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Mozgovicz M, Fischer A, Brocard C, Jungbauer A, Lingg N. L-Arginine sulfate reduces irreversible protein binding in immobilized metal affinity chromatography. J Chromatogr A 2023; 1706:464246. [PMID: 37541058 DOI: 10.1016/j.chroma.2023.464246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/17/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
Immobilized metal affinity chromatography (IMAC) is a powerful technique for capture and purification of relevant biopharmaceuticals in complex biological matrices. However, protein recovery can be drastically compromised due to surface induced spreading and unfolding of the analyte, leading to fouling of the stationary phase. Here, we report on the kinetics of irreversible adsorption of a protease on an IMAC resin in a time span ranging from minutes to several hours. This trend correlated with the thermal data measured by nano differential scanning calorimetry, and showed a time-dependent change in protein unfolding temperature. Our results highlight that 'soft' proteins show a strong time dependent increase in irreversible adsorption. Furthermore, commonly used co-solvents for preservation of the native protein conformation are tested for their ability to reduce fouling. Thermal data suggests that the amino acid l-arginine is beneficial in preventing unfolding, which was confirmed in batch adsorption experiments. The choice of counter-ions has to be considered when using this amino acid. These results show that l-arginine sulfate decelerates the irreversible adsorption kinetics of proteins on the IMAC stationary phase to a greater extent than l-arginine chloride.
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Affiliation(s)
- Markus Mozgovicz
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andreas Fischer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Cécile Brocard
- Biopharma Process Science Austria, Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Alois Jungbauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nico Lingg
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Vienna, Austria.
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2
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Kröß C, Engele P, Sprenger B, Fischer A, Lingg N, Baier M, Öhlknecht C, Lier B, Oostenbrink C, Cserjan-Puschmann M, Striedner G, Jungbauer A, Schneider R. PROFICS: A bacterial selection system for directed evolution of proteases. J Biol Chem 2021; 297:101095. [PMID: 34418435 PMCID: PMC8446807 DOI: 10.1016/j.jbc.2021.101095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 12/31/2022] Open
Abstract
Proteases serve as important tools in biotechnology and as valuable drugs or drug targets. Efficient protein engineering methods to study and modulate protease properties are thus of great interest for a plethora of applications. We established PROFICS (PRotease Optimization via Fusion-Inhibited Carbamoyltransferase-based Selection), a bacterial selection system, which enables the optimization of proteases for biotechnology, therapeutics or diagnosis in a simple overnight process. During the PROFICS process, proteases are selected for their ability to specifically cut a tag from a reporter enzyme and leave a native N-terminus. Precise and efficient cleavage after the recognition sequence reverses the phenotype of an Escherichia coli knockout strain deficient in an essential enzyme of pyrimidine synthesis. A toolbox was generated to select for proteases with different preferences for P1' residues (the residue immediately following the cleavage site). The functionality of PROFICS is demonstrated with viral proteases and human caspase-2. PROFICS improved caspase-2 activity up to 25-fold after only one round of mutation and selection. Additionally, we found a significantly improved tolerance for all P1' residues caused by a mutation in a substrate interaction site. We showed that this improved activity enables cells containing the new variant to outgrow cells containing all other mutants, facilitating its straightforward selection. Apart from optimizing enzymatic activity and P1' tolerance, PROFICS can be used to reprogram specificities, erase off-target activity, optimize expression via tags/codon usage, or even to screen for potential drug-resistance-conferring mutations in therapeutic targets such as viral proteases in an unbiased manner.
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Affiliation(s)
- Christina Kröß
- acib GmbH, Graz, Austria; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Petra Engele
- acib GmbH, Graz, Austria; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Bernhard Sprenger
- acib GmbH, Graz, Austria; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Andreas Fischer
- acib GmbH, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nico Lingg
- acib GmbH, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magdalena Baier
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christoph Öhlknecht
- acib GmbH, Graz, Austria; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Bettina Lier
- acib GmbH, Graz, Austria; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- acib GmbH, Graz, Austria; Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Monika Cserjan-Puschmann
- acib GmbH, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Striedner
- acib GmbH, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alois Jungbauer
- acib GmbH, Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Rainer Schneider
- acib GmbH, Graz, Austria; Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria.
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Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins 2020; 88:1303-1318. [PMID: 32432825 PMCID: PMC7497161 DOI: 10.1002/prot.25950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
The N-terminal cleavage of fusion tags to restore the native N-terminus of recombinant proteins is a challenging task and up to today, protocols need to be optimized for different proteins individually. Within this work, we present a novel protease that was designed in-silico to yield enhanced promiscuity toward different N-terminal amino acids. Two mutations in the active-site amino acids of human Caspase-2 were determined to increase the recognition of branched amino-acids, which show only poor binding capabilities in the unmutated protease. These mutations were determined by sequential and structural comparisons of Caspase-2 and Caspase-3 and their effect was additionally predicted using free-energy calculations. The two mutants proposed in the in-silico studies were expressed and in-vitro experiments confirmed the simulation results. Both mutants showed not only enhanced activities toward branched amino acids, but also smaller, unbranched amino acids. We believe that the created mutants constitute an important step toward generalized procedures to restore original N-termini of recombinant fusion proteins.
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Affiliation(s)
- Christoph Öhlknecht
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Drazen Petrov
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
| | - Petra Engele
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Christina Kröß
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Bernhard Sprenger
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | | | - Nico Lingg
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center of Molecular Biosciences InnsbruckUniversity of InnsbruckInnsbruckAustria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and SimulationUniversity of Natural Resources and Life SciencesViennaAustria
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Mitrasinovic PM. Quantum Mechanics/Molecular Mechanics Study on Caspase-2 Recognition by Peptide Inhibitors. Acta Chim Slov 2020; 67:876-884. [PMID: 33533429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023] Open
Abstract
For a variety of biological and medical reasons, the ongoing development of humane caspase-2 inhibitors is of vital importance. Herein, a hybrid (Quantum Mechanics/Molecular Mechanics - QM/MM), two-layered molecular model is derived in order to understand better the affinity and specificity of peptide inhibitor interaction with caspase-2. By taking care of both the unique structural features and the catalytic activity of human caspase-2, the critical enzyme residues (E217, R378, N379, T380, and Y420) with the peptide inhibitor are treated at QM level (the Self-Consistent-Charge Density-Functional Tight-Binding method with the Dispersion correction (SCC-DFTB-D)), while the remaining part of the complex is treated at MM level (AMBER force field). The QM/MM binding free energies (BFEs) are well-correlated with the experimental observations and indicate that caspase-2 uniquely prefers a penta-peptide such as VDVAD. The sequence of VDVAD is varied in a systematic fashion by considering the physicochemical properties of every constitutive amino acid and its substituent, and the corresponding BFE with the inhibition constant (Ki) is evaluated. The values of Ki for several caspase-2:peptide complexes are found to be within the experimental range (between 0.01 nM and 1 ?M). The affinity order is: VELAD (Ki=0.081 nM) > VDVAD (Ki=0.23 nM) > VEIAD (Ki=0.61 nM) > VEVAD (Ki=3.7 nM) > VDIAD (Ki=4.5 nM) etc. An approximate condition needed to be satisfied by the kinetic parameters (the Michaelis constant - KM and the specificity constant - kcat/KM) for competitive inhibition is reported. The estimated values of kcat/KM, being within the experimentally established range (between 10-4 and 10-1 ?M-1 s-1), indicate that VELAD and VDVAD are most specific to caspase-2. These two particular peptides are nearly 1.5, 3 and 4 times more specific to the receptor than VEIAD, VEVAD and VDIAD respectively. Additional kinetic threshold, aimed to discriminate tightly bound inhibitors, is given.
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5
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Abstract
Caspase-2 is the most evolutionarily conserved member of the mammalian caspase family and has been implicated in both apoptotic and non-apoptotic signaling pathways, including tumor suppression, cell cycle regulation, and DNA repair. A myriad of signaling molecules is associated with the tight regulation of caspase-2 to mediate multiple cellular processes far beyond apoptotic cell death. This review provides a comprehensive overview of the literature pertaining to possible sophisticated molecular mechanisms underlying the multifaceted process of caspase-2 activation and to highlight its interplay between factors that promote or suppress apoptosis in a complicated regulatory network that determines the fate of a cell from its birth and throughout its life.
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Pham DD, Bruelle C, Thi Do H, Pajanoja C, Jin C, Srinivasan V, Olkkonen VM, Eriksson O, Jauhiainen M, Lalowski M, Lindholm D. Caspase-2 and p75 neurotrophin receptor (p75NTR) are involved in the regulation of SREBP and lipid genes in hepatocyte cells. Cell Death Dis 2019; 10:537. [PMID: 31296846 PMCID: PMC6624261 DOI: 10.1038/s41419-019-1758-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 06/11/2019] [Indexed: 12/16/2022]
Abstract
Lipid-induced toxicity is part of several human diseases, but the mechanisms involved are not fully understood. Fatty liver is characterized by the expression of different growth and tissue factors. The neurotrophin, nerve growth factor (NGF) and its pro-form, pro-NGF, are present in fatty liver together with p75 neurotrophin receptor (p75NTR). Stimulation of human Huh7 hepatocyte cells with NGF and pro-NGF induced Sterol-regulator-element-binding protein-2 (SREBP2) activation and increased Low-Density Lipoprotein Receptor (LDLR) expression. We observed that phosphorylation of caspase-2 by p38 MAPK was essential for this regulation involving a caspase-3-mediated cleavage of SREBP2. RNA sequencing showed that several genes involved in lipid metabolism were altered in p75NTR-deficient mouse liver. The same lipogenic genes were downregulated in p75NTR gene-engineered human Huh7 cells and reciprocally upregulated by stimulation of p75NTRs. In the knock-out mice the serum cholesterol and triglyceride levels were reduced, suggesting a physiological role of p75NTRs in whole-body lipid metabolism. Taken together, this study shows that p75NTR signaling influences a network of genes involved in lipid metabolism in liver and hepatocyte cells. Modulation of p75NTR signaling may be a target to consider in various metabolic disorders accompanied by increased lipid accumulation.
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Affiliation(s)
- Dan Duc Pham
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Céline Bruelle
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Hai Thi Do
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Ceren Pajanoja
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Congyu Jin
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
| | - Vignesh Srinivasan
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Vesa M Olkkonen
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Ove Eriksson
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
| | - Matti Jauhiainen
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Maciej Lalowski
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland
- HiLiFE, Meilahti Clinical Proteomics Core Facility, Helsinki, Finland
| | - Dan Lindholm
- Medicum, Department of Biochemistry and Developmental Biology, Medical Faculty, University of Helsinki, POB 63, FI-00014, Helsinki, Finland.
- Minerva Foundation Institute for Medical Research, Biomedicum 2, Tukholmankatu 8, FI-00290, Helsinki, Finland.
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Ren X, Yu X, Gao B, Liu P, Li J. Characterization of three caspases and their pathogen-induced expression pattern in Portunus trituberculatus. Fish Shellfish Immunol 2017; 66:189-197. [PMID: 28478258 DOI: 10.1016/j.fsi.2017.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 06/07/2023]
Abstract
Caspases are a family of proteases involved in many important biological processes including apoptosis and inflammation. In this study, we analyzed the expression patterns and effects on immune response in various tissues of the edible crab Portunus trituberculatus. PtCas 2, PtCas 3 and PtCas 4 share overall sequence identities of 55.88%-74.86%, 8.47%-46.54% and 20.11%-50.87%, respectively, with their other crustacean species. PtCas 2, PtCas 3 and PtCas 4 have the same caspase domain and catalytic site found in known caspases. The expression levels of the three caspases differed between tissues. Following bacterial and viral infection, the expression levels of the three caspases reached a maximum level at 24 h post-infection (hpi) in case of bacteria, whereas it was 48 hpi in virus. Moreover, the WSSV, Vibrio alginolyticus or V. parahaemolyticus induced the activities of PtCas 2-4 in a time-dependent manner. These results indicate an involvement of caspases in bacterial and viral induced immune response and demonstrate for the first time that PtCas 2, PtCas 3 and PtCas 4 are essential for optimal response to bacterial and virus infection in crabs.
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Affiliation(s)
- Xianyun Ren
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Xuan Yu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China; College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Baoquan Gao
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Ping Liu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Jian Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, PR China; Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, PR China.
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Abstract
Apoptosis (programmed cell death) is essential machinery for multicellular organisms. Apoptosis plays an important role in cell differentiation, damaged cell elimination and immune system homeostasis. This review is focused on various mechanisms of signal transduction through caspase-2 which believed to be one of the most enigmatical protease involved in apoptosis. Caspase-2 is activated upon stimulation by such agents as genotoxic stress, death receptors ligation, ER stress, metabolic changes, etc. In addition, caspase-2 may act as a tumor suppressor and has been implicated in cell response to oxidative stress and neurodegenerative progression during ischemic brain damage. Thus, variety of signal pathways triggered by caspase-2 place this protease apart from other members of the family and suggests a prominent role in apoptosis. Here, we analyse different functions of this unique caspase and discuss possible applications of accumulated knowledge in advanced oncology and medicine.
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Tinnikov AA, Samuels HH. A novel cell lysis approach reveals that caspase-2 rapidly translocates from the nucleus to the cytoplasm in response to apoptotic stimuli. PLoS One 2013; 8:e61085. [PMID: 23596516 PMCID: PMC3626589 DOI: 10.1371/journal.pone.0061085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/07/2013] [Indexed: 11/22/2022] Open
Abstract
Unlike other caspases, caspase-2 appears to be a nuclear protein although immunocytochemical studies have suggested that it may also be localized to the cytosol and golgi. Where and how caspase-2 is activated in response to apoptotic signals is not clear. Earlier immunocytochemistry studies suggest that caspase-2 is activated in the nucleus and through cleavage of BID leads to increased mitochondrial permeability. More recent studies using bimolecular fluorescence complementation found that caspase-2 oligomerization that leads to activation only occurs in the cytoplasm. Thus, apoptotic signals may lead to activation of caspase-2 which may already reside in the cytoplasm or lead to release of nuclear caspase-2 to the extra-nuclear cytoplasmic compartment. It has not been possible to study release of nuclear caspase-2 to the cytoplasm by cell fractionation studies since cell lysis is known to release nuclear caspase-2 to the extra-nuclear fraction. This is similar to what is known about unliganded nuclear estrogen receptor-α (ERα ) when cells are disrupted. In this study we found that pre-treatment of cells with N-ethylmaleimide (NEM), which alkylates cysteine thiol groups in proteins, completely prevents redistribution of caspase-2 and ERα from the nucleus to the extra-nuclear fraction when cells are lysed. Using this approach we provide evidence that apoptotic signals rapidly leads to a shift of caspase-2 from the nucleus to the extra-nuclear fraction, which precedes the detection of apoptosis. These findings are consistent with a model where apoptotic signals lead to a rapid shift of caspase-2 from the nucleus to the cytoplasm where activation occurs.
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Affiliation(s)
- Alexander A. Tinnikov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Herbert H. Samuels
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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Abstract
Caspase-2, the most evolutionarily conserved member in the human caspase family, may play important roles in stress-induced apoptosis, cell cycle regulation, and tumor suppression. In biochemical assays, caspase-2 uniquely prefers a pentapeptide (such as VDVAD) rather than a tetrapeptide, as required for efficient cleavage by other caspases. We investigated the molecular basis for pentapeptide specificity using peptide analog inhibitors and substrates that vary at the P5 position. We determined the crystal structures of apo caspase-2, caspase-2 in complex with peptide inhibitors VDVAD-CHO, ADVAD-CHO, and DVAD-CHO, and a T380A mutant of caspase-2 in complex with VDVAD-CHO. Two residues, Thr-380 and Tyr-420, are identified to be critical for the P5 residue recognition; mutation of the two residues reduces the catalytic efficiency by about 4- and 40-fold, respectively. The structures also provide a series of snapshots of caspase-2 in different catalytic states, shedding light on the mechanism of capase-2 activation, substrate binding, and catalysis. By comparing the apo and inhibited caspase-2 structures, we propose that the disruption of a non-conserved salt bridge between Glu-217 and the invariant Arg-378 is important for the activation of caspase-2. These findings broaden our understanding of caspase-2 substrate specificity and catalysis.
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Affiliation(s)
- Yinyan Tang
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA
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11
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Schweizer A, Roschitzki-Voser H, Amstutz P, Briand C, Gulotti-Georgieva M, Prenosil E, Binz HK, Capitani G, Baici A, Plückthun A, Grütter MG. Inhibition of Caspase-2 by a Designed Ankyrin Repeat Protein: Specificity, Structure, and Inhibition Mechanism. Structure 2007; 15:625-36. [PMID: 17502107 DOI: 10.1016/j.str.2007.03.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 03/09/2007] [Accepted: 03/14/2007] [Indexed: 11/29/2022]
Abstract
Specific and potent caspase inhibitors are indispensable for the dissection of the intricate pathways leading to apoptosis. We selected a designed ankyrin repeat protein (DARPin) from a combinatorial library that inhibits caspase-2 in vitro with a subnanomolar inhibition constant and, in contrast to the peptidic caspase inhibitors, with very high specificity for this particular caspase. The crystal structure of this inhibitor (AR_F8) in complex with caspase-2 reveals the molecular basis for the specificity and, together with kinetic analyses, the allosteric mechanism of inhibition. The structure also shows a conformation of the active site that can be exploited for the design of inhibitory compounds. AR_F8 is a specific inhibitor of an initiator caspase and has the potential to help identify the function of caspase-2 in the complex biological apoptotic signaling network.
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Affiliation(s)
- Andreas Schweizer
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Tinel A, Janssens S, Lippens S, Cuenin S, Logette E, Jaccard B, Quadroni M, Tschopp J. Autoproteolysis of PIDD marks the bifurcation between pro-death caspase-2 and pro-survival NF-kappaB pathway. EMBO J 2006; 26:197-208. [PMID: 17159900 PMCID: PMC1782377 DOI: 10.1038/sj.emboj.7601473] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 11/06/2006] [Indexed: 01/08/2023] Open
Abstract
Upon DNA damage, a complex called the PIDDosome is formed and either signals NF-kappaB activation and thus cell survival or alternatively triggers caspase-2 activation and apoptosis. PIDD (p53-induced protein with a death domain) is constitutively processed giving rise to a 48-kDa N-terminal fragment containing the leucine-rich repeats (LRRs, PIDD-N) and a 51-kDa C-terminal fragment containing the death domain (DD, PIDD-C). The latter undergoes further cleavage resulting in a 37-kDa fragment (PIDD-CC). Here we show that processing occurs at S446 (generating PIDD-C) and S588 (generating PIDD-CC) by an auto-processing mechanism similar to that found in the nuclear pore protein Nup98/96 and inteins. Auto-cleavage of PIDD determines the outcome of the downstream signaling events. Whereas initially formed PIDD-C mediates the activation of NF-kappaB via the recruitment of RIP1 and NEMO, subsequent formation of PIDD-CC causes caspase-2 activation and thus cell death. A non-cleavable PIDD mutant is unable to translocate from the cytoplasm to the nucleus and loses both activities. In this way, auto-proteolysis of PIDD might participate in the orchestration of the DNA damage-induced life and death signaling pathways.
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Affiliation(s)
- Antoine Tinel
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Sophie Janssens
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Saskia Lippens
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Solange Cuenin
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Emmanuelle Logette
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Bastienne Jaccard
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- Protein Analysis Facility, University of Lausanne, Epalinges, Switzerland
| | - Manfredo Quadroni
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- Protein Analysis Facility, University of Lausanne, Epalinges, Switzerland
| | - Jürg Tschopp
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, CH-1066 Epalinges, Switzerland. Tel.: +41 21 692 5738; Fax: +41 21 692 6705; E-mail:
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Coureuil M, Fouchet P, Prat M, Letallec B, Barroca V, Dos Santos C, Racine C, Allemand I. Caspase-independent death of meiotic and postmeiotic cells overexpressing p53: calpain involvement. Cell Death Differ 2006; 13:1927-37. [PMID: 16528385 DOI: 10.1038/sj.cdd.4401887] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In a model of male sterility (MTp53) owing to enforced p53 expression in spermatocytes II and spermatids of transgenic mice, we focused on the role of caspases. Most of them are expressed in all differentiation stages, but only the transcriptional levels of caspase-2 and caspase-3 are modified in MTp53 germ cells. In normal testis, cleaved caspase-3 and caspase-9 are detected during the elongation of spermatids. Despite this constitutive presence of caspases during terminal differentiation, calpains are the main effectors of germ cell loss in MTp53 testes: calpain 1 RNA levels are increased, caspase-3-like activity is markedly decreased while calpain activity is higher and the calpain inhibitor E64d ((2S, 3S)-trans-epoxysuccinyl-L-leucylamido-3-methylbutane ethyl ester) reduces TUNEL labeling in MTp53 testis, whereas pancaspase inhibitor zVADfmk (N-benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone) has no effect. Our work suggests that despite the presence, and potent involvement, of caspases in male haploid cell maturation, calpains are the executioners of the death of terminally differentiating germ cells.
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Affiliation(s)
- M Coureuil
- Département de Radiobiologie et Radiopathologie (DRR), CEA/Institut Nationale de la Santé et de la Recherche Médicale Unité 566/Université Paris VII, 60 avenue du général Leclerc, BP6, Fontenay aux Roses Cedex 92265, France
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