1
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Nguyen D, Osterlund E, Kale J, Andrews DW. The C-terminal sequences of Bcl-2 family proteins mediate interactions that regulate cell death. Biochem J 2024; 481:903-922. [PMID: 38985308 DOI: 10.1042/bcj20210352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024]
Abstract
Programmed cell death via the both intrinsic and extrinsic pathways is regulated by interactions of the Bcl-2 family protein members that determine whether the cell commits to apoptosis via mitochondrial outer membrane permeabilization (MOMP). Recently the conserved C-terminal sequences (CTSs) that mediate localization of Bcl-2 family proteins to intracellular membranes, have been shown to have additional protein-protein binding functions that contribute to the functions of these proteins in regulating MOMP. Here we review the pivotal role of CTSs in Bcl-2 family interactions including: (1) homotypic interactions between the pro-apoptotic executioner proteins that cause MOMP, (2) heterotypic interactions between pro-apoptotic and anti-apoptotic proteins that prevent MOMP, and (3) heterotypic interactions between the pro-apoptotic executioner proteins and the pro-apoptotic direct activator proteins that promote MOMP.
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Affiliation(s)
- Dang Nguyen
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
- Biological Sciences Platform, Odette Cancer Program, Sunnybrook Research Institute, Toronto, Canada
| | - Elizabeth Osterlund
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Science, McMaster University, Hamilton, Canada
| | - Justin Kale
- Biological Sciences Platform, Odette Cancer Program, Sunnybrook Research Institute, Toronto, Canada
| | - David W Andrews
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Canada
- Biological Sciences Platform, Odette Cancer Program, Sunnybrook Research Institute, Toronto, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Canada
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2
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Subas Satish HP, Iyer S, Shi MX, Wong AW, Fischer KC, Wardak AZ, Lio D, Brouwer JM, Uren RT, Czabotar PE, Miller MS, Kluck RM. A novel inhibitory BAK antibody enables assessment of non-activated BAK in cancer cells. Cell Death Differ 2024; 31:711-721. [PMID: 38582955 PMCID: PMC11164899 DOI: 10.1038/s41418-024-01289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024] Open
Abstract
BAX and BAK are pro-apoptotic members of the BCL2 family that are required to permeabilize the mitochondrial outer membrane. The proteins can adopt a non-activated monomeric conformation, or an activated conformation in which the exposed BH3 domain facilitates binding either to a prosurvival protein or to another activated BAK or BAX protein to promote pore formation. Certain cancer cells are proposed to have high levels of activated BAK sequestered by MCL1 or BCLXL, thus priming these cells to undergo apoptosis in response to BH3 mimetic compounds that target MCL1 or BCLXL. Here we report the first antibody, 14G6, that is specific for the non-activated BAK conformer. A crystal structure of 14G6 Fab bound to BAK revealed a binding site encompassing both the α1 helix and α5-α6 hinge regions of BAK, two sites involved in the unfolding of BAK during its activation. In mitochondrial experiments, 14G6 inhibited BAK unfolding triggered by three diverse BAK activators, supporting crucial roles for both α1 dissociation and separation of the core (α2-α5) and latch (α6-α9) regions in BAK activation. 14G6 bound the majority of BAK in several leukaemia cell lines, and binding decreased following treatment with BH3 mimetics, indicating only minor levels of constitutively activated BAK in those cells. In summary, 14G6 provides a new means of assessing BAK status in response to anti-cancer treatments.
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Affiliation(s)
- Hema Preethi Subas Satish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Sweta Iyer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Melissa X Shi
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Agnes W Wong
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Karla C Fischer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ahmad Z Wardak
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daisy Lio
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jason M Brouwer
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rachel T Uren
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michelle S Miller
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Ruth M Kluck
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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3
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Miller MS, Cowan AD, Brouwer JM, Smyth ST, Peng L, Wardak AZ, Uren RT, Luo C, Roy MJ, Shah S, Tan Z, Reid GE, Colman PM, Czabotar PE. Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids. FEBS J 2024; 291:2335-2353. [PMID: 38088212 DOI: 10.1111/febs.17031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/07/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
The B-cell lymphoma 2 (BCL2) family members, BCL2-associated protein X (BAX) and BCL2 homologous antagonist killer (BAK), are required for programmed cell death via the mitochondrial pathway. When cells are stressed, damaged or redundant, the balance of power between the BCL2 family of proteins shifts towards BAX and BAK, allowing their transition from an inactive, monomeric state to a membrane-active oligomeric form that releases cytochrome c from the mitochondrial intermembrane space. That oligomeric state has an essential intermediate, a symmetric homodimer of BAX or BAK. Here we describe crystal structures of dimers of the core domain of BAX, comprising its helices α2-α5. These structures provide an atomic resolution description of the interactions that drive BAX homo-dimerisation and insights into potential interaction between core domain dimers and membrane lipids. The previously identified BAK lipid-interacting sites are not conserved with BAX and are likely to determine the differences between them in their interactions with lipids. We also describe structures of heterodimers of BAK/BAX core domains, yielding further insight into the differences in lipid binding between BAX and BAK.
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Affiliation(s)
- Michelle S Miller
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Angus D Cowan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Jason M Brouwer
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Sean T Smyth
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Liuyu Peng
- School of Chemistry, University of Melbourne, Parkville, Vic., Australia
| | - Ahmad Z Wardak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Rachel T Uren
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Cindy Luo
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Michael J Roy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Sayali Shah
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Ziwen Tan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Gavin E Reid
- School of Chemistry, University of Melbourne, Parkville, Vic., Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Vic., Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Peter M Colman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
- Department of Medical Biology, University of Melbourne, Parkville, Vic., Australia
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4
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Zhang Z, Hou L, Liu D, Luan S, Huang M, Zhao L. Directly targeting BAX for drug discovery: Therapeutic opportunities and challenges. Acta Pharm Sin B 2024; 14:2378-2401. [PMID: 38828138 PMCID: PMC11143528 DOI: 10.1016/j.apsb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 06/05/2024] Open
Abstract
For over two decades, the development of B-cell lymphoma-2 (Bcl-2) family therapeutics has primarily focused on anti-apoptotic proteins, resulting in the first-in-class drugs called BH3 mimetics, especially for Bcl-2 inhibitor Venetoclax. The pro-apoptotic protein Bcl-2-associated X protein (BAX) plays a crucial role as the executioner protein of the mitochondrial regulated cell death, contributing to organismal development, tissue homeostasis, and immunity. The dysregulation of BAX is closely associated with the onset and progression of diseases characterized by pathologic cell survival or death, such as cancer, neurodegeneration, and heart failure. In addition to conducting thorough investigations into the physiological modulation of BAX, research on the regulatory mechanisms of small molecules identified through biochemical screening approaches has prompted the identification of functional and potentially druggable binding sites on BAX, as well as diverse all-molecule BAX modulators. This review presents recent advancements in elucidating the physiological and pharmacological modulation of BAX and in identifying potentially druggable binding sites on BAX. Furthermore, it highlights the structural and mechanistic insights into small-molecule modulators targeting diverse binding surfaces or conformations of BAX, offering a promising avenue for developing next-generation apoptosis modulators to treat a wide range of diseases associated with dysregulated cell death by directly targeting BAX.
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Affiliation(s)
- Zhenwei Zhang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Linghui Hou
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Dan Liu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Shenglin Luan
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd., Shenzhen 518000, China
| | - Min Huang
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Linxiang Zhao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
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5
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Yuan Z, van Delft MF, Li MX, Sumardy F, Smith BJ, Huang DCS, Lessene G, Khakam Y, Jin R, He S, Smith NA, Birkinshaw RW, Czabotar PE, Dewson G. Key residues in the VDAC2-BAK complex can be targeted to modulate apoptosis. PLoS Biol 2024; 22:e3002617. [PMID: 38696533 PMCID: PMC11098506 DOI: 10.1371/journal.pbio.3002617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/16/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024] Open
Abstract
BAK and BAX execute intrinsic apoptosis by permeabilising the mitochondrial outer membrane. Their activity is regulated through interactions with pro-survival BCL-2 family proteins and with non-BCL-2 proteins including the mitochondrial channel protein VDAC2. VDAC2 is important for bringing both BAK and BAX to mitochondria where they execute their apoptotic function. Despite this important function in apoptosis, while interactions with pro-survival family members are well characterised and have culminated in the development of drugs that target these interfaces to induce cancer cell apoptosis, the interaction between BAK and VDAC2 remains largely undefined. Deep scanning mutagenesis coupled with cysteine linkage identified key residues in the interaction between BAK and VDAC2. Obstructive labelling of specific residues in the BH3 domain or hydrophobic groove of BAK disrupted this interaction. Conversely, mutating specific residues in a cytosol-exposed region of VDAC2 stabilised the interaction with BAK and inhibited BAK apoptotic activity. Thus, this VDAC2-BAK interaction site can potentially be targeted to either inhibit BAK-mediated apoptosis in scenarios where excessive apoptosis contributes to disease or to promote BAK-mediated apoptosis for cancer therapy.
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Affiliation(s)
- Zheng Yuan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Mark F. van Delft
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Mark Xiang Li
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Australia
| | - Fransisca Sumardy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - David C. S. Huang
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Guillaume Lessene
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, Melbourne, Australia
| | - Yelena Khakam
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
| | - Ruitao Jin
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
- Research School of Biology, Australian National University, Canberra, Australia
| | - Sitong He
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Richard W. Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Peter E. Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Australia
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6
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Lim D, Jeong DE, Shin HC, Choi JS, Seo J, Kim SJ, Ku B. Crystal structure of Bak bound to the BH3 domain of Bnip5, a noncanonical BH3 domain-containing protein. Proteins 2024; 92:44-51. [PMID: 37553948 DOI: 10.1002/prot.26568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/10/2023]
Abstract
The activation or inactivation of B-cell lymphoma-2 (Bcl-2) antagonist/killer (Bak) is critical for controlling mitochondrial outer membrane permeabilization-dependent apoptosis. Its pro-apoptotic activity is controlled by intermolecular interactions with the Bcl-2 homology 3 (BH3) domain, which is accommodated in the hydrophobic pocket of Bak. Bcl-2-interacting protein 5 (Bnip5) is a noncanonical BH3 domain-containing protein that interacts with Bak. Bnip5 is characterized by its controversial effects on the regulation of the pro-apoptotic activity of Bak. In the present study, we determined the crystal structure of Bak bound to Bnip5 BH3. The intermolecular association appeared to be typical at first glance, but we found that it is maintained by tight hydrophobic interactions together with hydrogen/ionic bonds, which accounts for their high binding affinity with a dissociation constant of 775 nM. Structural analysis of the complex showed that Bnip5 interacts with Bak in a manner similar to that of the Bak-activating pro-apoptotic factor peroxisomal testis-enriched protein 1, particularly in the destabilization of the intramolecular electrostatic network of Bak. Our structure is considered to reflect the initial point of drastic and consecutive conformational and stoichiometric changes in Bak induced by Bnip5 BH3, which helps in explaining the effects of Bnip5 in regulating Bak-mediated apoptosis.
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Affiliation(s)
- Dahwan Lim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biochemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Da Eun Jeong
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Ho-Chul Shin
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Joon Sig Choi
- Department of Biochemistry, Chungnam National University, Daejeon, Republic of Korea
| | - Jinho Seo
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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7
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Dehghan S, Kheshtchin N, Hassannezhad S, Soleimani M. Cell death classification: A new insight based on molecular mechanisms. Exp Cell Res 2023; 433:113860. [PMID: 38013091 DOI: 10.1016/j.yexcr.2023.113860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 11/29/2023]
Abstract
Cells tend to disintegrate themselves or are forced to undergo such destructive processes in critical circumstances. This complex cellular function necessitates various mechanisms and molecular pathways in order to be executed. The very nature of cell death is essentially important and vital for maintaining homeostasis, thus any type of disturbing occurrence might lead to different sorts of diseases and dysfunctions. Cell death has various modalities and yet, every now and then, a new type of this elegant procedure gets to be discovered. The diversity of cell death compels the need for a universal organizing system in order to facilitate further studies, therapeutic strategies and the invention of new methods of research. Considering all that, we attempted to review most of the known cell death mechanisms and sort them all into one arranging system that operates under a simple but subtle decision-making (If \ Else) order as a sorting algorithm, in which it decides to place and sort an input data (a type of cell death) into its proper set, then a subset and finally a group of cell death. By proposing this algorithm, the authors hope it may solve the problems regarding newer and/or undiscovered types of cell death and facilitate research and therapeutic applications of cell death.
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Affiliation(s)
- Sepehr Dehghan
- Department of Medical Basic Sciences, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nasim Kheshtchin
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Maryam Soleimani
- Department of Medical Basic Sciences, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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8
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Cheng P, Hou Y, Bian M, Fang X, Liu Y, Rao Y, Cao S, Liu Y, Zhang S, Chen Y, Dong X, Liu Z. Parkin-mediated ubiquitination inhibits BAK apoptotic activity by blocking its canonical hydrophobic groove. Commun Biol 2023; 6:1260. [PMID: 38087033 PMCID: PMC10716173 DOI: 10.1038/s42003-023-05650-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BAK permeabilizes the mitochondrial outer membrane, causing apoptosis. This apoptotic activity of BAK is stimulated by binding prodeath activators within its canonical hydrophobic groove. Parkin, an E3 ubiquitin (Ub) ligase, can ubiquitinate BAK, which inhibits BAK apoptotic activity. However, the molecular mechanism underlying the inhibition of ubiquitination remains structurally uncharacterized. Here, we utilize truncated and soluble BAK to construct a mimetic of K113-ubiquitinated BAK (disulfide-linked UbG76C ~ BAKK113C) and further present its NMR-derived structure model. The classical L8-I44-H68-V70 hydrophobic patch of the conjugated Ub subunit binds within the canonical hydrophobic groove of BAK. This Ub occludes the binding of prodeath BID activators in the groove and impairs BID-triggered BAK activation and membrane permeabilization. Reduced interaction between Ub and BAK subunits allows BID to activate K113-ubiquitinated BAK. These mechanistic insights suggest a nonsignaling function of Ub in that it directly antagonizes stimuli targeting Ub-modified proteins rather than by recruiting downstream partners for cellular messaging.
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Affiliation(s)
- Peng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuzhu Hou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingxing Bian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xueru Fang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuanfang Rao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuo Cao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanjun Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuai Zhang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yanke Chen
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xu Dong
- Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, 430074, China.
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
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9
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King LE, Hohorst L, García-Sáez AJ. Expanding roles of BCL-2 proteins in apoptosis execution and beyond. J Cell Sci 2023; 136:jcs260790. [PMID: 37994778 DOI: 10.1242/jcs.260790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
The proteins of the BCL-2 family are known as key regulators of apoptosis, with interactions between family members determining permeabilisation of the mitochondrial outer membrane (MOM) and subsequent cell death. However, the exact mechanism through which they form the apoptotic pore responsible for MOM permeabilisation (MOMP), the structure and specific components of this pore, and what roles BCL-2 proteins play outside of directly regulating MOMP are incompletely understood. Owing to the link between apoptosis dysregulation and disease, the BCL-2 proteins are important targets for drug development. With the development and clinical use of drugs targeting BCL-2 proteins showing success in multiple haematological malignancies, enhancing the efficacy of these drugs, or indeed developing novel drugs targeting BCL-2 proteins is of great interest to treat cancer patients who have developed resistance or who suffer other disease types. Here, we review our current understanding of the molecular mechanism of MOMP, with a particular focus on recently discovered roles of BCL-2 proteins in apoptosis and beyond, and discuss what implications these functions might have in both healthy tissues and disease.
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Affiliation(s)
- Louise E King
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne 50931, Germany
| | - Lisa Hohorst
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne 50931, Germany
| | - Ana J García-Sáez
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne 50931, Germany
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10
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Czabotar PE, Garcia-Saez AJ. Mechanisms of BCL-2 family proteins in mitochondrial apoptosis. Nat Rev Mol Cell Biol 2023; 24:732-748. [PMID: 37438560 DOI: 10.1038/s41580-023-00629-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/14/2023]
Abstract
The proteins of the BCL-2 family are key regulators of mitochondrial apoptosis, acting as either promoters or inhibitors of cell death. The functional interplay and balance between the opposing BCL-2 family members control permeabilization of the outer mitochondrial membrane, leading to the release of activators of the caspase cascade into the cytosol and ultimately resulting in cell death. Despite considerable research, our knowledge about the mechanisms of the BCL-2 family of proteins remains insufficient, which complicates cell fate predictions and does not allow us to fully exploit these proteins as targets for drug discovery. Detailed understanding of the formation and molecular architecture of the apoptotic pore in the outer mitochondrial membrane remains a holy grail in the field, but new studies allow us to begin constructing a structural model of its arrangement. Recent literature has also revealed unexpected activities for several BCL-2 family members that challenge established concepts of how they regulate mitochondrial permeabilization. In this Review, we revisit the most important advances in the field and integrate them into a new structure-function-based classification of the BCL-2 family members that intends to provide a comprehensive model for BCL-2 action in apoptosis. We close this Review by discussing the potential of drugging the BCL-2 family in diseases characterized by aberrant apoptosis.
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Affiliation(s)
- Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Ana J Garcia-Saez
- Membrane Biophysics, Institute of Genetics, CECAD, University of Cologne, Cologne, Germany.
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11
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Wei H, Wang H, Wang G, Qu L, Jiang L, Dai S, Chen X, Zhang Y, Chen Z, Li Y, Guo M, Chen Y. Structures of p53/BCL-2 complex suggest a mechanism for p53 to antagonize BCL-2 activity. Nat Commun 2023; 14:4300. [PMID: 37463921 DOI: 10.1038/s41467-023-40087-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Mitochondrial apoptosis is strictly controlled by BCL-2 family proteins through a subtle network of protein interactions. The tumor suppressor protein p53 triggers transcription-independent apoptosis through direct interactions with BCL-2 family proteins, but the molecular mechanism is not well understood. In this study, we present three crystal structures of p53-DBD in complex with the anti-apoptotic protein BCL-2 at resolutions of 2.3-2.7 Å. The structures show that two loops of p53-DBD penetrate directly into the BH3-binding pocket of BCL-2. Structure-based mutations at the interface impair the p53/BCL-2 interaction. Specifically, the binding sites for p53 and the pro-apoptotic protein Bax in the BCL-2 pocket are mostly identical. In addition, formation of the p53/BCL-2 complex is negatively correlated with the formation of BCL-2 complexes with pro-apoptotic BCL-2 family members. Defects in the p53/BCL-2 interaction attenuate p53-mediated cell apoptosis. Overall, our study provides a structural basis for the interaction between p53 and BCL-2, and suggests a molecular mechanism by which p53 regulates transcription-independent apoptosis by antagonizing the interaction of BCL-2 with pro-apoptotic BCL-2 family members.
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Affiliation(s)
- Hudie Wei
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Haolan Wang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Genxin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Lingzhi Qu
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Longying Jiang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuyan Dai
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaojuan Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ye Zhang
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhuchu Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Youjun Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430072, China
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Wuhan University, Wuhan, 430071, China
| | - Ming Guo
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Yongheng Chen
- Department of Oncology, NHC Key Laboratory of Cancer Proteomics & State Local Joint Engineering Laboratroy for Anticancer Drugs, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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12
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Chen M, Hu L, Bao X, Ye K, Li Y, Zhang Z, Kaufmann SH, Xiao J, Dai H. Eltrombopag directly activates BAK and induces apoptosis. Cell Death Dis 2023; 14:394. [PMID: 37393297 PMCID: PMC10314921 DOI: 10.1038/s41419-023-05918-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 06/10/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Small molecule direct BAK activators can potentially be used for the development of anti-cancer drugs or as tools to study BAK activation. The thrombopoietin receptor agonist eltrombopag (Eltro) inhibits BAX activation and BAX-mediated apoptosis. Here we report that, in contrast to its function as a BAX inhibitor, Eltro directly binds BAK but induces its activation in vitro. Moreover, Eltro induces or sensitizes BAK-dependent cell death in mouse embryonic fibroblasts (MEFs) and Jurkat cells. Chemical shift perturbation analysis by NMR indicates that Eltro binds to the BAK α4/α6/α7 groove to initiate BAK activation. Further molecular docking by HADDOCK suggests that several BAK residues, including R156, F157, and H164, play an important role in the interaction with Eltro. The introduction of an R156E mutation in the BAK α4/α6/α7 groove not only decreases Eltro binding and Eltro-induced BAK activation in vitro but also diminishes Eltro-induced apoptosis. Thus, our data suggest that Eltro directly induces BAK activation and BAK-dependent apoptosis, providing a starting point for the future development of more potent and selective direct BAK activators.
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Affiliation(s)
- Meng Chen
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- University of Science and Technology of China, Hefei, 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Lei Hu
- School of Preclinical Medicine, Wannan Medical College, Wuhu, 241002, China
| | - Xuyuan Bao
- Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiqin Ye
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yunjian Li
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Zhiyong Zhang
- Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jun Xiao
- Department of Urology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
| | - Haiming Dai
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
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13
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Lim D, Choe SH, Jin S, Lee S, Kim Y, Shin HC, Choi JS, Oh DB, Kim SJ, Seo J, Ku B. Structural basis for proapoptotic activation of Bak by the noncanonical BH3-only protein Pxt1. PLoS Biol 2023; 21:e3002156. [PMID: 37315086 DOI: 10.1371/journal.pbio.3002156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Bak is a critical executor of apoptosis belonging to the Bcl-2 protein family. Bak contains a hydrophobic groove where the BH3 domain of proapoptotic Bcl-2 family members can be accommodated, which initiates its activation. Once activated, Bak undergoes a conformational change to oligomerize, which leads to mitochondrial destabilization and the release of cytochrome c into the cytosol and eventual apoptotic cell death. In this study, we investigated the molecular aspects and functional consequences of the interaction between Bak and peroxisomal testis-specific 1 (Pxt1), a noncanonical BH3-only protein exclusively expressed in the testis. Together with various biochemical approaches, this interaction was verified and analyzed at the atomic level by determining the crystal structure of the Bak-Pxt1 BH3 complex. In-depth biochemical and cellular analyses demonstrated that Pxt1 functions as a Bak-activating proapoptotic factor, and its BH3 domain, which mediates direct intermolecular interaction with Bak, plays a critical role in triggering apoptosis. Therefore, this study provides a molecular basis for the Pxt1-mediated novel pathway for the activation of apoptosis and expands our understanding of the cell death signaling coordinated by diverse BH3 domain-containing proteins.
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Affiliation(s)
- Dahwan Lim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - So-Hui Choe
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sein Jin
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Seulgi Lee
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Younjin Kim
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Ho-Chul Shin
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Joon Sig Choi
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Doo-Byoung Oh
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Korea
| | - Jinho Seo
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Korea
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14
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Flores-Romero H, Dadsena S, García-Sáez AJ. Mitochondrial pores at the crossroad between cell death and inflammatory signaling. Mol Cell 2023; 83:843-856. [PMID: 36931255 DOI: 10.1016/j.molcel.2023.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 03/18/2023]
Abstract
Mitochondria are cellular organelles with a major role in many cellular processes, including not only energy production, metabolism, and calcium homeostasis but also regulated cell death and innate immunity. Their proteobacterial origin makes them a rich source of potent immune agonists, normally hidden within the mitochondrial membrane barriers. Alteration of mitochondrial permeability through mitochondrial pores thus provides efficient mechanisms not only to communicate mitochondrial stress to the cell but also as a key event in the integration of cellular responses. In this regard, eukaryotic cells have developed diverse signaling networks that sense and respond to the release of mitochondrial components into the cytosol and play a key role in controlling cell death and inflammatory pathways. Modulating pore formation at mitochondria through direct or indirect mechanisms may thus open new opportunities for therapy. In this review, we discuss the current understanding of the structure and molecular mechanisms of mitochondrial pores and how they function at the interface between cell death and inflammatory signaling to regulate cellular outcomes.
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Affiliation(s)
- Hector Flores-Romero
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Shashank Dadsena
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany
| | - Ana J García-Sáez
- Institute for Genetics, CECAD Research Center, University of Cologne, Cologne, Germany.
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15
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Gonzalo Ó, Benedi A, Vela L, Anel A, Naval J, Marzo I. Study of the Bcl-2 Interactome by BiFC Reveals Differences in the Activation Mechanism of Bax and Bak. Cells 2023; 12:cells12050800. [PMID: 36899936 PMCID: PMC10000386 DOI: 10.3390/cells12050800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Evasion of apoptosis is one of the hallmarks of cancer cells. Proteins of the Bcl-2 family are key regulators of the intrinsic pathway of apoptosis, and alterations in some of these proteins are frequently found in cancer cells. Permeabilization of the outer mitochondrial membrane, regulated by pro- and antiapoptotic members of the Bcl-2 family of proteins, is essential for the release of apoptogenic factors leading to caspase activation, cell dismantlement, and death. Mitochondrial permeabilization depends on the formation of oligomers of the effector proteins Bax and Bak after an activation event mediated by BH3-only proteins and regulated by antiapoptotic members of the Bcl-2 family. In the present work, we have studied interactions between different members of the Bcl-2 family in living cells via the BiFC technique. Despite the limitations of this technique, present data suggest that native proteins of the Bcl-2 family acting inside living cells establish a complex network of interactions, which would fit nicely into "mixed" models recently proposed by others. Furthermore, our results point to differences in the regulation of Bax and Bak activation by proteins of the antiapoptotic and BH3-only subfamilies. We have also applied the BiFC technique to explore the different molecular models proposed for Bax and Bak oligomerization. Bax and Bak's mutants lacking the BH3 domain were still able to associate and give BiFC signals, suggesting the existence of alternative surfaces of interaction between two Bax or Bak molecules. These results agree with the widely accepted symmetric model for the dimerization of these proteins and also suggest that other regions, different from the α6 helix, could be involved in the oligomerization of BH3-in groove dimers.
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16
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Aguilar F, Yu S, Grant RA, Swanson S, Ghose D, Su BG, Sarosiek KA, Keating AE. Peptides from human BNIP5 and PXT1 and non-native binders of pro-apoptotic BAK can directly activate or inhibit BAK-mediated membrane permeabilization. Structure 2023; 31:265-281.e7. [PMID: 36706751 PMCID: PMC9992319 DOI: 10.1016/j.str.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/24/2022] [Accepted: 01/02/2023] [Indexed: 01/27/2023]
Abstract
Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed "activation" and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics.
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Affiliation(s)
- Fiona Aguilar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacey Yu
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sebastian Swanson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dia Ghose
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristopher A Sarosiek
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Program in Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA; John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Dai H, Peterson KL, Flatten KS, Meng XW, Venkatachalam A, Correia C, Ramirez-Alvarado M, Pang YP, Kaufmann SH. A BAK subdomain that binds mitochondrial lipids selectively and releases cytochrome C. Cell Death Differ 2023; 30:794-808. [PMID: 36376382 PMCID: PMC9984382 DOI: 10.1038/s41418-022-01083-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/16/2022] Open
Abstract
How BAK and BAX induce mitochondrial outer membrane (MOM) permeabilization (MOMP) during apoptosis is incompletely understood. Here we have used molecular dynamics simulations, surface plasmon resonance, and assays for membrane permeabilization in vitro and in vivo to assess the structure and function of selected BAK subdomains and their derivatives. Results of these studies demonstrate that BAK helical regions α5 and α6 bind the MOM lipid cardiolipin. While individual peptides corresponding to these helical regions lack the full biological activity of BAK, tandem peptides corresponding to α4-α5, α5-α6, or α6-α7/8 can localize exogenous proteins to mitochondria, permeabilize liposomes composed of MOM lipids, and cause MOMP in the absence of the remainder of the BAK protein. Importantly, the ability of these tandem helices to induce MOMP under cell-free conditions is diminished by mutations that disrupt the U-shaped helix-turn-helix structure of the tandem peptides or decrease their lipid binding. Likewise, BAK-induced apoptosis in intact cells is diminished by CLS1 gene interruption, which decreases mitochondrial cardiolipin content, or by BAK mutations that disrupt the U-shaped tandem peptide structure or diminish lipid binding. Collectively, these results suggest that BAK structural rearrangements during apoptosis might mobilize helices involved in specific protein-lipid interactions that are critical for MOMP.
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Affiliation(s)
- Haiming Dai
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
| | - Kevin L Peterson
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Karen S Flatten
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - X Wei Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Cristina Correia
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | | | - Yuan-Ping Pang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
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18
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Huang AS, Chin HS, Reljic B, Djajawi TM, Tan IKL, Gong JN, Stroud DA, Huang DCS, van Delft MF, Dewson G. Mitochondrial E3 ubiquitin ligase MARCHF5 controls BAK apoptotic activity independently of BH3-only proteins. Cell Death Differ 2023; 30:632-646. [PMID: 36171332 PMCID: PMC9984372 DOI: 10.1038/s41418-022-01067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/08/2022] Open
Abstract
Intrinsic apoptosis is principally governed by the BCL-2 family of proteins, but some non-BCL-2 proteins are also critical to control this process. To identify novel apoptosis regulators, we performed a genome-wide CRISPR-Cas9 library screen, and it identified the mitochondrial E3 ubiquitin ligase MARCHF5/MITOL/RNF153 as an important regulator of BAK apoptotic function. Deleting MARCHF5 in diverse cell lines dependent on BAK conferred profound resistance to BH3-mimetic drugs. The loss of MARCHF5 or its E3 ubiquitin ligase activity surprisingly drove BAK to adopt an activated conformation, with resistance to BH3-mimetics afforded by the formation of inhibitory complexes with pro-survival proteins MCL-1 and BCL-XL. Importantly, these changes to BAK conformation and pro-survival association occurred independently of BH3-only proteins and influence on pro-survival proteins. This study identifies a new mechanism by which MARCHF5 regulates apoptotic cell death by restraining BAK activating conformation change and provides new insight into how cancer cells respond to BH3-mimetic drugs. These data also highlight the emerging role of ubiquitin signalling in apoptosis that may be exploited therapeutically.
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Affiliation(s)
- Allan Shuai Huang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Hui San Chin
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Boris Reljic
- Bio21 Molecular Science & Biotechnology Institute, 30 Flemington Road, Parkville, Melbourne, 3052, Australia
- Department of Biochemistry and Pharmacology Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Tirta M Djajawi
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Iris K L Tan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Jia-Nan Gong
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- NHC Key Laboratory of Human Disease Comparative Medicine, The Institute of Laboratory Animal Sciences, the Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical Disease, Beijing, China
| | - David A Stroud
- Bio21 Molecular Science & Biotechnology Institute, 30 Flemington Road, Parkville, Melbourne, 3052, Australia
- Department of Biochemistry and Pharmacology Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - David C S Huang
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Mark F van Delft
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia.
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19
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Moldoveanu T. Apoptotic mitochondrial poration by a growing list of pore-forming BCL-2 family proteins. Bioessays 2023; 45:e2200221. [PMID: 36650950 PMCID: PMC9975053 DOI: 10.1002/bies.202200221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/19/2023]
Abstract
The pore-forming BCL-2 family proteins are effectors of mitochondrial poration in apoptosis initiation. Two atypical effectors-BOK and truncated BID (tBID)-join the canonical effectors BAK and BAX. Gene knockout revealed developmental phenotypes in the absence the effectors, supporting their roles in vivo. During apoptosis effectors are activated and change shape from dormant monomers to dynamic oligomers that associate with and permeabilize mitochondria. BID is activated by proteolysis, BOK accumulates on inhibition of its degradation by the E3 ligase gp78, while BAK and BAX undergo direct activation by BH3-only initiators, autoactivation, and crossactivation. Except tBID, effector oligomers on the mitochondria appear as arcs and rings in super-resolution microscopy images. The BH3-in-groove dimers of BAK and BAX, the tBID monomers, and uncharacterized BOK species are the putative building blocks of apoptotic pores. Effectors interact with lipids and bilayers but the mechanism of membrane poration remains elusive. I discuss effector-mediated mitochondrial poration.
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Affiliation(s)
- Tudor Moldoveanu
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences,Correspondence:
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20
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Sekar G, Singh G, Qin X, Guibao CD, Schwam B, Inde Z, Grace CR, Zhang W, Slavish PJ, Lin W, Chen T, Lee RE, Rankovic Z, Sarosiek K, Moldoveanu T. Small molecule SJ572946 activates BAK to initiate apoptosis. iScience 2022; 25:105064. [PMID: 36147946 PMCID: PMC9485059 DOI: 10.1016/j.isci.2022.105064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/29/2022] [Accepted: 08/30/2022] [Indexed: 01/11/2023] Open
Abstract
Poration of the outer mitochondrial membrane by the effector BCL-2 proteins BAK and BAX initiates apoptosis. BH3-only initiators BID and BIM trigger conformational changes in BAK and BAX transforming them from globular dormant proteins to oligomers of the apoptotic pores. Small molecules that can directly activate effectors are being sought for applications in cancer treatment. Here, we describe the small molecule SJ572946, discovered in a fragment-based screen that binds to the activation groove of BAK and selectively triggers BAK activation over that of BAX in liposome and mitochondrial permeabilization assays. SJ572946 independently kills BAK-expressing BCL2allKO HCT116 cells revealing on target cellular activity. In combination with apoptotic inducers and BH3 mimetics, SJ572946 kills experimental cancer cell lines. SJ572946 also cooperates with the endogenous BAK activator BID in activating a misfolded BAK mutant substantially impaired in activation. SJ572946 is a proof-of-concept tool for probing BAK-mediated apoptosis in preclinical cancer research.
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Affiliation(s)
- Giridhar Sekar
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Geetika Singh
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Children’s GMP, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xingping Qin
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Cristina D. Guibao
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Brittany Schwam
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zintis Inde
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Weixing Zhang
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - P. Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Kristopher Sarosiek
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston,02115 MA, USA,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard School of Public Health, Boston, 02115 MA, USA,Laboratory of Systems Pharmacology, Harvard Medical School, Boston,02115 MA, USA
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Roeck, AR 72205, USA,Corresponding author
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21
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Robin AY, Miller MS, Iyer S, Shi MX, Wardak AZ, Lio D, Smith NA, Smith BJ, Birkinshaw RW, Czabotar PE, Kluck RM, Colman PM. Structure of the BAK-activating antibody 7D10 bound to BAK reveals an unexpected role for the α1-α2 loop in BAK activation. Cell Death Differ 2022; 29:1757-1768. [PMID: 35279694 PMCID: PMC9433411 DOI: 10.1038/s41418-022-00961-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 02/13/2022] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
Pro-apoptotic BAK and BAX are activated by BH3-only proteins to permeabilise the outer mitochondrial membrane. The antibody 7D10 also activates BAK on mitochondria and its epitope has previously been mapped to BAK residues in the loop connecting helices α1 and α2 of BAK. A crystal structure of the complex between the Fv fragment of 7D10 and the BAK mutant L100A suggests a possible mechanism of activation involving the α1-α2 loop residue M60. M60 mutants of BAK have reduced stability and elevated sensitivity to activation by BID, illustrating that M60, through its contacts with residues in helices α1, α5 and α6, is a linchpin stabilising the inert, monomeric structure of BAK. Our data demonstrate that BAK's α1-α2 loop is not a passive covalent connector between secondary structure elements, but a direct restraint on BAK's activation.
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Affiliation(s)
- Adeline Y Robin
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Michelle S Miller
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Sweta Iyer
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Melissa X Shi
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Ahmad Z Wardak
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Daisy Lio
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Nicholas A Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Brian J Smith
- Department of Chemistry and Physics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Richard W Birkinshaw
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Peter E Czabotar
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
| | - Ruth M Kluck
- Blood Cells and Blood Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
| | - Peter M Colman
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.
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22
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Athanasopoulou K, Adamopoulos PG, Daneva GN, Scorilas A. Decoding the concealed transcriptional signature of the apoptosis-related BCL2 antagonist/killer 1 (BAK1) gene in human malignancies. Apoptosis 2022; 27:869-882. [DOI: 10.1007/s10495-022-01753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
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23
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At the Crossroads of Life and Death: The Proteins That Influence Cell Fate Decisions. Cancers (Basel) 2022; 14:cancers14112745. [PMID: 35681725 PMCID: PMC9179324 DOI: 10.3390/cancers14112745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cellular senescence and apoptosis were historically thought of as two distinct cell fate pathways. However, many of the proteins involved are integral to both pathways. In particular, the ability of p53 to regulate both senescence and apoptosis meant it was seen as the decisive factor in these decisions, yet questions remain about its ability to select on its own the most appropriate cell fate according to each situation. Therefore, cell fates are no longer considered fixed endpoints but dynamic states that can be shifted given the right combination of activation and/or inhibitions of cofactors. Abstract When a cell is damaged, it must decide how to respond. As a consequence of a variety of stresses, cells can induce well-regulated programmes such as senescence, a persistent proliferative arrest that limits their replication. Alternatively, regulated programmed cell death can be induced to remove the irreversibly damaged cells in a controlled manner. These programmes are mainly triggered and controlled by the tumour suppressor protein p53 and its complex network of effectors, but how it decides between these wildly different responses is not fully understood. This review focuses on the key proteins involved both in the regulation and induction of apoptosis and senescence to examine the key events that determine cell fate following damage. Furthermore, we examine how the regulation and activity of these proteins are altered during the progression of many chronic diseases, including cancer.
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24
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Sora V, Papaleo E. Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective. Front Mol Biosci 2022; 9:864874. [PMID: 35685242 PMCID: PMC9171138 DOI: 10.3389/fmolb.2022.864874] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is a mechanism of programmed cell death crucial in organism development, maintenance of tissue homeostasis, and several pathogenic processes. The B cell lymphoma 2 (BCL2) protein family lies at the core of the apoptotic process, and the delicate balance between its pro- and anti-apoptotic members ultimately decides the cell fate. BCL2 proteins can bind with each other and several other biological partners through the BCL2 homology domain 3 (BH3), which has been also classified as a possible Short Linear Motif and whose distinctive features remain elusive even after decades of studies. Here, we aim to provide an updated overview of the structural features characterizing BH3s and BH3-mediated interactions (with a focus on human proteins), elaborating on the plasticity of BCL2 proteins and the motif properties. We also discussed the implication of these findings for the discovery of interactors of the BH3-binding groove of BCL2 proteins and the design of mimetics for therapeutic purposes.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Elena Papaleo, ,
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25
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Protein-protein and protein-lipid interactions of pore-forming BCL-2 family proteins in apoptosis initiation. Biochem Soc Trans 2022; 50:1091-1103. [PMID: 35521828 DOI: 10.1042/bst20220323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 01/26/2023]
Abstract
Apoptosis is a common cell death program that is important in human health and disease. Signaling in apoptosis is largely driven through protein-protein interactions. The BCL-2 family proteins function in protein-protein interactions as key regulators of mitochondrial poration, the process that initiates apoptosis through the release of cytochrome c, which activates the apoptotic caspase cascade leading to cellular demolition. The BCL-2 pore-forming proteins BAK and BAX are the key executors of mitochondrial poration. We review the state of knowledge of protein-protein and protein-lipid interactions governing the apoptotic function of BAK and BAX, as determined through X-ray crystallography and NMR spectroscopy studies. BAK and BAX are dormant, globular α-helical proteins that participate in protein-protein interactions with other pro-death BCL-2 family proteins, transforming them into active, partially unfolded proteins that dimerize and associate with and permeabilize mitochondrial membranes. We compare the protein-protein interactions observed in high-resolution structures with those derived in silico by AlphaFold, making predictions based on combining experimental and in silico approaches to delineate the structural basis for novel protein-protein interaction complexes of BCL-2 family proteins.
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26
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The concept of intrinsic versus extrinsic apoptosis. Biochem J 2022; 479:357-384. [PMID: 35147165 DOI: 10.1042/bcj20210854] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Regulated cell death is a vital and dynamic process in multicellular organisms that maintains tissue homeostasis and eliminates potentially dangerous cells. Apoptosis, one of the better-known forms of regulated cell death, is activated when cell-surface death receptors like Fas are engaged by their ligands (the extrinsic pathway) or when BCL-2-family pro-apoptotic proteins cause the permeabilization of the mitochondrial outer membrane (the intrinsic pathway). Both the intrinsic and extrinsic pathways of apoptosis lead to the activation of a family of proteases, the caspases, which are responsible for the final cell demise in the so-called execution phase of apoptosis. In this review, I will first discuss the most common types of regulated cell death on a morphological basis. I will then consider in detail the molecular pathways of intrinsic and extrinsic apoptosis, discussing how they are activated in response to specific stimuli and are sometimes overlapping. In-depth knowledge of the cellular mechanisms of apoptosis is becoming more and more important not only in the field of cellular and molecular biology but also for its translational potential in several pathologies, including neurodegeneration and cancer.
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27
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Smith NA, Wardak AZ, Cowan AD, Colman PM, Czabotar PE, Smith BJ. The Bak core dimer focuses triacylglycerides in the membrane. Biophys J 2022; 121:347-360. [PMID: 34973947 PMCID: PMC8822611 DOI: 10.1016/j.bpj.2021.12.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 02/03/2023] Open
Abstract
Apoptosis, the intrinsic programmed cell death process, is mediated by the Bcl-2 family members Bak and Bax. Activation via formation of symmetric core dimers and oligomerization on the mitochondrial outer membrane (MOM) leads to permeabilization and cell death. Although this process is linked to the MOM, the role of the membrane in facilitating such pores is poorly understood. We recently described Bak core domain dimers, revealing lipid binding sites and an initial role of lipids in oligomerization. Here we describe simulations that identified localized clustering and interaction of triacylglycerides (TAGs) with a minimized Bak dimer construct. Coalescence of TAGs occurred beneath this Bak dimer, mitigating dimer-induced local membrane thinning and curvature in representative coarse-grain MOM and model membrane systems. Furthermore, the effects observed as a result of coarse-grain TAG cluster formation was concentration dependent, scaling from low physiological MOM concentrations to those found in other organelles. We find that increasing the TAG concentration in liposomes mimicking the MOM decreased the ability of activated Bak to permeabilize these liposomes. These results suggest that the presence of TAGs within a Bak-lipid membrane preserves membrane integrity and is associated with reduced membrane stress, suggesting a possible role of TAGs in Bak-mediated apoptosis.
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Affiliation(s)
- Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Ahmad Z. Wardak
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Angus D. Cowan
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter M. Colman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter E. Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia,Corresponding author
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28
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Singh G, Guibao CD, Seetharaman J, Aggarwal A, Grace CR, McNamara DE, Vaithiyalingam S, Waddell MB, Moldoveanu T. Structural basis of BAK activation in mitochondrial apoptosis initiation. Nat Commun 2022; 13:250. [PMID: 35017502 PMCID: PMC8752837 DOI: 10.1038/s41467-021-27851-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 12/14/2021] [Indexed: 12/31/2022] Open
Abstract
BCL-2 proteins regulate mitochondrial poration in apoptosis initiation. How the pore-forming BCL-2 Effector BAK is activated remains incompletely understood mechanistically. Here we investigate autoactivation and direct activation by BH3-only proteins, which cooperate to lower BAK threshold in membrane poration and apoptosis initiation. We define in trans BAK autoactivation as the asymmetric “BH3-in-groove” triggering of dormant BAK by active BAK. BAK autoactivation is mechanistically similar to direct activation. The structure of autoactivated BAK BH3-BAK complex reveals the conformational changes leading to helix α1 destabilization, which is a hallmark of BAK activation. Helix α1 is destabilized and restabilized in structures of BAK engaged by rationally designed, high-affinity activating and inactivating BID-like BH3 ligands, respectively. Altogether our data support the long-standing hit-and-run mechanism of BAK activation by transient binding of BH3-only proteins, demonstrating that BH3-induced structural changes are more important in BAK activation than BH3 ligand affinity. The authors show that the mechanism of BAK activation in mitochondrial apoptosis involves cooperation between direct activation by BH3-only protein BID and BAK autoactivation, providing a unifying basis for BAK triggering by BH3 ligands.
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Affiliation(s)
- Geetika Singh
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.,Integrative Biomedical Sciences Program, University of Tennessee Health Sciences Center, Memphis, TN, 38163, USA
| | - Cristina D Guibao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Anup Aggarwal
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Christy R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Dan E McNamara
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - M Brett Waddell
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tudor Moldoveanu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
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29
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Diepstraten ST, Anderson MA, Czabotar PE, Lessene G, Strasser A, Kelly GL. The manipulation of apoptosis for cancer therapy using BH3-mimetic drugs. Nat Rev Cancer 2022; 22:45-64. [PMID: 34663943 DOI: 10.1038/s41568-021-00407-4] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/02/2021] [Indexed: 12/14/2022]
Abstract
Apoptosis is a form of programmed cell death that is regulated by the balance between prosurvival and proapoptotic BCL-2 protein family members. Evasion of apoptosis is a hallmark of cancer that arises when this balance is tipped in favour of survival. One form of anticancer therapeutic, termed 'BH3-mimetic drugs', has been developed to directly activate the apoptosis machinery in malignant cells. These drugs bind to and inhibit specific prosurvival BCL-2 family proteins, thereby mimicking their interaction with the BH3 domains of proapoptotic BCL-2 family proteins. The BCL-2-specific inhibitor venetoclax is approved by the US Food and Drug Administration and many regulatory authorities worldwide for the treatment of chronic lymphocytic leukaemia and acute myeloid leukaemia. BH3-mimetic drugs targeting other BCL-2 prosurvival proteins have been tested in preclinical models of cancer, and drugs targeting MCL-1 or BCL-XL have advanced into phase I clinical trials for certain cancers. As with all therapeutics, efficacy and tolerability need to be carefully balanced to achieve a therapeutic window whereby there is significant anticancer activity with an acceptable safety profile. In this Review, we outline the current state of BH3-mimetic drugs targeting various prosurvival BCL-2 family proteins and discuss emerging data regarding primary and acquired resistance to these agents and approaches that may overcome this. We highlight issues that need to be addressed to further advance the clinical application of BH3-mimetic drugs, both alone and in combination with additional anticancer agents (for example, standard chemotherapeutic drugs or inhibitors of oncogenic kinases), for improved responses in patients with cancer.
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Affiliation(s)
- Sarah T Diepstraten
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Mary Ann Anderson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Department of Clinical Haematology, Royal Melbourne Hospital, Melbourne, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, VIC, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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30
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Flores‐Romero H, Hohorst L, John M, Albert M, King LE, Beckmann L, Szabo T, Hertlein V, Luo X, Villunger A, Frenzel LP, Kashkar H, Garcia‐Saez AJ. BCL‐2‐family protein tBID can act as a BAX‐like effector of apoptosis. EMBO J 2021; 41:e108690. [PMID: 34931711 PMCID: PMC8762556 DOI: 10.15252/embj.2021108690] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/14/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
During apoptosis, the BCL‐2‐family protein tBID promotes mitochondrial permeabilization by activating BAX and BAK and by blocking anti‐apoptotic BCL‐2 members. Here, we report that tBID can also mediate mitochondrial permeabilization by itself, resulting in release of cytochrome c and mitochondrial DNA, caspase activation and apoptosis even in absence of BAX and BAK. This previously unrecognized activity of tBID depends on helix 6, homologous to the pore‐forming regions of BAX and BAK, and can be blocked by pro‐survival BCL‐2 proteins. Importantly, tBID‐mediated mitochondrial permeabilization independent of BAX and BAK is physiologically relevant for SMAC release in the immune response against Shigella infection. Furthermore, it can be exploited to kill leukaemia cells with acquired venetoclax resistance due to lack of active BAX and BAK. Our findings define tBID as an effector of mitochondrial permeabilization in apoptosis and provide a new paradigm for BCL‐2 proteins, with implications for anti‐bacterial immunity and cancer therapy.
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Affiliation(s)
- Hector Flores‐Romero
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Lisa Hohorst
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Malina John
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Marie‐Christine Albert
- Institute for Molecular Immunology, and Center for Molecular Medicine Cologne (CMMC) Faculty of Medicine University Hospital of Cologne University of Cologne Cologne Germany
| | - Louise E King
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Laura Beckmann
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Department I of Internal Medicine University Hospital of Cologne Cologne Germany
- Center of Integrated Oncology ABCD University Hospital of Cologne Cologne Germany
| | - Tamas Szabo
- Division of Developmental Immunology Biocenter Medical University of Innsbruck Innsbruck Austria
| | - Vanessa Hertlein
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
| | - Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center University of Nebraska Medical Center Omaha ME USA
- Department of Pathology and Microbiology University of Nebraska Medical Center Omaha NE USA
| | - Andreas Villunger
- Division of Developmental Immunology Biocenter Medical University of Innsbruck Innsbruck Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria
| | - Lukas P Frenzel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Department I of Internal Medicine University Hospital of Cologne Cologne Germany
- Center of Integrated Oncology ABCD University Hospital of Cologne Cologne Germany
| | - Hamid Kashkar
- Institute for Molecular Immunology, and Center for Molecular Medicine Cologne (CMMC) Faculty of Medicine University Hospital of Cologne University of Cologne Cologne Germany
| | - Ana J Garcia‐Saez
- Institute for Genetics University of Cologne Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
- Interfaculty Institute of Biochemistry Eberhard‐Karls‐Universität Tübingen Tübingen Germany
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31
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VDAC2 and the BCL-2 family of proteins. Biochem Soc Trans 2021; 49:2787-2795. [PMID: 34913469 PMCID: PMC8786305 DOI: 10.1042/bst20210753] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022]
Abstract
The BCL-2 protein family govern whether a cell dies or survives by controlling mitochondrial apoptosis. As dysregulation of mitochondrial apoptosis is a common feature of cancer cells, targeting protein–protein interactions within the BCL-2 protein family is a key strategy to seize control of apoptosis and provide favourable outcomes for cancer patients. Non-BCL-2 family proteins are emerging as novel regulators of apoptosis and are potential drug targets. Voltage dependent anion channel 2 (VDAC2) can regulate apoptosis. However, it is unclear how this occurs at the molecular level, with conflicting evidence in the literature for its role in regulating the BCL-2 effector proteins, BAK and BAX. Notably, VDAC2 is required for efficient BAX-mediated apoptosis, but conversely inhibits BAK-mediated apoptosis. This review focuses on the role of VDAC2 in apoptosis, discussing the current knowledge of the interaction between VDAC2 and BCL-2 family proteins and the recent development of an apoptosis inhibitor that targets the VDAC2–BAK interaction.
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32
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Discovery, development and application of drugs targeting BCL-2 pro-survival proteins in cancer. Biochem Soc Trans 2021; 49:2381-2395. [PMID: 34515749 PMCID: PMC8589430 DOI: 10.1042/bst20210749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
The discovery of a new class of small molecule compounds that target the BCL-2 family of anti-apoptotic proteins is one of the great success stories of basic science leading to translational outcomes in the last 30 years. The eponymous BCL-2 protein was identified over 30 years ago due to its association with cancer. However, it was the unveiling of the biochemistry and structural biology behind it and its close relatives’ mechanism(s)-of-action that provided the inspiration for what are now known as ‘BH3-mimetics’, the first clinically approved drugs designed to specifically inhibit protein–protein interactions. Herein, we chart the history of how these drugs were discovered, their evolution and application in cancer treatment.
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33
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Sandow JJ, Tan IK, Huang AS, Masaldan S, Bernardini JP, Wardak AZ, Birkinshaw RW, Ninnis RL, Liu Z, Dalseno D, Lio D, Infusini G, Czabotar PE, Webb AI, Dewson G. Dynamic reconfiguration of pro-apoptotic BAK on membranes. EMBO J 2021; 40:e107237. [PMID: 34523147 DOI: 10.15252/embj.2020107237] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 08/02/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
BAK and BAX, the effectors of intrinsic apoptosis, each undergo major reconfiguration to an activated conformer that self-associates to damage mitochondria and cause cell death. However, the dynamic structural mechanisms of this reconfiguration in the presence of a membrane have yet to be fully elucidated. To explore the metamorphosis of membrane-bound BAK, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS). The HDX-MS profile of BAK on liposomes comprising mitochondrial lipids was consistent with known solution structures of inactive BAK. Following activation, HDX-MS resolved major reconfigurations in BAK. Mutagenesis guided by our HDX-MS profiling revealed that the BCL-2 homology (BH) 4 domain maintains the inactive conformation of BAK, and disrupting this domain is sufficient for constitutive BAK activation. Moreover, the entire N-terminal region preceding the BAK oligomerisation domains became disordered post-activation and remained disordered in the activated oligomer. Removal of the disordered N-terminus did not impair, but rather slightly potentiated, BAK-mediated membrane permeabilisation of liposomes and mitochondria. Together, our HDX-MS analyses reveal new insights into the dynamic nature of BAK activation on a membrane, which may provide new opportunities for therapeutic targeting.
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Affiliation(s)
- Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Iris Kl Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Alan S Huang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Shashank Masaldan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Jonathan P Bernardini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ahmad Z Wardak
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Robert L Ninnis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Ziyan Liu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Destiny Dalseno
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Daisy Lio
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Giuseppi Infusini
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Vic., Australia
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34
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Sperl LE, Rührnößl F, Schiller A, Haslbeck M, Hagn F. High-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane. EMBO J 2021; 40:e107159. [PMID: 34523144 PMCID: PMC8521305 DOI: 10.15252/embj.2020107159] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 08/09/2021] [Accepted: 08/20/2021] [Indexed: 12/21/2022] Open
Abstract
Permeabilization of the outer mitochondrial membrane by pore-forming Bcl2 proteins is a crucial step for the induction of apoptosis. Despite a large set of data suggesting global conformational changes within pro-apoptotic Bak during pore formation, high-resolution structural details in a membrane environment remain sparse. Here, we used NMR and HDX-MS (Hydrogen deuterium exchange mass spectrometry) in lipid nanodiscs to gain important high-resolution structural insights into the conformational changes of Bak at the membrane that are dependent on a direct activation by BH3-only proteins. Furthermore, we determined the first high-resolution structure of the Bak transmembrane helix. Upon activation, α-helix 1 in the soluble domain of Bak dissociates from the protein and adopts an unfolded and dynamic potentially membrane-bound state. In line with this finding, comparative protein folding experiments with Bak and anti-apoptotic BclxL suggest that α-helix 1 in Bak is a metastable structural element contributing to its pro-apoptotic features. Consequently, mutagenesis experiments aimed at stabilizing α-helix 1 yielded Bak variants with delayed pore-forming activity. These insights will contribute to a better mechanistic understanding of Bak-mediated membrane permeabilization.
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Affiliation(s)
- Laura E Sperl
- Bavarian NMR Center at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Florian Rührnößl
- Center for Functional Protein Assemblies and Department of ChemistryTechnical University of MunichGarchingGermany
| | - Anita Schiller
- Bavarian NMR Center at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Haslbeck
- Center for Functional Protein Assemblies and Department of ChemistryTechnical University of MunichGarchingGermany
| | - Franz Hagn
- Bavarian NMR Center at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
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35
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BAX mitochondrial integration is regulated allosterically by its α1-α2 loop. Cell Death Differ 2021; 28:3270-3281. [PMID: 34135480 DOI: 10.1038/s41418-021-00815-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 11/08/2022] Open
Abstract
The conformational changes converting BAX from an inert cytosolic monomer into the homo-oligomers that permeabilize the mitochondrial outer membrane (MOM) are crucial steps toward apoptosis. Here, we have explored the potential role of the BAX α1-α2 loop in this process by three mutagenic approaches: replacing loop segments with cognate loop regions from closely related proteins, alanine scanning and analysis of BAX α1-α2 loop missense mutations observed in tumours. Responsiveness to a death signal, such as tBID, was reduced by mutations in the N-terminal but not C-terminal half of the loop. N-terminal loop variants, which were enriched in tumours, impaired MOM integration by allosterically reducing exposure of the BAX α9 transmembrane anchor. Most C-terminal loop variants reduced BAX stability, leading to increased BAX apoptotic function in some variants. Thus, our systematic mutagenesis suggests that the two halves of the α1-α2 loop have distinct functions. We show that the N-terminal half of the loop (its first nine residues) comprises an important allosteric regulator of BAX activation by setting the proportion of MOM-integrated BAX following a death signal. The enrichment of N-terminal loop mutations in tumours indicates that they may promote tumour cell survival and underscore the loop as a target for therapeutic manipulation of BAX function.
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36
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Lv F, Qi F, Zhang Z, Wen M, Kale J, Piai A, Du L, Wang S, Zhou L, Yang Y, Wu B, Liu Z, Del Rosario J, Pogmore J, Chou JJ, Andrews DW, Lin J, OuYang B. An amphipathic Bax core dimer forms part of the apoptotic pore wall in the mitochondrial␣membrane. EMBO J 2021; 40:e106438. [PMID: 34101209 PMCID: PMC8280806 DOI: 10.15252/embj.2020106438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/17/2021] [Accepted: 04/27/2021] [Indexed: 02/01/2023] Open
Abstract
Bax proteins form pores in the mitochondrial outer membrane to initiate apoptosis. This might involve their embedding in the cytosolic leaflet of the lipid bilayer, thus generating tension to induce a lipid pore with radially arranged lipids forming the wall. Alternatively, Bax proteins might comprise part of the pore wall. However, there is no unambiguous structural evidence for either hypothesis. Using NMR, we determined a high-resolution structure of the Bax core region, revealing a dimer with the nonpolar surface covering the lipid bilayer edge and the polar surface exposed to water. The dimer tilts from the bilayer normal, not only maximizing nonpolar interactions with lipid tails but also creating polar interactions between charged residues and lipid heads. Structure-guided mutations demonstrate the importance of both types of protein-lipid interactions in Bax pore assembly and core dimer configuration. Therefore, the Bax core dimer forms part of the proteolipid pore wall to permeabilize mitochondria.
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Affiliation(s)
- Fujiao Lv
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Fei Qi
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Zhi Zhang
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Maorong Wen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Justin Kale
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Alessandro Piai
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lingyu Du
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuqing Wang
- School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Liujuan Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yaqing Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Juan Del Rosario
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Justin Pogmore
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - James J Chou
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David W Andrews
- Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Jialing Lin
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Stephenson Cancer Center, Oklahoma City, OK, USA
| | - Bo OuYang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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37
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Li K, van Delft MF, Dewson G. Too much death can kill you: inhibiting intrinsic apoptosis to treat disease. EMBO J 2021; 40:e107341. [PMID: 34037273 DOI: 10.15252/embj.2020107341] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/11/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
Apoptotic cell death is implicated in both physiological and pathological processes. Since many types of cancerous cells intrinsically evade apoptotic elimination, induction of apoptosis has become an attractive and often necessary cancer therapeutic approach. Conversely, some cells are extremely sensitive to apoptotic stimuli leading to neurodegenerative disease and immune pathologies. However, due to several challenges, pharmacological inhibition of apoptosis is still only a recently emerging strategy to combat pathological cell loss. Here, we describe several key steps in the intrinsic (mitochondrial) apoptosis pathway that represent potential targets for inhibitors in disease contexts. We also discuss the mechanisms of action, advantages and limitations of small-molecule and peptide-based inhibitors that have been developed to date. These inhibitors serve as important research tools to dissect apoptotic signalling and may foster new treatments to reduce unwanted cell loss.
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Affiliation(s)
- Kaiming Li
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
| | - Mark F van Delft
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Royal Parade, Melbourne, VIC, Australia
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38
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Birkinshaw RW, Iyer S, Lio D, Luo CS, Brouwer JM, Miller MS, Robin AY, Uren RT, Dewson G, Kluck RM, Colman PM, Czabotar PE. Structure of detergent-activated BAK dimers derived from the inert monomer. Mol Cell 2021; 81:2123-2134.e5. [PMID: 33794146 DOI: 10.1016/j.molcel.2021.03.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Accepted: 03/09/2021] [Indexed: 01/27/2023]
Abstract
A body of data supports the existence of core (α2-α5) dimers of BAK and BAX in the oligomeric, membrane-perturbing conformation of these essential apoptotic effector molecules. Molecular structures for these dimers have only been captured for truncated constructs encompassing the core domain alone. Here, we report a crystal structure of BAK α2-α8 dimers (i.e., minus its flexible N-terminal helix and membrane-anchoring C-terminal segment) that has been obtained through the activation of monomeric BAK with the detergent C12E8. Core dimers are evident, linked through the crystal by contacts via latch (α6-α8) domains. This crystal structure shows activated BAK dimers with the extended latch domain present. Our data provide direct evidence for the conformational change converting BAK from inert monomer to the functional dimer that destroys mitochondrial integrity. This dimer is the smallest functional unit for recombinant BAK or BAX described so far.
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Affiliation(s)
- Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Sweta Iyer
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Daisy Lio
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Cindy S Luo
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jason M Brouwer
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michelle S Miller
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Adeline Y Robin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Rachel T Uren
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Grant Dewson
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Ruth M Kluck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter M Colman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia.
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Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc. PLoS One 2021; 16:e0251459. [PMID: 33989344 PMCID: PMC8121366 DOI: 10.1371/journal.pone.0251459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Synaptic plasticity is vital for brain function and memory formation. One of the key proteins in long-term synaptic plasticity and memory is the activity-regulated cytoskeleton-associated protein (Arc). Mammalian Arc forms virus-like capsid structures in a process requiring the N-terminal domain and contains two C-terminal lobes that are structural homologues to retroviral capsids. Drosophila has two isoforms of Arc, dArc1 and dArc2, with low sequence similarity to mammalian Arc, but lacking a large N-terminal domain. Both dArc isoforms are related to the Ty3/gypsy retrotransposon capsid, consisting of N- and C-terminal lobes. Structures of dArc1, as well as capsids formed by both dArc isoforms, have been recently determined. We carried out structural characterization of the four individual dArc lobe domains. As opposed to the corresponding mammalian Arc lobe domains, which are monomeric, the dArc lobes were all oligomeric in solution, indicating a strong propensity for homophilic interactions. A truncated N-lobe from dArc2 formed a domain-swapped dimer in the crystal structure, resulting in a novel dimer interaction that could be relevant for capsid assembly or other dArc functions. This domain-swapped structure resembles the dimeric protein C of flavivirus capsids, as well as the structure of histones dimers, domain-swapped transcription factors, and membrane-interacting BAK domains. The strong oligomerization properties of the isolated dArc lobe domains explain the ability of dArc to form capsids in the absence of any large N-terminal domain, in contrast to the mammalian protein.
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40
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Pogmore JP, Uehling D, Andrews DW. Pharmacological Targeting of Executioner Proteins: Controlling Life and Death. J Med Chem 2021; 64:5276-5290. [PMID: 33939407 DOI: 10.1021/acs.jmedchem.0c02200] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Small-molecule mediated modulation of protein interactions of Bcl-2 (B-cell lymphoma-2) family proteins was clinically validated in 2015 when Venetoclax, a selective inhibitor of the antiapoptotic protein BCL-2, achieved breakthrough status designation by the FDA for treatment of lymphoid malignancies. Since then, substantial progress has been made in identifying inhibitors of other interactions of antiapoptosis proteins. However, targeting their pro-apoptotic counterparts, the "executioners" BAX, BAK, and BOK that both initiate and commit the cell to dying, has lagged behind. However, recent publications demonstrate that these proteins can be positively or negatively regulated using small molecule tool compounds. The results obtained with these molecules suggest that pharmaceutical regulation of apoptosis will have broad implications that extend beyond activating cell death in cancer. We review recent advances in identifying compounds and their utility in the exogenous control of life and death by regulating executioner proteins, with emphasis on the prototype BAX.
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Affiliation(s)
- Justin P Pogmore
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 1M1, Canada
| | - David W Andrews
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1J7, Canada.,Biological Sciences, Sunnybrook Research Institute, University of Toronto, Toronto, Ontario M4N 3M5, Canada
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41
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Johnstone BA, Christie MP, Morton CJ, Parker MW. X-ray crystallography shines a light on pore-forming toxins. Methods Enzymol 2021; 649:1-46. [PMID: 33712183 DOI: 10.1016/bs.mie.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A common form of cellular attack by pathogenic bacteria is to secrete pore-forming toxins (PFTs). Capable of forming transmembrane pores in various biological membranes, PFTs have also been identified in a diverse range of other organisms such as sea anemones, earthworms and even mushrooms and trees. The mechanism of pore formation by PFTs is associated with substantial conformational changes in going from the water-soluble to transmembrane states of the protein. The determination of the crystal structures for numerous PFTs has shed much light on our understanding of these proteins. Other than elucidating the atomic structural details of PFTs and the conformational changes that must occur for pore formation, crystal structures have revealed structural homology that has led to the discovery of new PFTs and new PFT families. Here we review some key crystallographic results together with complimentary approaches for studying PFTs. We discuss how these studies have impacted our understanding of PFT function and guided research into biotechnical applications.
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Affiliation(s)
- Bronte A Johnstone
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michelle P Christie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Craig J Morton
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.
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42
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43
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Schnetler R, Fanucchi S, Moldoveanu T, Koorsen G. Linker Histone H1.2 Directly Activates BAK through the K/RVVKP Motif on the C-Terminal Domain. Biochemistry 2020; 59:3332-3346. [PMID: 32786407 DOI: 10.1021/acs.biochem.0c00373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
H1.2 is a key mediator of apoptosis following DNA double-strand breaks. The link between H1.2 and canonical apoptotic pathways is unclear. One study found that H1.2 stimulates cytochrome c (Cyt c) release; in contrast, apoptosis-inducing factor was found to be released in another study. The C-terminal domain (CTD) of H1.2 has been implicated in the latter pathway, but activation of the proapoptotic protein BCL-2 homologous antagonist/killer (BAK) is a common denominator in both pathways. This study aimed to determine whether the CTD of H1.2 is also responsible for mitochondrial Cyt c release and whether a previously identified K/RVVKP motif in the CTD mediates the response. This study investigated if H1.2 mediates apoptosis induction through direct interaction with BAK. We established that the CTD of H1.2 stimulates mitochondrial Cyt c release in vitro in a mitochondrial permeability transition-independent manner and that the substitution of a single valine with threonine in the K/RVVKP motif abolishes Cyt c release. Additionally, we showed that H1.2 directly interacts with BAK with weak affinity and that the CTD of H1.2 mediates this binding. Using two 20-amino acid peptides derived from the CTD of H1.2 and H1.1 (K/RVVKP motif inclusive), we determined the main residues involved in the direct interaction with BAK. We propose that H1.2 operates through the K/RVVKP motif by directly activating BAK through inter- and intramolecular interactions. These findings expand the view of H1.2 as a signal-transducing molecule that can activate apoptosis in a BAK-dependent manner.
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Affiliation(s)
- Rozanné Schnetler
- Department of Biochemistry, University of Johannesburg, Corner Kingsway and University Roads, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
| | - Sylvia Fanucchi
- Department of Molecular and Cell Biology, University of the Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa
| | - Tudor Moldoveanu
- Department of Structural Biology and Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Gerrit Koorsen
- Department of Biochemistry, University of Johannesburg, Corner Kingsway and University Roads, P.O. Box 524, Auckland Park, Johannesburg 2006, South Africa
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44
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Cowan AD, Smith NA, Sandow JJ, Kapp EA, Rustam YH, Murphy JM, Brouwer JM, Bernardini JP, Roy MJ, Wardak AZ, Tan IK, Webb AI, Gulbis JM, Smith BJ, Reid GE, Dewson G, Colman PM, Czabotar PE. BAK core dimers bind lipids and can be bridged by them. Nat Struct Mol Biol 2020; 27:1024-1031. [DOI: 10.1038/s41594-020-0494-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 12/27/2022]
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45
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Diversity in the intrinsic apoptosis pathway of nematodes. Commun Biol 2020; 3:478. [PMID: 32859965 PMCID: PMC7456325 DOI: 10.1038/s42003-020-01208-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022] Open
Abstract
Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic nematode taxa representing four evolutionary clades (I, III, IV and V). Unlike in C. elegans, 15 species possess multiple (two to five) BCL-2-like proteins, and some do not have any recognisable BCL-2 sequences. Functional studies provided no evidence that BAX/BAK proteins have evolved in nematodes, and structural studies of a BCL-2 protein from the basal clade I revealed it lacks a functionally important feature of the C. elegans orthologue. Clade I CED-4/APAF-1 proteins also possess WD40-repeat sequences associated with apoptosome assembly, not present in C. elegans, or other nematode taxa studied.
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46
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Abstract
Bax and Bak, two functionally similar, pro-apoptotic proteins of the Bcl-2 family, are known as the gateway to apoptosis because of their requisite roles as effectors of mitochondrial outer membrane permeabilization (MOMP), a major step during mitochondria-dependent apoptosis. The mechanism of how cells turn Bax/Bak from inert molecules into fully active and lethal effectors had long been the focal point of a major debate centered around two competing, but not mutually exclusive, models: direct activation and indirect activation. After intensive research efforts for over two decades, it is now widely accepted that to initiate apoptosis, some of the BH3-only proteins, a subclass of the Bcl-2 family, directly engage Bax/Bak to trigger their conformational transformation and activation. However, a series of recent discoveries, using previously unavailable CRISPR-engineered cell systems, challenge the basic premise that undergirds the consensus and provide evidence for a novel and surprisingly simple model of Bax/Bak activation: the membrane (lipids)-mediated spontaneous model. This review will discuss the evidence, rationale, significance, and implications of this new model.
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Affiliation(s)
- Xu Luo
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Alaska Medical Center, Omaha, ME, 68198-7696, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Katelyn L O'Neill
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Alaska Medical Center, Omaha, ME, 68198-7696, USA
| | - Kai Huang
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Alaska Medical Center, Omaha, ME, 68198-7696, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
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47
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Ye K, Meng WX, Sun H, Wu B, Chen M, Pang YP, Gao J, Wang H, Wang J, Kaufmann SH, Dai H. Characterization of an alternative BAK-binding site for BH3 peptides. Nat Commun 2020; 11:3301. [PMID: 32620849 PMCID: PMC7335050 DOI: 10.1038/s41467-020-17074-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 06/05/2020] [Indexed: 01/30/2023] Open
Abstract
Many cellular stresses are transduced into apoptotic signals through modification or up-regulation of the BH3-only subfamily of BCL2 proteins. Through direct or indirect mechanisms, these proteins activate BAK and BAX to permeabilize the mitochondrial outer membrane. While the BH3-only proteins BIM, PUMA, and tBID have been confirmed to directly activate BAK through its canonical BH3 binding groove, whether the BH3-only proteins BMF, HRK or BIK can directly activate BAK is less clear. Here we show that BMF and HRK bind and directly activate BAK. Through NMR studies, site-directed mutagenesis, and advanced molecular dynamics simulations, we also find that BAK activation by BMF and possibly HRK involves a previously unrecognized binding groove formed by BAK α4, α6, and α7 helices. Alterations in this groove decrease the ability of BMF and HRK to bind BAK, permeabilize membranes and induce apoptosis, suggesting a potential role for this BH3-binding site in BAK activation. Mitochondrial apoptosis is controlled by BCL2 family proteins, and the BH3-only proteins often act as sensors that transmit apoptotic signals. Here the authors show how the BH3-only proteins BMF and HRK can directly activate the BCL2 protein BAK and interact with BAK through an alternative binding groove.
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Affiliation(s)
- Kaiqin Ye
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Wei X Meng
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hongbin Sun
- School of Food and Biological Engineering, Zhenzhou University of Light Industry, Zhenzhou, 450002, China
| | - Bo Wu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, High Magnetic Field Laboratory, HFIPS, Chinese Academy of Sciences, Hefei, 230031, China
| | - Meng Chen
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yuan-Ping Pang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jia Gao
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Hongzhi Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China.,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China
| | - Junfeng Wang
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, High Magnetic Field Laboratory, HFIPS, Chinese Academy of Sciences, Hefei, 230031, China
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA. .,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Haiming Dai
- Anhui Province Key Laboratory of Medical Physics and Technology, Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China. .,Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, China.
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48
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Suraweera CD, Anasir MI, Chugh S, Javorsky A, Impey RE, Hasan Zadeh M, Soares da Costa TP, Hinds MG, Kvansakul M. Structural insight into tanapoxvirus-mediated inhibition of apoptosis. FEBS J 2020; 287:3733-3750. [PMID: 32412687 DOI: 10.1111/febs.15365] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/26/2020] [Accepted: 05/12/2020] [Indexed: 01/07/2023]
Abstract
Premature programmed cell death or apoptosis of cells is a strategy utilized by multicellular organisms to counter microbial threats. Tanapoxvirus (TANV) is a large double-stranded DNA virus belonging to the poxviridae that causes mild monkeypox-like infections in humans and primates. TANV encodes for a putative apoptosis inhibitory protein 16L. We show that TANV16L is able to bind to a range of peptides spanning the BH3 motif of human proapoptotic Bcl-2 proteins and is able to counter growth arrest of yeast induced by human Bak and Bax. We then determined the crystal structures of TANV16L bound to three identified interactors, Bax, Bim and Puma BH3. TANV16L adopts a globular Bcl-2 fold comprising 7 α-helices and utilizes the canonical Bcl-2 binding groove to engage proapoptotic host cell Bcl-2 proteins. Unexpectedly, TANV16L is able to adopt both a monomeric and a domain-swapped dimeric topology where the α1 helix from one protomer is swapped into a neighbouring unit. Despite adopting two different oligomeric forms, the canonical ligand binding groove in TANV16L remains unchanged from monomer to domain-swapped dimer. Our results provide a structural and mechanistic basis for tanapoxvirus-mediated inhibition of host cell apoptosis and reveal the capacity of Bcl-2 proteins to adopt differential oligomeric states whilst maintaining the canonical ligand binding groove in an unchanged state. DATABASE: Structural data are available in the Protein Data Bank (PDB) under the accession numbers 6TPQ, 6TQQ and 6TRR.
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Affiliation(s)
- Chathura D Suraweera
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Mohd Ishtiaq Anasir
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Srishti Chugh
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Airah Javorsky
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Rachael E Impey
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Mohammad Hasan Zadeh
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Tatiana P Soares da Costa
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Mark G Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
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49
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Panuzzo C, Jovanovski A, Pergolizzi B, Pironi L, Stanga S, Fava C, Cilloni D. Mitochondria: A Galaxy in the Hematopoietic and Leukemic Stem Cell Universe. Int J Mol Sci 2020; 21:ijms21113928. [PMID: 32486249 PMCID: PMC7312164 DOI: 10.3390/ijms21113928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/24/2020] [Accepted: 05/28/2020] [Indexed: 12/17/2022] Open
Abstract
Mitochondria are the main fascinating energetic source into the cells. Their number, shape, and dynamism are controlled by the cell’s type and current behavior. The perturbation of the mitochondrial inward system via stress response and/or oncogenic insults could activate several trafficking molecular mechanisms with the intention to solve the problem. In this review, we aimed to clarify the crucial pathways in the mitochondrial system, dissecting the different metabolic defects, with a special emphasis on hematological malignancies. We investigated the pivotal role of mitochondria in the maintenance of hematopoietic stem cells (HSCs) and their main alterations that could induce malignant transformation, culminating in the generation of leukemic stem cells (LSCs). In addition, we presented an overview of LSCs mitochondrial dysregulated mechanisms in terms of (1) increasing in oxidative phosphorylation program (OXPHOS), as a crucial process for survival and self-renewal of LSCs,(2) low levels of reactive oxygen species (ROS), and (3) aberrant expression of B-cell lymphoma 2 (Bcl-2) with sustained mitophagy. Furthermore, these peculiarities may represent attractive new “hot spots” for mitochondrial-targeted therapy. Finally, we remark the potential of the LCS metabolic effectors to be exploited as novel therapeutic targets.
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Affiliation(s)
- Cristina Panuzzo
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
- Correspondence: (C.P.); (D.C.)
| | - Aleksandar Jovanovski
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
| | - Barbara Pergolizzi
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
| | - Lucrezia Pironi
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
| | - Serena Stanga
- Department of Neuroscience Rita Levi Montalcini, 10124 Turin, Italy;
- Neuroscience Institute Cavalieri Ottolenghi, University of Turin, 10043 Orbassano, Italy
| | - Carmen Fava
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (A.J.); (B.P.); (L.P.); (C.F.)
- Correspondence: (C.P.); (D.C.)
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50
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Robust autoactivation for apoptosis by BAK but not BAX highlights BAK as an important therapeutic target. Cell Death Dis 2020; 11:268. [PMID: 32327636 PMCID: PMC7181796 DOI: 10.1038/s41419-020-2463-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 02/08/2023]
Abstract
BAK and BAX, which drive commitment to apoptosis, are activated principally by certain BH3-only proteins that bind them and trigger major rearrangements. One crucial conformation change is exposure of their BH3 domain which allows BAK or BAX to form homodimers, and potentially to autoactivate other BAK and BAX molecules to ensure robust pore formation and cell death. Here, we test whether full-length BAK or mitochondrial BAX that are specifically activated by antibodies can then activate other BAK or BAX molecules. We found that antibody-activated BAK efficiently activated BAK as well as mitochondrial or cytosolic BAX, but antibody-activated BAX unexpectedly proved a poor activator. Notably, autoactivation by BAK involved transient interactions, as BAK and BAX molecules it activated could dissociate and homodimerize. The results suggest that BAK-driven autoactivation may play a substantial role in apoptosis, including recruitment of BAX to the mitochondria. Hence, directly targeting BAK rather than BAX may prove particularly effective in inhibiting unwanted apoptosis, or alternatively, inducing apoptosis in cancer cells.
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