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Kumutima J, Yao XQ, Hamelberg D. Post-translational Modifications of Cyclophilin D Fine-Tune Its Conformational Dynamics and Activity: Implications for Its Mitochondrial Function. J Phys Chem B 2022; 126:10844-10853. [PMID: 36529932 DOI: 10.1021/acs.jpcb.2c06208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mitochondria are the powerhouse of a cell, whose disruption due to mitochondrial pore opening can cause cell death, leading to necrosis and many other diseases. The peptidyl-prolyl cis-trans isomerase cyclophilin D (CypD) is a key player in the regulation of the mitochondrial pore. The activity of CypD can be modulated by the post-translational modification (PTM). However, the detailed mechanism of this functional modulation is not well understood. Here, we investigate the catalytic mechanism of unmodified and modified CypD by calculating the reaction free energy profiles and characterizing the function-related conformational dynamics using molecular dynamics simulations and associated analyses. Our results show that unmodified and modified CypD considerably lower the isomerization free energy barrier compared to a free peptide substrate, supporting the catalytic activity of CypD in the simulation systems. The unmodified CypD reduces the free energy difference between the cis and trans states of the peptide substrate, suggesting a stronger binding affinity of CypD toward cis, consistent with experiments. In contrast, phosphorylated CypD further stabilizes trans, leading to a lower catalytic rate in the trans-to-cis direction. The differential catalytic activities of the unmodified and phosphorylated CypD are due to a significant shift of the conformational ensemble upon phosphorylation under different functional states. Interestingly, the local flexibility is both reduced and enhanced at distinct regions by phosphorylation, which is explained by a "seesaw" model of flexibility modulation. The allosteric pathway between the phosphorylation site and a distal site displaying substantial conformational changes upon phosphorylation is also identified, which is influenced by the presence of the substrate or the substrate conformation. Similar conclusions are obtained for the acetylation of CypD using the same peptide substrate and the influence of substrate sequence is also examined. Our work may serve as the basis for the understanding of other PTMs and PTM-initiated allosteric regulations in CypD.
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Kumutima J, Yao XQ, Hamelberg D. p53 Is Potentially Regulated by Cyclophilin D in the Triple-Proline Loop of the DNA Binding Domain. Biochemistry 2021; 60:597-606. [PMID: 33591178 DOI: 10.1021/acs.biochem.0c00946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The multifunctional protein p53 is the central molecular sensor of cellular stresses. The canonical function of p53 is to transcriptionally activate target genes in response to, for example, DNA damage that may trigger apoptosis. Recently, p53 was also found to play a role in the regulation of necrosis, another type of cell death featured by the mitochondrial permeability transition (mPT). In this process, p53 directly interacts with the mPT regulator cyclophilin D, the detailed mechanism of which however remains poorly understood. Here, we report a comprehensive computational investigation of the p53-cyclophilin D interaction using molecular dynamics simulations and associated analyses. We have identified the specific cyclophilin D binding site on p53 that is located at proline 151 in the DNA binding domain. As a peptidyl-prolyl isomerase, cyclophilin D binds p53 and catalyzes the cis-trans isomerization of the peptide bond preceding proline 151. We have also characterized the effect of such an isomerization and found that the p53 domain in the cis state is overall more rigid than the trans state except for the local region around proline 151. Dynamical changes upon isomerization occur in both local and distal regions, indicating an allosteric effect elicited by the isomerization. We present potential allosteric communication pathways between proline 151 and distal sites, including the DNA binding surface. Our work provides, for the first time, a model for how cyclophilin D binds p53 and regulates its activity by switching the configuration of a specific site.
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Biasutto L, Azzolini M, Szabò I, Zoratti M. The mitochondrial permeability transition pore in AD 2016: An update. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:2515-30. [PMID: 26902508 DOI: 10.1016/j.bbamcr.2016.02.012] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 12/13/2022]
Abstract
Over the past 30years the mitochondrial permeability transition - the permeabilization of the inner mitochondrial membrane due to the opening of a wide pore - has progressed from being considered a curious artifact induced in isolated mitochondria by Ca(2+) and phosphate to a key cell-death-inducing process in several major pathologies. Its relevance is by now universally acknowledged and a pharmacology targeting the phenomenon is being developed. The molecular nature of the pore remains to this day uncertain, but progress has recently been made with the identification of the FOF1 ATP synthase as the probable proteic substrate. Researchers sharing this conviction are however divided into two camps: these believing that only the ATP synthase dimers or oligomers can form the pore, presumably in the contact region between monomers, and those who consider that the ring-forming c subunits in the FO sector actually constitute the walls of the pore. The latest development is the emergence of a new candidate: Spastic Paraplegia 7 (SPG7), a mitochondrial AAA-type membrane protease which forms a 6-stave barrel. This review summarizes recent developments of research on the pathophysiological relevance and on the molecular nature of the mitochondrial permeability transition pore. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.
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Affiliation(s)
- Lucia Biasutto
- CNR Neuroscience Institute, Viale G. Colombo 3, 35121 Padova, Italy; University of Padova, Department of Biomedical Sciences, Viale G. Colombo 3, 35121 Padova, Italy
| | - Michele Azzolini
- CNR Neuroscience Institute, Viale G. Colombo 3, 35121 Padova, Italy; University of Padova, Department of Biomedical Sciences, Viale G. Colombo 3, 35121 Padova, Italy
| | - Ildikò Szabò
- CNR Neuroscience Institute, Viale G. Colombo 3, 35121 Padova, Italy; University of Padova, Department of Biology, Viale G. Colombo 3, 35121 Padova, Italy
| | - Mario Zoratti
- CNR Neuroscience Institute, Viale G. Colombo 3, 35121 Padova, Italy; University of Padova, Department of Biomedical Sciences, Viale G. Colombo 3, 35121 Padova, Italy.
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Warne J, Pryce G, Hill JM, Shi X, Lennerås F, Puentes F, Kip M, Hilditch L, Walker P, Simone MI, Chan AWE, Towers GJ, Coker AR, Duchen MR, Szabadkai G, Baker D, Selwood DL. Selective Inhibition of the Mitochondrial Permeability Transition Pore Protects against Neurodegeneration in Experimental Multiple Sclerosis. J Biol Chem 2016; 291:4356-73. [PMID: 26679998 PMCID: PMC4813465 DOI: 10.1074/jbc.m115.700385] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/09/2015] [Indexed: 12/23/2022] Open
Abstract
The mitochondrial permeability transition pore is a recognized drug target for neurodegenerative conditions such as multiple sclerosis and for ischemia-reperfusion injury in the brain and heart. The peptidylprolyl isomerase, cyclophilin D (CypD, PPIF), is a positive regulator of the pore, and genetic down-regulation or knock-out improves outcomes in disease models. Current inhibitors of peptidylprolyl isomerases show no selectivity between the tightly conserved cyclophilin paralogs and exhibit significant off-target effects, immunosuppression, and toxicity. We therefore designed and synthesized a new mitochondrially targeted CypD inhibitor, JW47, using a quinolinium cation tethered to cyclosporine. X-ray analysis was used to validate the design concept, and biological evaluation revealed selective cellular inhibition of CypD and the permeability transition pore with reduced cellular toxicity compared with cyclosporine. In an experimental autoimmune encephalomyelitis disease model of neurodegeneration in multiple sclerosis, JW47 demonstrated significant protection of axons and improved motor assessments with minimal immunosuppression. These findings suggest that selective CypD inhibition may represent a viable therapeutic strategy for MS and identify quinolinium as a mitochondrial targeting group for in vivo use.
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Affiliation(s)
- Justin Warne
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Gareth Pryce
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom, the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom
| | - Julia M Hill
- the Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom
| | - Xiao Shi
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Felicia Lennerås
- the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom
| | - Fabiola Puentes
- the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom
| | - Maarten Kip
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Laura Hilditch
- the Medical Research Council Centre for Medical Molecular Biology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Paul Walker
- Cyprotex Discovery Ltd., 100 Barbirolli Square, Manchester M2 3AB, United Kingdom, and
| | - Michela I Simone
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - A W Edith Chan
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Greg J Towers
- the Medical Research Council Centre for Medical Molecular Biology, Division of Infection and Immunity, University College London, London WC1E 6BT, United Kingdom
| | - Alun R Coker
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Michael R Duchen
- the Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom
| | - Gyorgy Szabadkai
- the Department of Cell and Developmental Biology, University College London, London WC1E 6BT, United Kingdom, the Department of Biomedical Sciences, University of Padua, Padua 35122, Italy
| | - David Baker
- the Neuroimmunology Unit, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, United Kingdom,
| | - David L Selwood
- From the Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, United Kingdom,
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