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Abstract
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) - RNA-guided Cas9 endonuclease system has provided a fast and efficient method for precise genome editing in diverse mammalian species, including humans. The CRISPR/Cas9 technology allows generation of modifications into site-specific locations of the selected genes in one major step by carrying deletions, insertions or DNA donor-directed precise sequence modifications. Cas9 forms a nucleoprotein complex with a sequence-specific guide RNA to create double-stranded breaks in complementary DNA target. Further, double-stranded break repair machinery leads to the intended gene modifications. The CRISPR/Cas9 system is widely used technique for genome modification, editing and other biotechnology applications, such as functional annotation, a system for visualization of specific genomic loci and transcriptional control of genes. CRISPR/Cas9-mediated manipulation of the laboratory animal genomes has contributed to the understanding of gene functions and has become a popular approach for modeling human disorders. Furthermore, the growing application of CRISPR-Cas9 system to human genes emerges as an extremely powerful technology for the molecular characterization and treatment of human disease. In this review we present the essential principles of CRISPR/Cas9 technology and the recent advances in its use in translational biomedicine.
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Affiliation(s)
- Elena I Leonova
- Institute of Translational Biomedicine St. Petersburg State University, Saint Petersburg, Russia
- University of Science and Technology, Sochi, Russia,
| | - Raul R Gainetdinov
- Institute of Translational Biomedicine St. Petersburg State University, Saint Petersburg, Russia
- St. Petersburg State University Hospital, St. Petersburg State University, Saint Petersburg, Russia
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2
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Álvarez Ó, Fernández-Martínez JL, Corbeanu AC, Fernández-Muñiz Z, Kloczkowski A. Predicting protein tertiary structure and its uncertainty analysis via particle swarm sampling. J Mol Model 2019; 25:79. [PMID: 30810816 PMCID: PMC7586042 DOI: 10.1007/s00894-019-3956-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 02/05/2019] [Indexed: 10/27/2022]
Abstract
We discuss the relationship between the problem of protein tertiary structure prediction from the amino acid sequence and the uncertainty analysis. The algorithm presented in this paper belongs to the category of decoy-based modeling, where different known protein models are used to establish a low dimensional space via principal component analysis. The low dimensional space is utilized to perform an energy optimization via a family of very explorative particle swarm optimizers to find the global minimum. The aim of this procedure is to get a representative sample of the nonlinear equivalent region, that is, protein models that have their energy lower than a certain energy bound. The posterior analysis of this family provides very valuable information about the backbone structure of the native conformation and its possible alternate states. This methodology has the advantage of being simple and fast and can help refine the tertiary protein structure. We comprehensively illustrate the performance of our algorithm on one protein from the CASP-9 protein structure prediction experiment. We also provide a theoretical analysis of the energy landscape found in the tertiary structure protein inverse problem, explaining why model reduction techniques (principal component analysis in this case) serve to alleviate the ill-posed character of this high dimensional optimization problem. In addition, we expand the computational benchmark with a summary of other CASP-9 proteins in the Appendix.
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Affiliation(s)
- Óscar Álvarez
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo C. Federico García Lorca, 18, 33007, Oviedo, Spain
| | - Juan Luis Fernández-Martínez
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo C. Federico García Lorca, 18, 33007, Oviedo, Spain.
| | - Ana Cernea Corbeanu
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo C. Federico García Lorca, 18, 33007, Oviedo, Spain
| | - Zulima Fernández-Muñiz
- Group of Inverse Problems, Optimization and Machine Learning, Department of Mathematics, University of Oviedo C. Federico García Lorca, 18, 33007, Oviedo, Spain
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
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3
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Han J, Goldstein LA, Hou W, Chatterjee S, Burns TF, Rabinowich H. HSP90 inhibition targets autophagy and induces a CASP9-dependent resistance mechanism in NSCLC. Autophagy 2018; 14:958-971. [PMID: 29561705 PMCID: PMC6103412 DOI: 10.1080/15548627.2018.1434471] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Macroautophagy/autophagy has emerged as a resistance mechanism to anticancer drug treatments that induce metabolic stress. Certain tumors, including a subset of KRAS-mutant NSCLCs have been shown to be addicted to autophagy, and potentially vulnerable to autophagy inhibition. Currently, autophagy inhibition is being tested in the clinic as a therapeutic component for tumors that utilize this degradation process as a drug resistance mechanism. The current study provides evidence that HSP90 (heat shock protein 90) inhibition diminishes the expression of ATG7, thereby impeding the cellular capability of mounting an effective autophagic response in NSCLC cells. Additionally, an elevation in the expression level of CASP9 (caspase 9) prodomain in KRAS-mutant NSCLC cells surviving HSP90 inhibition appears to serve as a cell survival mechanism. Initial characterization of this survival mechanism suggests that the altered expression of CASP9 is mainly ATG7 independent; it does not involve the apoptotic activity of CASP9; and it localizes to a late endosomal and pre-lysosomal phase of the degradation cascade. HSP90 inhibitors are identified here as a pharmacological approach for targeting autophagy via destabilization of ATG7, while an induced expression of CASP9, but not its apoptotic activity, is identified as a resistance mechanism to the cellular stress brought about by HSP90 inhibition.
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Affiliation(s)
- Jie Han
- a Department of Pathology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Leslie A Goldstein
- a Department of Pathology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Wen Hou
- a Department of Pathology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Suman Chatterjee
- b Department of Medicine, Division of Hematology-Oncology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Timothy F Burns
- b Department of Medicine, Division of Hematology-Oncology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
| | - Hannah Rabinowich
- a Department of Pathology , University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute , Pittsburgh , PA , USA
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den Hamer A, Lemmens LJM, Nijenhuis MAD, Ottmann C, Merkx M, de Greef TFA, Brunsveld L. Small-Molecule-Induced and Cooperative Enzyme Assembly on a 14-3-3 Scaffold. Chembiochem 2017; 18:331-335. [PMID: 27897387 PMCID: PMC5299510 DOI: 10.1002/cbic.201600631] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 11/21/2016] [Indexed: 12/23/2022]
Abstract
Scaffold proteins regulate cell signalling by promoting the proximity of putative interaction partners. Although they are frequently applied in cellular settings, fundamental understanding of them in terms of, amongst other factors, quantitative parameters has been lagging behind. Here we present a scaffold protein platform that is based on the native 14-3-3 dimeric protein and is controllable through the action of a small-molecule compound, thus permitting study in an in vitro setting and mathematical description. Robust small-molecule regulation of caspase-9 activity through induced dimerisation on the 14-3-3 scaffold was demonstrated. The individual parameters of this system were precisely determined and used to develop a mathematical model of the scaffolding concept. This model was used to elucidate the strong cooperativity of the enzyme activation mediated by the 14-3-3 scaffold. This work provides an entry point for the long-needed quantitative insights into scaffold protein functioning and paves the way for the optimal use of reengineered 14-3-3 proteins as chemically inducible scaffolds in synthetic systems.
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Affiliation(s)
- Anniek den Hamer
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Minke A. D. Nijenhuis
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Christian Ottmann
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Maarten Merkx
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Luc Brunsveld
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
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5
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Bohnuud T, Luo L, Wodak SJ, Vajda S, Bonvin AM, Weng Z, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins 2017; 85:10-16. [PMID: 27172383 PMCID: PMC5817996 DOI: 10.1002/prot.25063] [Citation(s) in RCA: 25] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 05/08/2016] [Indexed: 12/20/2022]
Abstract
Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases. Proteins 2016; 85:10-16. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Tanggis Bohnuud
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Lingqi Luo
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Shoshana J. Wodak
- VIB Structural Biology Research Center, VUB Pleinlaan 2, 1050 Brussels
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Alexandre M.J.J. Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, 3584CH, the Netherlands
| | - Zhiping Weng
- Biochemistry and Molecular Pharmacology University of Massachusetts Medical School Worcester MA United States
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Department of Applied Mathematics and Statistics, Stony Brook University NY, USA
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Sawai H. Induction of Apoptosis in TNF-Treated L929 Cells in the Presence of Necrostatin-1. Int J Mol Sci 2016; 17:ijms17101678. [PMID: 27739412 PMCID: PMC5085711 DOI: 10.3390/ijms17101678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 08/03/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 12/20/2022] Open
Abstract
It has been shown that necroptosis—caspase-independent programmed necrotic cell death—can be induced by treatment with tumor necrosis factor (TNF) in the L929 murine fibrosarcoma cell line, even in the absence of a caspase inhibitor. Although it was reported that necrostatin-1—a specific inhibitor of necroptosis—inhibited TNF-induced necroptosis in L929 cells, it has not been elucidated whether the cells eventually die by apoptosis in the presence of necrostatin-1. In this paper, induction of apoptosis was demonstrated in TNF-treated L929 cells in the presence of necrostatin-1. Co-treatment with cycloheximide expedited apoptosis induction in necrostatin-1/TNF-treated L929 cells: typical apoptotic morphological changes, including membrane blebbing and nuclear fragmentation, induction of caspase-3 activity, proteolytic activation of caspases-3, -8, and -9, and cleavage of poly(ADP-ribose) polymerase (PARP) (a well-known substrate of caspase-3) were observed. Moreover, co-treatment with Z-VAD-fmk (a pan-caspase inhibitor) inhibited apoptosis by completely inhibiting caspases, resulting in a shift from apoptosis to necroptosis. In contrast, co-treatment with Z-Asp-CH2-DCB (a caspase inhibitor preferential to caspase-3) inhibited apoptosis without expediting necroptosis. These results indicate that apoptosis can be induced in TNF-treated L929 cells when the cells are protected from necroptosis, and support the notion that partial activation of caspase-8 in the presence of a caspase inhibitor preferential to caspase-3 suppresses both apoptosis and necroptosis.
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Affiliation(s)
- Hirofumi Sawai
- Department of Internal Medicine, Osaka Dental University, Hirakata 573-1121, Japan.
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7
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Kang YF, Qiao HX, Xin LZ, Ge LP. Chain elongation analog of resveratrol as potent cancer chemoprevention agent. J Physiol Biochem 2016; 72:445-52. [PMID: 27160168 DOI: 10.1007/s13105-016-0487-3] [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: 01/26/2016] [Accepted: 04/12/2016] [Indexed: 11/26/2022]
Abstract
Resveratrol is identified as a natural cancer chemoprevention agent. There has been a lot of interest in designing and developing resveratrol analogs with cancer chemoprevention activity superior to that of parent molecule and exploring their action mechanism in the past several decades. In this study, we have synthesized resveratrol analogs of compounds A-C via conjugated chain elongation based on isoprene unit retention strategy. Remarkably, cytotoxic activity analysis results indicated that compound B possesses the best proliferation inhibition activity for NCI-H460 cells in all the test compounds. Intriguingly, compound B displayed a higher cytotoxicity against human non-small cell lung cancer cells (NCI-H460) compared to normal human embryonic lung fibroblasts (MRC-5). Afterward, flow cytometry analysis showed that compound B would induce cell apoptosis. We further researched the action mechanism. When NCI-H460 cells were incubated by compound B for 6 or 9 h, respectively, the intracellular reactive oxygen species (ROS) level was enhanced obviously. With elevation of intracellular ROS level, flow cytometry measurement verified mitochondrial transmembrane potential collapse, which was accompanied by the up-regulation of Bax and down-regulation of Bcl-2. More interestingly, compound B increased the expression of caspase-9 and caspase-3, which induced cell apoptosis. Moreover, compound B arrested cell cycle in G0/G1 phase. These are all to provide useful information for designing resveratrol-based chemoprevention agent and understanding the action mechanism.
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Affiliation(s)
- Yan-Fei Kang
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou, 075000, Hebei Province, People's Republic of China.
| | - Hai-Xia Qiao
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou, 075000, Hebei Province, People's Republic of China
| | - Long-Zuo Xin
- College of Agriculture and Forestry Science and Technology, Hebei North University, Zhangjiakou, 075000, Hebei, China
| | - Li-Ping Ge
- College of Laboratory Medicine, Hebei North University, 11 Diamond Street South, Zhangjiakou, 075000, Hebei Province, People's Republic of China
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8
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Wang J, Luttrell J, Zhang N, Khan S, Shi N, Wang MX, Kang JQ, Wang Z, Xu D. Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling. Adv Exp Med Biol 2016; 939:39-61. [PMID: 27807743 PMCID: PMC6829626 DOI: 10.1007/978-981-10-1503-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia. Protein structure prediction and modeling were also applied in nucleotide-gated channels and their interaction interfaces to investigate their roles in brain and heart cells. In molecular mechanism studies of plants, rice salinity tolerance mechanism was studied via structure modeling on crucial proteins identified by systems biology analysis; trait-associated protein-protein interactions were modeled, which sheds some light on the roles of mutations in soybean oil/protein content. In the age of precision medicine, we believe protein structure prediction and modeling will play more and more important roles in investigating biomedical mechanism of diseases and drug design.
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Affiliation(s)
- Juexin Wang
- Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Joseph Luttrell
- School of Computing, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA
| | - Ning Zhang
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Saad Khan
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - NianQing Shi
- Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin, Room 8418, 1111 Highland Ave, Madison, WI, 53706, USA
| | - Michael X Wang
- Department of Pathology and Anatomical Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zheng Wang
- School of Computing, University of Southern Mississippi, 118 College Drive, Hattiesburg, MS, 39406, USA
| | - Dong Xu
- Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
- Informatics Institute, University of Missouri, Columbia, MO, 65211, USA.
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Yang G, Zhang W, Qin Q, Wang J, Zheng H, Xiong W, Yuan J. Mono(2-ethylhexyl) phthalate induces apoptosis in p53-silenced L02 cells via activation of both mitochondrial and death receptor pathways. Environ Toxicol 2015; 30:1178-1191. [PMID: 24706461 DOI: 10.1002/tox.21990] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 11/04/2013] [Revised: 03/21/2014] [Accepted: 03/23/2014] [Indexed: 06/03/2023]
Abstract
Mono(2-ethylhexyl) phthalate (MEHP) is one of the main metabolites of di(2-ethylhexyl) phthalate. The evidence shows that DEHP may exert its toxic effects primarily via MEHP, which is 10-fold more potent than its parent compound in toxicity in vitro. MEHP-induced apoptosis is mediated by either p53-dependent or -independent pathway. However, the detailed mechanism of its toxicity remains unclear. In this study, immortalized normal human liver cell line L02 was chosen, as an in vitro model of nonmalignant liver, to elucidate the role of p53 in MEHP-induced apoptosis. The cells were treated with MEHP (6.25, 12.50, 25.00, 50.00, and 100.00 μM) for 24 and 36 h, then small interfering RNA (siRNA) was used to specifically silence p53 gene of L02 cells. The results indicated that MEHP caused oxidative DNA damage and apoptosis in L02 cells were associated with the p53 signaling pathway. Further study found that MEHP (50.00 and 100.00 μM) induced apoptosis in p53-silenced L02 cells, along with the up-regulations of Fas and FasL proteins as well as increased the Bax/Bcl-2 ratio and Caspase 3, 8, and 9 activities. Additionally, both FasL inhibitor (AF-016) and Caspase inhibitor N-benzyloxycarbonyl-Val-Ala-Asp- fluoromethylketone (Z-VAD-FMK) could prevent the cell apoptosis induced by MEHP. The findings suggested that MEHP-induced apoptosis in L02 cells involving a Caspases-mediated mitochondrial signaling pathway and/or death receptor pathway. p53 was not absolutely necessary for MEHP-induced L02 cell apoptosis.
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Affiliation(s)
- Guangtao Yang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenjuan Zhang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Qizhi Qin
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Jing Wang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Hongyan Zheng
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Wei Xiong
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
| | - Jing Yuan
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, People's Republic of China
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10
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Shan H, Yan R, Diao J, Lin L, Wang S, Zhang M, Zhang R, Wei J. Involvement of caspases and their upstream regulators in myocardial apoptosis in a rat model of selenium deficiency-induced dilated cardiomyopathy. J Trace Elem Med Biol 2015; 31:85-91. [PMID: 26004897 DOI: 10.1016/j.jtemb.2015.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 02/24/2015] [Accepted: 03/24/2015] [Indexed: 12/19/2022]
Abstract
Keshan disease is an endemic dilated cardiomyopathy (DCM) which is closely related with selenium-deficient diet in China. In the previous study, we reported that the low selenium status plays a pivotal role in the myocardial apoptosis in the DCM rats, however, the underlying mechanism remains unclear. The present study aimed to determine whether the intrinsic, extrinsic pathways and the upstream regulators were involved in the myocardial apoptosis of selenium deficiency-induced DCM rats. Therefore, the rat model of endemic DCM was induced by a selenium-deficient diet for 12 weeks. Accompanied with significant dilation and impaired systolic function of left ventricle, an enhanced myocardial apoptosis was detected by TUNEL assay. Western blot analysis showed remarkably increased protein levels of cleaved caspase-3, caspase-8, caspase-9, and cytosolic cytochrome c released from the mitochondria. In addition, the immunoreactivities of p53 and Bax were significantly up-regulated, while the anti-apoptotic Bcl-2 family members Bcl-2 and Bcl-X(L) were down-regulated. Furthermore, appropriate selenium supplement for another 4 weeks could partially reverse all the above changes. In conclusion, the intrinsic, extrinsic pathways and the upstream regulators such as p53, Bax, Bcl-2, and Bcl-X(L )were all involved in selenium deficiency-induced myocardial apoptosis.
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Affiliation(s)
- Hu Shan
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Rui Yan
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Jiayu Diao
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Lin Lin
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China
| | - Suqin Wang
- Department of Cardiology, Henan Provincial People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, 450003, China
| | - Ming Zhang
- Key Laboratory of Trace Elements and Endemic Disease of Ministry of Health, Xi'an Jiaotong University School of Medicine, 76 Yantaxi Road, Xi'an, Shaanxi 710061, China
| | - Rong Zhang
- Key Laboratory of Trace Elements and Endemic Disease of Ministry of Health, Xi'an Jiaotong University School of Medicine, 76 Yantaxi Road, Xi'an, Shaanxi 710061, China
| | - Jin Wei
- Department of Cardiology, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China; Department of Endemic Disease, The Second Affiliated Hospital, Xi'an Jiaotong University School of Medicine, 157 Xiwu Road, Xi'an, Shaanxi 710004, China.
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11
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Manavalan B, Lee J, Lee J. Random forest-based protein model quality assessment (RFMQA) using structural features and potential energy terms. PLoS One 2014; 9:e106542. [PMID: 25222008 PMCID: PMC4164442 DOI: 10.1371/journal.pone.0106542] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 08/06/2014] [Indexed: 01/28/2023] Open
Abstract
Recently, predicting proteins three-dimensional (3D) structure from its sequence information has made a significant progress due to the advances in computational techniques and the growth of experimental structures. However, selecting good models from a structural model pool is an important and challenging task in protein structure prediction. In this study, we present the first application of random forest based model quality assessment (RFMQA) to rank protein models using its structural features and knowledge-based potential energy terms. The method predicts a relative score of a model by using its secondary structure, solvent accessibility and knowledge-based potential energy terms. We trained and tested the RFMQA method on CASP8 and CASP9 targets using 5-fold cross-validation. The correlation coefficient between the TM-score of the model selected by RFMQA (TMRF) and the best server model (TMbest) is 0.945. We benchmarked our method on recent CASP10 targets by using CASP8 and 9 server models as a training set. The correlation coefficient and average difference between TMRF and TMbest over 95 CASP10 targets are 0.984 and 0.0385, respectively. The test results show that our method works better in selecting top models when compared with other top performing methods. RFMQA is available for download from http://lee.kias.re.kr/RFMQA/RFMQA_eval.tar.gz.
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Affiliation(s)
- Balachandran Manavalan
- Center for In Silico Protein Science, School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Juyong Lee
- Center for In Silico Protein Science, School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
| | - Jooyoung Lee
- Center for In Silico Protein Science, School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea
- * E-mail:
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12
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Arrouss I, Nemati F, Roncal F, Wislez M, Dorgham K, Vallerand D, Rabbe N, Karboul N, Carlotti F, Bravo J, Mazier D, Decaudin D, Rebollo A. Specific targeting of caspase-9/PP2A interaction as potential new anti-cancer therapy. PLoS One 2013; 8:e60816. [PMID: 23637769 PMCID: PMC3634037 DOI: 10.1371/journal.pone.0060816] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 03/03/2013] [Indexed: 01/02/2023] Open
Abstract
PURPOSE PP2A is a serine/threonine phosphatase critical to physiological processes, including apoptosis. Cell penetrating peptides are molecules that can translocate into cells without causing membrane damage. Our goal was to develop cell-penetrating fusion peptides specifically designed to disrupt the caspase-9/PP2A interaction and evaluate their therapeutic potential in vitro and in vivo. EXPERIMENTAL DESIGN We generated a peptide containing a penetrating sequence associated to the interaction motif between human caspase-9 and PP2A (DPT-C9h), in order to target their association. Using tumour cell lines, primary human cells and primary human breast cancer (BC) xenografts, we investigated the capacity of DPT-C9h to provoke apoptosis in vitro and inhibition of tumour growth (TGI) in vivo. DPT-C9h was intraperitoneally administered at doses from 1 to 25 mg/kg/day for 5 weeks. Relative Tumour Volume (RTV) was calculated. RESULTS We demonstrated that DPT-C9h specifically target caspase-9/PP2A interaction in vitro and in vivo and induced caspase-9-dependent apoptosis in cancer cell lines. DPT-C9h also induced significant TGI in BC xenografts models. The mouse-specific peptide DPT-C9 also induced TGI in lung (K-Ras model) and breast cancer (PyMT) models. DPT-C9h has a specific effect on transformed B cells isolated from chronic lymphocytic leukemia patients without any effect on primary healthy cells. Finally, neither toxicity nor immunogenic responses were observed. CONCLUSION Using the cell-penetrating peptides blocking caspase-9/PP2A interactions, we have demonstrated that DPT-C9h had a strong therapeutic effect in vitro and in vivo in mouse models of tumour progression.
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Affiliation(s)
- Issam Arrouss
- Inserm UMRS 945, Hôpital Pitié Salpêtrière, Université Pierre et Marie Curie, Paris, France
| | - Fariba Nemati
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | - Fernando Roncal
- Centro Nacional de Biotecnologia, Campus de Cantoblanco, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marie Wislez
- URF Pierre et Marie Curie, Hôpital Tenon, Paris, France
| | - Karim Dorgham
- Inserm UMRS 945, Hôpital Pitié Salpêtrière, Université Pierre et Marie Curie, Paris, France
| | - David Vallerand
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | | | - Narjesse Karboul
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
| | - Françoise Carlotti
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeronimo Bravo
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
| | - Dominique Mazier
- Inserm UMRS 945, Hôpital Pitié Salpêtrière, Université Pierre et Marie Curie, Paris, France
| | - Didier Decaudin
- Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, Paris, France
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Angelita Rebollo
- Inserm UMRS 945, Hôpital Pitié Salpêtrière, Université Pierre et Marie Curie, Paris, France
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13
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Affiliation(s)
- Ken A Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794-5252, USA.
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14
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Bacardit J, Widera P, Márquez-Chamorro A, Divina F, Aguilar-Ruiz JS, Krasnogor N. Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features. Bioinformatics 2012; 28:2441-8. [PMID: 22833524 DOI: 10.1093/bioinformatics/bts472] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 11/12/2022] Open
Abstract
MOTIVATION The prediction of a protein's contact map has become in recent years, a crucial stepping stone for the prediction of the complete 3D structure of a protein. In this article, we describe a methodology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of a variety of structural aspects of protein residues, (ii) an ensemble strategy used to facilitate the training process and (iii) a rule-based machine learning system from which we can extract human-readable explanations of the predictor and derive useful information about the contact map representation. RESULTS The main part of the evaluation is the comparison against the sequence-based contact prediction methods from CASP9, where our method presented the best rank in five out of the six evaluated metrics. We also assess the impact of the size of the ensemble used in our predictor to show the trade-off between performance and training time of our method. Finally, we also study the rule sets generated by our machine learning system. From this analysis, we are able to estimate the contribution of the attributes in our representation and how these interact to derive contact predictions. AVAILABILITY http://icos.cs.nott.ac.uk/servers/psp.html. CONTACT natalio.krasnogor@nottingham.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jaume Bacardit
- Interdisciplinary Computing and Complex Systems research group, School of Computer Science, University of Nottingham, Nottingham, NG8 1BB, UK
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15
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Conus S, Pop C, Snipas SJ, Salvesen GS, Simon HU. Cathepsin D primes caspase-8 activation by multiple intra-chain proteolysis. J Biol Chem 2012; 287:21142-51. [PMID: 22528489 PMCID: PMC3375537 DOI: 10.1074/jbc.m111.306399] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [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: 09/21/2011] [Revised: 04/13/2012] [Indexed: 11/06/2022] Open
Abstract
During the resolution of inflammatory responses, neutrophils rapidly undergo apoptosis. A direct and fast activation of caspase-8 by cathepsin D was shown to be crucial in the initial steps of neutrophil apoptosis. Nevertheless, the activation mechanism of caspase-8 remains unclear. Here, by using site-specific mutants of caspase-8, we show that both cathepsin D-mediated proteolysis and homodimerization of caspase-8 are necessary to generate an active caspase-8. At acidic pH, cathepsin D specifically cleaved caspase-8 but not the initiator caspase-9 or -10 and significantly increased caspase-8 activity in dimerizing conditions. These events were completely abolished by pepstatin A, a pharmacological inhibitor of cathepsin D. The cathepsin D intra-chain proteolysis greatly stabilized the active site of caspase-8. Moreover, the main caspase-8 fragment generated by cathepsin D cleavage could be affinity-labeled with the active site probe biotin-VAD-fluoromethyl ketone, suggesting that this fragment is enzymatically active. Importantly, in an in vitro cell-free assay, the addition of recombinant human caspase-8 protein, pre-cleaved by cathepsin D, was followed by caspase-3 activation. Our data therefore indicate that cathepsin D is able to initiate the caspase cascade by direct activation of caspase-8. As cathepsin D is ubiquitously expressed, this may represent a general mechanism to induce apoptosis in a variety of immune and nonimmune cells.
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Affiliation(s)
- Sébastien Conus
- Institute of Pharmacology, University of Bern, CH-3010 Bern, Switzerland.
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16
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Huber K, Ghosh S, Hardy JA. Inhibition of caspase-9 by stabilized peptides targeting the dimerization interface. Biopolymers 2012; 98:451-65. [PMID: 23203690 PMCID: PMC3544179 DOI: 10.1002/bip.22080] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/29/2012] [Accepted: 04/04/2012] [Indexed: 11/09/2022]
Abstract
Caspases comprise a family of dimeric cysteine proteases that control apoptotic programmed cell death and are therefore critical in both organismal development and disease. Specific inhibition of individual caspases has been repeatedly attempted, but has not yet been attained. Caspase-9 is an upstream or initiator caspase that is regulated differently from all other caspases, as interaction with natural inhibitor X-linked inhibitor of apoptosis protein (XIAP)-baculovirus inhibitory repeat 3 (BIR3) occurs at the dimer interface maintaining caspase-9 in an inactive monomeric state. One route to caspase-9-specific inhibition is to mimic this interaction, which has been localized to the α5 helix of XIAP-BIR3. We have developed three types of stabilized peptides derived from the α5 helix, using incorporation of aminoisobutyric acid, the avian pancreatic polypeptide (aPP)-scaffold or aliphatic staples. The stabilized peptides are helical in solution and achieve up to 32 μM inhibition, indicating that this allosteric site at the caspase-9 dimerization interface is regulatable with low-molecular weight synthetic ligands and is thus a druggable site. The most potent peptides against caspase-9 activity are the aPP-scaffolded peptides. Other caspases, which are not regulated by dimerization, should not be inactivated by these peptides. Given that all of the peptides attain helical structures but cannot recapitulate the high-affinity inhibition of the intact BIR3 domain, it has become clear that interactions of caspase-9 with the BIR3 exosite are essential for high-affinity binding. These results explain why the full XIAP-BIR3 domain is required for maximal inhibition and suggest a path forward for achieving allosteric inhibition at the dimerization interface using peptides or small molecules.
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Affiliation(s)
- Kristen Huber
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | | | - Jeanne A. Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
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17
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Fisher AA, Labenski MT, Malladi S, Gokhale V, Bowen ME, Milleron RS, Bratton SB, Monks TJ, Lau SS. Quinone Electrophiles Selectively Adduct “Electrophile Binding Motifs” within Cytochrome c. Biochemistry 2007; 46:11090-100. [PMID: 17824617 DOI: 10.1021/bi700613w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrophiles generated endogenously, or via the metabolic bioactivation of drugs and other environmental chemicals, are capable of binding to a variety of nucleophilic sites within proteins. Factors that determine site selective susceptibility to electrophile-mediated post-translational modifications, and the consequences of such alterations, remain largely unknown. To identify and characterize chemical-mediated protein adducts, electrophiles with known toxicity were utilized. Hydroquinone, and its mercapturic acid pathway metabolites, cause renal proximal tubular cell necrosis and nephrocarcinogenicity in rats. The adverse effects of HQ and its thioether metabolites are in part a consequence of their oxidation to the corresponding electrophilic 1,4-benzoquinones (BQ). We now report that BQ and 2-(N-acetylcystein-S-yl)benzoquinone (NAC-BQ) preferentially bind to solvent-exposed lysine-rich regions within cytochrome c. Furthermore, we have identified specific glutamic acid residues within cytochrome c as novel sites of NAC-BQ adduction. The microenvironment at the site of adduction governs both the initial specificity and the structure of the final adduct. The solvent accessibility and local pKa of the adducted and neighboring amino acids contribute to the selectivity of adduction. Postadduction chemistry subsequently alters the nature of the final adduct. Using molecular modeling, the impact of BQ and NAC-BQ adduction on cytochrome c was visualized, revealing the spatial rearrangement of critical residues necessary for protein-protein interactions. Consequently, BQ-adducted cytochrome c fails to initiate caspase-3 activation in native lysates and also inhibits Apaf-1 oligomerization into an apoptosome complex in a purely reconstituted system. In summary, a combination of mass spectroscopic, molecular modeling, and biochemical approaches confirms that electrophile-protein adducts produce structural alterations that influence biological function.
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Affiliation(s)
- Ashley A Fisher
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, Tucson, Arizona 85721, USA
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18
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Gao Z, Tian Y, Wang J, Yin Q, Wu H, Li YM, Jiang X. A dimeric Smac/diablo peptide directly relieves caspase-3 inhibition by XIAP. Dynamic and cooperative regulation of XIAP by Smac/Diablo. J Biol Chem 2007; 282:30718-27. [PMID: 17724022 PMCID: PMC3202417 DOI: 10.1074/jbc.m705258200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Caspase activation, the executing event of apoptosis, is under deliberate regulation. IAP proteins inhibit caspase activity, whereas Smac/Diablo antagonizes IAP. XIAP, a ubiquitous IAP, can inhibit both caspase-9, the initiator caspase of the mitochondrial apoptotic pathway, and the downstream effector caspases, caspase-3 and caspase-7. Smac neutralizes XIAP inhibition of caspase-9 by competing for binding of the BIR3 domain of XIAP with caspase-9, whereas how Smac liberates effector caspases from XIAP inhibition is not clear. It is generally believed that binding of Smac with IAP generates a steric hindrance that prevents XIAP from inhibiting effector caspases, and therefore small molecule mimics of Smac are not able to reverse inhibition of the effector caspases. Surprisingly, we show here that binding of a dimeric Smac N-terminal peptide with the BIR2 domain of XIAP effectively antagonizes inhibition of caspase-3 by XIAP. Further, we defined the dynamic and cooperative interaction of Smac with XIAP: binding of Smac with the BIR3 domain anchors the subsequent binding of Smac with the BIR2 domain, which in turn attenuates the caspase-3 inhibitory function of XIAP. We also show that XIAP homotrimerizes via its C-terminal Ring domain, making its inhibitory activity toward caspase-3 more susceptible to Smac.
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Affiliation(s)
- Zhonghua Gao
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
| | - Yuan Tian
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
| | - Junru Wang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
| | - Qian Yin
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
- Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021
| | - Hao Wu
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
- Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021
| | - Yue-Ming Li
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
| | - Xuejun Jiang
- Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021
- Graduate School of Biomedical Sciences, Weill Medical College of Cornell University, New York, NY 10021
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Allan LA, Clarke PR. Phosphorylation of caspase-9 by CDK1/cyclin B1 protects mitotic cells against apoptosis. Mol Cell 2007; 26:301-10. [PMID: 17466630 DOI: 10.1016/j.molcel.2007.03.019] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 12/08/2006] [Accepted: 03/16/2007] [Indexed: 10/23/2022]
Abstract
Proliferating metazoan cells respond to damage that has the potential to cause genomic instability by restricting the cell division cycle or by initiating apoptosis. The molecular mechanisms determining the balance between these responses are not well understood. Here, we show that the apoptotic initiator protease caspase-9 is regulated during the cell cycle through periodic phosphorylation at an inhibitory site, Thr125. This site is phosphorylated by CDK1/cyclin B1 during mitosis and in response to microtubule poisons that arrest cells at this stage of the cell cycle. Using an RNA interference strategy, we show that induction of apoptosis from mitosis in response to these drugs is caspase-9 dependent and is greatly increased when endogenous caspase-9 is replaced by a nonphosphorylatable mutant. Thus, phosphorylation of caspase-9 at Thr125 sets the threshold for activation of the intrinsic apoptotic pathway during the cell cycle, restrains apoptosis during mitosis, and determines sensitivity to antimitotic drugs.
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Affiliation(s)
- Lindsey A Allan
- Biomedical Research Centre, Level 5, Ninewells Hospital and Medical School, University of Dundee, Dundee, Scotland, UK
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20
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Reis MIR, do Vale A, Pinto C, Nascimento DS, Costa-Ramos C, Silva DSP, Silva MT, Dos Santos NMS. First molecular cloning and characterisation of caspase-9 gene in fish and its involvement in a gram negative septicaemia. Mol Immunol 2006; 44:1754-64. [PMID: 16989898 DOI: 10.1016/j.molimm.2006.07.293] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Revised: 07/14/2006] [Accepted: 07/20/2006] [Indexed: 12/18/2022]
Abstract
Caspase-9 is an initiator caspase in the apoptotic process whose function is to activate effector caspases that are downstream in the mitochondrial pathway of apoptosis. This work reports for the first time the complete sequencing and characterisation of caspase-9 in fish. A 1924bp cDNA of sea bass caspase-9 was obtained, consisting of 1308bp open reading frame coding for 435 amino acids, 199bp of the 5'-UTR and 417bp of the 3'-UTR including a canonical polyadenilation signal 10 nucleotides upstream the polyadenilation tail. The sequence retains the pentapeptide active-site motif (QACGG) and the putative cleavage sites at Asp(121), Asp(325) and Asp(343). The sequence of sea bass caspase-9 exhibits a very close homology to the sequences of caspase-9 from other vertebrates, particularly with the putative caspases-9 of Danio rerio and Tetraodon nigroviridis (77.5 and 75.4% similarity, respectively), justifying the fact that the phylogenetic analysis groups these species together with sea bass. The sea bass caspase-9 gene exists as a single copy gene and is organised in 9 introns and 10 exons. The sea bass caspase-9 showed a basal expression in all the organs analysed, although weaker in spleen. The expression of sea bass caspase-9 in the head kidney of sea bass infected with the Photobacterium damselae ssp. piscicida (Phdp) strain PP3, showed increased expression from 0 to 12h returning to control levels at 24h. Caspase-9 activity was detected in Phdp infected sea bass head kidney from 18 to 48h post-infection, when the fish were with advanced septicaemia.
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Affiliation(s)
- Marta I R Reis
- Fish Immunology and Vaccinology, IBMC-Instituto de Biologia Molecular e Celular, R. do Campo Alegre 823, 4150-180 Porto, Portugal
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