054.2011.01536.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Proteolysis is an irreversible post-translational modification that regulates many intra- and intercellular processes, including essential go/no-go decisions during cell proliferation, development and cell death. Hundreds of protease-coding genes have been identified in plants, but few have been linked to specific substrates. Conversely, proteolytic processes are frequently observed in plant biology but rarely have they been ascribed to specific proteases. In mammalian systems, unbiased system-wide proteomics analyses of protease activities have recently been tremendously successful in the identification of protease substrate repertoires, also known as substrate degradomes. Knowledge of the substrate degradome is key to understand the role of proteases in vivo. Quantitative shotgun proteomic studies have been successful in identifying protease substrates, but while simple to perform they are biased toward abundant proteins and do not reveal precise cleavage sites. Current degradomics techniques overcome these limitations by focusing on the information-rich amino- and carboxy-terminal peptides of the original mature proteins and the protease-generated neo-termini. Targeted quantitative analysis of protein termini identifies precise cleavage sites in protease substrates with exquisite sensitivity and dynamic range in in vitro and in vivo systems. This review provides an overview of state-of-the-art methods for enrichment of protein terminal peptides, and their application to protease research. These emerging degradomics techniques promise to clarify the elusive biological roles of proteases and proteolysis in plants.
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Affiliation(s)
- Pitter F Huesgen
- Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada V6T 1Z3.
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Chou JS, Impens F, Gevaert K, Davies PL. m-Calpain activation in vitro does not require autolysis or subunit dissociation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:864-72. [PMID: 21549862 DOI: 10.1016/j.bbapap.2011.04.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 03/25/2011] [Accepted: 04/12/2011] [Indexed: 11/17/2022]
Abstract
Calpains are Ca(2+)-dependent, intracellular cysteine proteases involved in many physiological functions. How calpains are activated in the cell is unknown because the average intracellular concentration of Ca(2+) is orders of magnitude lower than that needed for half-maximal activation of the enzyme in vitro. Two of the proposed mechanisms by which calpains can overcome this Ca(2+) concentration differential are autoproteolysis (autolysis) and subunit dissociation, both of which could release constraints on the core by breaking the link between the anchor helix and the small subunit to allow the active site to form. By measuring the rate of autolysis at different sites in calpain, we show that while the anchor helix is one of the first targets to be cut, this occurs in the same time-frame as several potentially inactivating cleavages in Domain III. Thus autolytic activation would overlap with inactivation. We also show that the small subunit does not dissociate from the large subunit, but is proteolyzed to a 40-45k heterodimer of Domains IV and VI. It is likely that this autolysis-generated heterodimer has previously been misidentified as the small subunit homodimer produced by subunit dissociation. We propose a model for m-calpain activation that does not involve either autolysis or subunit dissociation.
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Affiliation(s)
- Jordan S Chou
- Department of Biochemistry, Queen's University, Kingston, ON, Canada K7L 3N6
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Methods for the proteomic identification of protease substrates. Curr Opin Chem Biol 2009; 13:503-9. [PMID: 19729334 DOI: 10.1016/j.cbpa.2009.07.026] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Accepted: 07/31/2009] [Indexed: 01/07/2023]
Abstract
Proteolysis is a key regulatory post-translational modification in diverse cellular processes including programed cell death, immune function, and development. Tracking proteolytic events has become a focus of researchers assessing the downstream consequences of protease activation. In this review we summarize unbiased methods for identifying protease substrates and tracking the extent of cleavage, a field termed 'degradomics'. These include one-dimensional and two-dimensional gel-based methods for identifying protease substrates, N-terminal peptide identification methods for simultaneously identifying substrates and cleavage sites, and approaches for the quantitation of cleavage events during endogenous proteolysis. Individual methods have identified more than 300 caspase-cleaved targets during apoptosis suggesting broad future applications for these technologies.
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Cauwe B, Martens E, Proost P, Opdenakker G. Multidimensional degradomics identifies systemic autoantigens and intracellular matrix proteins as novel gelatinase B/MMP-9 substrates. Integr Biol (Camb) 2009; 1:404-26. [PMID: 20023747 DOI: 10.1039/b904701h] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The action radius of matrix metalloproteinases or MMPs is not restricted to massive extracellular matrix (ECM) degradation, it extends to the proteolysis of numerous secreted and membrane-bound proteins. Although many instances exist in which cells disintegrate, often in conjunction with induction of MMPs, the intracellular MMP substrate repertoire or degradome remains relatively unexplored. We started an unbiased exploration of the proteolytic modification of intracellular proteins by MMPs, using gelatinase B/MMP-9 as a model enzyme. To this end, multidimensional degradomics technology was developed by the integration of broadly available biotechniques. In this way, 100-200 MMP-9 candidate substrates were isolated, of which 69 were identified. Integration of these results with the known biological functions of the substrates revealed many novel MMP-9 substrates from the intracellular matrix (ICM), such as actin, tubulin, gelsolin, moesin, ezrin, Arp2/3 complex subunits, filamin B and stathmin. About 2/3 of the identified candidates were autoantigens described in multiple autoimmune conditions and in cancer (e.g. annexin I, nucleolin, citrate synthase, HMGB1, alpha-enolase, histidyl-tRNA synthetase, HSP27, HSC70, HSP90, snRNP D3). These findings led to the insight that MMPs and other proteases may have novel (immuno)regulatory properties by the clearance of toxic and immunogenic burdens of abundant ICM proteins released after extensive necrosis. In line with the extracellular processing of organ-specific autoantigens, proteolysis might also assist in the generation of immunodominant 'neo-epitopes' from systemic autoantigens. The study of proteolysis of ICM molecules, autoantigens, alarmins and other crucial intracellular molecules may result in the discovery of novel roles for proteolytic modification.
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Affiliation(s)
- Bénédicte Cauwe
- Department of Microbiology and Immunology, Laboratory of Immunobiology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, Leuven, Belgium
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