1
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Mayse LA, Movileanu L. Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets. Int J Mol Sci 2023; 24:12095. [PMID: 37569469 PMCID: PMC10418385 DOI: 10.3390/ijms241512095] [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: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.
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Affiliation(s)
- Lauren A. Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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2
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Heslop KA, Burger P, Kappler C, Solanki AK, Gooz M, Peterson YK, Mills C, Benton T, Duncan SA, Woster PM, Maldonado EN. Small molecules targeting the NADH-binding pocket of VDAC modulate mitochondrial metabolism in hepatocarcinoma cells. Biomed Pharmacother 2022; 150:112928. [PMID: 35447542 PMCID: PMC9400819 DOI: 10.1016/j.biopha.2022.112928] [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: 02/11/2022] [Revised: 03/25/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022] Open
Abstract
Voltage dependent anion channels (VDAC) control the flux of most anionic respiratory substrates, ATP, ADP, and small cations, crossing the outer mitochondrial membrane. VDAC closure contributes to the partial suppression of mitochondrial metabolism that favors the Warburg phenotype of cancer cells. Recently, it has been shown that NADH binds to a specific pocket in the inner surface of VDAC1, also conserved in VDAC2 and 3, closing the channel. We hypothesized that binding of small molecules to the NADH pocket, maintain VDAC in an open configuration by preventing closure induced by NADH and possible other endogenous regulators. We screened in silico, the South Carolina Compound Collection SC3 (~ 100,000 proprietary molecules), using shape-based queries of the NADH binding region of VDAC. After molecular docking of selected compounds, we physically screened candidates using mitochondrial membrane potential (ΔΨm), as an overall readout of mitochondrial metabolism. We identified SC18, as the most potent compound. SC18 bound to VDAC1, as assessed by a thermal shift assay. Short-term treatment with SC18 decreased ΔΨm in SNU-449 and HepG2 human hepatocarcinoma cells. Mitochondrial depolarization was similar in wild type, VDAC1/2, 1/3, and 2/3 double KO HepG2 cells indicating that the effect of SC18 was not VDAC isoform-dependent. In addition, SC18 decreased mitochondrial NADH and cellular ATP production; and increased basal respiration. Long-term exposure to SC18, decreased cell proliferation as determined by wound-healing and cell viability assays. In summary, SC18 is a novel VDAC-targeting small molecule that induces mitochondrial dysfunction and inhibits cell proliferation.
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Affiliation(s)
- Kareem A Heslop
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Pieter Burger
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Christiana Kappler
- Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Ashish K Solanki
- Nephrology Division, Medical University of South Carolina, Charleston, SC, USA
| | - Monika Gooz
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Yuri K Peterson
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Catherine Mills
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Thomas Benton
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Stephen A Duncan
- Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Patrick M Woster
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Eduardo N Maldonado
- Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC, USA; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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3
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Najbauer EE, Tekwani Movellan K, Giller K, Benz R, Becker S, Griesinger C, Andreas LB. Structure and Gating Behavior of the Human Integral Membrane Protein VDAC1 in a Lipid Bilayer. J Am Chem Soc 2022; 144:2953-2967. [PMID: 35164499 PMCID: PMC8874904 DOI: 10.1021/jacs.1c09848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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The voltage-dependent
anion channel (VDAC), the most abundant protein
in the outer mitochondrial membrane, is responsible for the transport
of all ions and metabolites into and out of mitochondria. Larger than
any of the β-barrel structures determined to date by magic-angle
spinning (MAS) NMR, but smaller than the size limit of cryo-electron
microscopy (cryo-EM), VDAC1’s 31 kDa size has long been a bottleneck
in determining its structure in a near-native lipid bilayer environment.
Using a single two-dimensional (2D) crystalline sample of human VDAC1
in lipids, we applied proton-detected fast magic-angle spinning NMR
spectroscopy to determine the arrangement of β strands. Combining
these data with long-range restraints from a spin-labeled sample,
chemical shift-based secondary structure prediction, and previous
MAS NMR and atomic force microscopy (AFM) data, we determined the
channel’s structure at a 2.2 Å root-mean-square deviation
(RMSD). The structure, a 19-stranded β-barrel, with an N-terminal
α-helix in the pore is in agreement with previous data in detergent,
which was questioned due to the potential for the detergent to perturb
the protein’s functional structure. Using a quintuple mutant
implementing the channel’s closed state, we found that dynamics
are a key element in the protein’s gating behavior, as channel
closure leads to the destabilization of not only the C-terminal barrel
residues but also the α2 helix. We showed that cholesterol,
previously shown to reduce the frequency of channel closure, stabilizes
the barrel relative to the N-terminal helix. Furthermore, we observed
channel closure through steric blockage by a drug shown to selectively
bind to the channel, the Bcl2-antisense oligonucleotide G3139.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Roland Benz
- Life Sciences and Chemistry, Jacobs University of Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
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4
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Homocysteine-Thiolactone Modulates Gating of Mitochondrial Voltage-Dependent Anion Channel (VDAC) and Protects It from Induced Oxidative Stress. J Membr Biol 2022; 255:79-97. [PMID: 35103807 DOI: 10.1007/s00232-022-00215-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/10/2022] [Indexed: 12/26/2022]
Abstract
The gating of the Voltage-Dependent Anion Channel (VDAC) is linked to oxidative stress through increased generation of mitochondrial ROS with increasing mitochondrial membrane potential (ΔΨm). It has been already reported that H2O2 increases the single-channel conductance of VDAC on a bilayer lipid membrane. On the other hand, homocysteine (Hcy) has been reported to induce mitochondria-mediated cell death. It is argued that the thiol-form of homocysteine, HTL could be the plausible molecule responsible for the alteration in the function of proteins, such as VDAC. It is hypothesized that HTL interacts with VDAC that causes functional abnormalities. An investigation was undertaken to study the interaction of HTL with VDAC under H2O2 induced oxidative stress through biophysical and electrophysiological methods. Fluorescence spectroscopic studies indicate that HTL interacts with VDAC, but under induced oxidative stress the effect is prevented partially. Similarly, bilayer electrophysiology studies suggest that HTL shows a reduction in VDAC single-channel conductance, but the effects are partially prevented under an oxidative environment. Gly172 and His181 are predicted through bioinformatics tools to be the most plausible binding residues of HTL in Rat VDAC. The binding of HTL and H2O2 with VDAC appears to be cooperative as per our analysis of experimental data in the light of the Hill-Langmuir equation. The binding energies are estimated to be - 4.7 kcal mol-1 and - 2.8 kcal mol-1, respectively. The present in vitro studies suggest that when mitochondrial VDAC is under oxidative stress, the effects of amino acid metabolites like HTL are suppressed.
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The Molecular Mechanism of Human Voltage-Dependent Anion Channel 1 Blockade by the Metallofullerenol Gd@C82(OH)22: An In Silico Study. Biomolecules 2022; 12:biom12010123. [PMID: 35053271 PMCID: PMC8773804 DOI: 10.3390/biom12010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
The endohedral metallofullerenol Gd@C82(OH)22 has been identified as a possible antineoplastic agent that can inhibit both the growth and metastasis of cancer cells. Despite these potentially important effects, our understanding of the interactions between Gd@C82(OH)22 and biomacromolecules remains incomplete. Here, we study the interaction between Gd@C82(OH)22 and the human voltage-dependent anion channel 1 (hVDAC1), the most abundant porin embedded in the mitochondrial outer membrane (MOM), and a potential druggable target for novel anticancer therapeutics. Using in silico approaches, we observe that Gd@C82(OH)22 molecules can permeate and form stable interactions with the pore of hVDAC1. Further, this penetration can occur from either side of the MOM to elicit blockage of the pore. The binding between Gd@C82(OH)22 and hVDAC1 is largely driven by long-range electrostatic interactions. Analysis of the binding free energies indicates that it is thermodynamically more favorable for Gd@C82(OH)22 to bind to the hVDAC1 pore when it enters the channel from inside the membrane rather than from the cytoplasmic side of the protein. Multiple factors contribute to the preferential penetration, including the surface electrostatic landscape of hVDAC1 and the unique physicochemical properties of Gd@C82(OH)22. Our findings provide insights into the potential molecular interactions of macromolecular biological systems with the Gd@C82(OH)22 nanodrug.
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6
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Gong J, Zhu M, Zhan M, Xi C, Xu Z, Shui Y, Shen H. PcVDAC promotes WSSV infection by regulating the apoptotic activity of haemocytes in Procambarus clarkii. Comp Biochem Physiol B Biochem Mol Biol 2021; 259:110697. [PMID: 34798242 DOI: 10.1016/j.cbpb.2021.110697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022]
Abstract
Apoptosis is programmed cell death that is strictly regulated by a series of related genes and is of great importance in resisting pathogen invasion and maintaining cell environment homeostasis. Among apoptotic proteins, the voltage-dependent anion channel protein (VDAC) plays a key role in the mitochondrial apoptosis pathway because of its close connection with changes in mitochondrial membrane potential. However, the role of VDAC in apoptosis and immune regulation in Procambarus clarkii is poorly understood. In this study, the VDAC gene in P. clarkii (PcVDAC) was cloned by rapid amplification of cDNA ends (RACE) technology. The gene was found to have a total length of 2277 bp, including a 194-bp 5'-UTR, 1234-bp 3'-UTR and 849-bp open reading frame (ORF), and to encode 282 amino acids. PcVDAC was expressed in all tissues tested, and its expression was upregulated after white spot syndrome virus (WSSV) infection (P < 0.05). The RNA interference (RNAi) method was used to explore the role of PcVDAC in WSSV infection. The results showed that the number of WSSV copies in haemocytes was significantly reduced after RNAi (P < 0.05), and the survival rate was significantly increased. In addition, after RNAi, the apoptosis rate was significantly increased (P < 0.05), the mitochondrial membrane potential was reduced (P < 0.01), and the expression of caspase-3 and other genes was upregulated (P < 0.05). These results indicate that PcVDAC promotes the replication of WSSV in P. clarkii by inhibiting haemocytes apoptosis. Therefore, the results presented in this paper provide new insights into the immune response of P. clarkii infected with WSSV.
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Affiliation(s)
- Jie Gong
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Mengru Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Ming Zhan
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changjun Xi
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Zenghong Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Yan Shui
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Huaishun Shen
- Wuxi Fisheries College, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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7
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Heslop KA, Milesi V, Maldonado EN. VDAC Modulation of Cancer Metabolism: Advances and Therapeutic Challenges. Front Physiol 2021; 12:742839. [PMID: 34658929 PMCID: PMC8511398 DOI: 10.3389/fphys.2021.742839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/25/2021] [Indexed: 12/16/2022] Open
Abstract
Most anionic metabolites including respiratory substrates, glycolytic adenosine triphosphate (ATP), and small cations that enter mitochondria, and mitochondrial ATP moving to the cytosol, cross the outer mitochondrial membrane (OMM) through voltage dependent anion channels (VDAC). The closed states of VDAC block the passage of anionic metabolites, and increase the flux of small cations, including calcium. Consequently, physiological or pharmacological regulation of VDAC opening, by conditioning the magnitude of both anion and cation fluxes, is a major contributor to mitochondrial metabolism. Tumor cells display a pro-proliferative Warburg phenotype characterized by enhanced aerobic glycolysis in the presence of partial suppression of mitochondrial metabolism. The heterogeneous and flexible metabolic traits of most human tumors render cells able to adapt to the constantly changing energetic and biosynthetic demands by switching between predominantly glycolytic or oxidative phenotypes. Here, we describe the biological consequences of changes in the conformational state of VDAC for cancer metabolism, the mechanisms by which VDAC-openers promote cancer cell death, and the advantages of VDAC opening as a valuable pharmacological target. Particular emphasis is given to the endogenous regulation of VDAC by free tubulin and the effects of VDAC-tubulin antagonists in cancer cells. Because of its function and location, VDAC operates as a switch to turn-off mitochondrial metabolism (closed state) and increase aerobic glycolysis (pro-Warburg), or to turn-on mitochondrial metabolism (open state) and decrease glycolysis (anti-Warburg). A better understanding of the role of VDAC regulation in tumor progression is relevant both for cancer biology and for developing novel cancer chemotherapies.
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Affiliation(s)
- Kareem A Heslop
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Veronica Milesi
- Facultad de Ciencias Exactas, Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP), UNLP, CONICET, CIC PBA, La Plata, Argentina
| | - Eduardo N Maldonado
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, United States.,Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
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8
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Molecular mechanism of thiamine pyrophosphate import into mitochondria: a molecular simulation study. J Comput Aided Mol Des 2021; 35:987-1007. [PMID: 34406552 DOI: 10.1007/s10822-021-00414-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
The import of thiamine pyrophosphate (TPP) through both mitochondrial membranes was studied using a total of 3-µs molecular dynamics simulations. Regarding the translocation through the mitochondrial outer membrane, our simulations support the conjecture that TPP uses the voltage-dependent anion channel, the major pore of this membrane, for its passage to the intermembrane space, as its transport presents significant analogies with that used by other metabolites previously studied, in particular with ATP. As far as passing through the mitochondrial inner membrane is concerned, our simulations show that the specific carrier of TPP has a single binding site that becomes accessible, through an alternating access mechanism. The preference of this transporter for TPP can be rationalized mainly by three residues located in the binding site that differ from those identified in the ATP/ADP carrier, the most studied member of the mitochondrial carrier family. The simulated transport mechanism of TPP highlights the essential role, at the energetic level, of the contributions coming from the formation and breakage of two networks of salt bridges, one on the side of the matrix and the other on the side of the intermembrane space, as well as the interactions, mainly of an ionic nature, formed by TPP upon its binding. The energy contribution provided by the cytosolic network establishes a lower barrier than that of the matrix network, which can be explained by the lower interaction energy of TPP on the matrix side or possibly a uniport activity.
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9
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NAD(H) Regulates the Permeability Transition Pore in Mitochondria through an External Site. Int J Mol Sci 2021; 22:ijms22168560. [PMID: 34445270 PMCID: PMC8395297 DOI: 10.3390/ijms22168560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/28/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
The opening of the permeability transition pore (mPTP) in mitochondria initiates cell death in numerous diseases. The regulation of mPTP by NAD(H) in the mitochondrial matrix is well established; however, the role of extramitochondrial (cytosolic) NAD(H) is still unclear. We studied the effect of added NADH and NAD+ on: (1) the Ca2+-retention capacity (CRC) of isolated rat liver, heart, and brain mitochondria; (2) the Ca2+-dependent mitochondrial swelling in media whose particles can (KCl) or cannot (sucrose) be extruded from the matrix by mitochondrial carriers; (3) the Ca2+-dependent mitochondrial depolarization and the release of entrapped calcein from mitochondria of permeabilized hepatocytes; and (4) the Ca2+-dependent mitochondrial depolarization and subsequent repolarization. NADH and NAD+ increased the CRC of liver, heart, and brain mitochondria 1.5-2.5 times, insignificantly affecting the rate of Ca2+-uptake and the free Ca2+ concentration in the medium. NAD(H) suppressed the Ca2+-dependent mitochondrial swelling both in KCl- and sucrose-based media but did not induce the contraction and repolarization of swollen mitochondria. By contrast, EGTA caused mitochondrial repolarization in both media and the contraction in KCl-based medium only. NAD(H) delayed the Ca2+-dependent depolarization and the release of calcein from individual mitochondria in hepatocytes. These data unambiguously demonstrate the existence of an external NAD(H)-dependent site of mPTP regulation.
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10
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Najbauer EE, Becker S, Giller K, Zweckstetter M, Lange A, Steinem C, de Groot BL, Griesinger C, Andreas LB. Structure, gating and interactions of the voltage-dependent anion channel. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:159-172. [PMID: 33782728 PMCID: PMC8071794 DOI: 10.1007/s00249-021-01515-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 12/14/2022]
Abstract
The voltage-dependent anion channel (VDAC) is one of the most highly abundant proteins found in the outer mitochondrial membrane, and was one of the earliest discovered. Here we review progress in understanding VDAC function with a focus on its structure, discussing various models proposed for voltage gating as well as potential drug targets to modulate the channel's function. In addition, we explore the sensitivity of VDAC structure to variations in the membrane environment, comparing DMPC-only, DMPC with cholesterol, and near-native lipid compositions, and use magic-angle spinning NMR spectroscopy to locate cholesterol on the outside of the β-barrel. We find that the VDAC protein structure remains unchanged in different membrane compositions, including conditions with cholesterol.
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Affiliation(s)
- Eszter E Najbauer
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Karin Giller
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
- Senior Research Group of Translational Structural Biology in Dementia, Deutsches Zentrum Für Neurodegenerative Erkrankungen (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
- Department of Neurology, University Medical Center Göttingen, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut Für Molekulare Pharmakologie, 13125, Berlin, Germany
- Institut Für Biologie, Humboldt-Universität Zu Berlin, 10115, Berlin, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
- Max-Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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11
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Shoshan-Barmatz V, Shteinfer-Kuzmine A, Verma A. VDAC1 at the Intersection of Cell Metabolism, Apoptosis, and Diseases. Biomolecules 2020; 10:E1485. [PMID: 33114780 PMCID: PMC7693975 DOI: 10.3390/biom10111485] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/02/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
The voltage-dependent anion channel 1 (VDAC1) protein, is an important regulator of mitochondrial function, and serves as a mitochondrial gatekeeper, with responsibility for cellular fate. In addition to control over energy sources and metabolism, the protein also regulates epigenomic elements and apoptosis via mediating the release of apoptotic proteins from the mitochondria. Apoptotic and pathological conditions, as well as certain viruses, induce cell death by inducing VDAC1 overexpression leading to oligomerization, and the formation of a large channel within the VDAC1 homo-oligomer. This then permits the release of pro-apoptotic proteins from the mitochondria and subsequent apoptosis. Mitochondrial DNA can also be released through this channel, which triggers type-Ι interferon responses. VDAC1 also participates in endoplasmic reticulum (ER)-mitochondria cross-talk, and in the regulation of autophagy, and inflammation. Its location in the outer mitochondrial membrane, makes VDAC1 ideally placed to interact with over 100 proteins, and to orchestrate the interaction of mitochondrial and cellular activities through a number of signaling pathways. Here, we provide insights into the multiple functions of VDAC1 and describe its involvement in several diseases, which demonstrate the potential of this protein as a druggable target in a wide variety of pathologies, including cancer.
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Affiliation(s)
- Varda Shoshan-Barmatz
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; (A.S.-K.); (A.V.)
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12
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Regulation of permeability transition pore opening in mitochondria by external NAD(H). Biochim Biophys Acta Gen Subj 2019; 1863:771-783. [PMID: 30763605 DOI: 10.1016/j.bbagen.2019.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The opening of the permeability transition pore (PTP) in mitochondria plays a critical role in the pathogenesis of numerous diseases. Mitochondrial matrix pyridine nucleotides are potent regulators of the PTP, but the role of extramitochondrial nucleotides is unclear. METHODS The PTP opening was explored in isolated mitochondria and mitochondria in permeabilized differentiated and undifferentiated cells in the presence of added NAD(P)(H) in combination with Mg2+, adenine nucleotides (AN), and the inhibitors of AN translocase (ANT), voltage-dependent anion channel (VDAC), and cyclophilin D. RESULTS Added NAD(H) and AN, but not NADP(H), inhibited the PTP opening with comparable potency. PTP suppression required neither NAD(H) oxidation nor reduction. The protective effects of NAD(H) and cyclosporin A were synergistic, and the effects of NAD(H) and millimolar AN were additive. The conformation-specific ANT inhibitors were unable to cancel the protective effect of NADH even under total ANT inhibition. Besides, NAD(H) activated the efflux of mitochondrial AN via ANT. VDAC ligand (Mg2+) and blockers (G3139 and 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid) potentiated and attenuated the protective effect of NAD(H), respectively. However, in embryonic and cancer (undifferentiated) cells, in contrast to isolated differentiated hepatocytes and cardiocytes, the suppression of PTP opening by NADH was negligible though all cells tested possessed a full set of VDAC isoforms. CONCLUSIONS The study revealed a novel mechanism of PTP regulation by external (cytosolic) NAD(H) through the allosteric site in the OM or the intermembrane space. GENERAL SIGNIFICANCE The mechanism might contribute to the resistance of differentiated cells under different pathological conditions including ischemia/reperfusion.
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13
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Van Liefferinge F, Krammer EM, Sengupta D, Prévost M. Lipid composition and salt concentration as regulatory factors of the anion selectivity of VDAC studied by coarse-grained molecular dynamics simulations. Chem Phys Lipids 2018; 220:66-76. [PMID: 30448398 DOI: 10.1016/j.chemphyslip.2018.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/08/2018] [Accepted: 11/12/2018] [Indexed: 12/27/2022]
Abstract
The voltage-dependent anion channel (VDAC) is a mitochondrial outer membrane protein whose fundamental function is to facilitate and regulate the flow of metabolites between the cytosol and the mitochondrial intermembrane space. Using coarse-grained molecular dynamics simulations, we investigated the dependence of VDAC selectivity towards small inorganic anions on two factors: the ionic strength and the lipid composition. In agreement with experimental data we found that VDAC becomes less anion selective with increasing salt concentration due to the screening of a few basic residues that point into the pore lumen. The molecular dynamics simulations provide insight into the regulation mechanism of VDAC selectivity by the composition in the lipid membrane and suggest that the ion distribution is differently modulated by POPE compared to the POPC bilayer. This occurs through the more persistent interactions of acidic residues located at both rims of the β-barrel with head groups of POPE which in turn impact the electrostatic potential and thereby the selectivity of the pore. This mechanism occurs not only in POPE single component membranes but also in a mixed POPE/POPC bilayer by an enrichment of POPE over POPC lipids on the surface of VDAC. Thus we show here that computationally-inexpensive coarse-grained simulations are able to capture, in a semi-quantitative way, essential features of VDAC anion selectivity and could pave the way toward a molecular level understanding of metabolite transport in natural membranes.
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Affiliation(s)
- F Van Liefferinge
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - E-M Krammer
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - D Sengupta
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411 008, India
| | - M Prévost
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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14
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Gupta R, Ghosh S. Phosphorylation of purified mitochondrial Voltage-Dependent Anion Channel by c-Jun N-terminal Kinase-3 modifies channel voltage-dependence. BIOCHIMIE OPEN 2017; 4:78-87. [PMID: 29450145 PMCID: PMC5802065 DOI: 10.1016/j.biopen.2017.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/02/2017] [Indexed: 02/05/2023]
Abstract
Voltage-Dependent Anion Channel (VDAC) phosphorylated by c-Jun N-terminal Kinase-3 (JNK3) was incorporated into the bilayer lipid membrane. Single-channel electrophysiological properties of the native and the phosphorylated VDAC were compared. The open probability versus voltage curve of the native VDAC displayed symmetry around the voltage axis, whereas that of the phosphorylated VDAC showed asymmetry. This result indicates that phosphorylation by JNK3 modifies voltage-dependence of VDAC.
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Affiliation(s)
- Rajeev Gupta
- Department of Physiology, All India Institute of Medical Sciences, New Delhi, India
| | - Subhendu Ghosh
- Department of Biophysics, University of Delhi South Campus, India
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15
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Briones R, Weichbrodt C, Paltrinieri L, Mey I, Villinger S, Giller K, Lange A, Zweckstetter M, Griesinger C, Becker S, Steinem C, de Groot BL. Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1. Biophys J 2016; 111:1223-1234. [PMID: 27653481 PMCID: PMC5034351 DOI: 10.1016/j.bpj.2016.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/17/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022] Open
Abstract
The voltage-dependent anion channel 1 (VDAC-1) is an important protein of the outer mitochondrial membrane that transports energy metabolites and is involved in apoptosis. The available structures of VDAC proteins show a wide β-stranded barrel pore, with its N-terminal α-helix (N-α) bound to its interior. Electrophysiology experiments revealed that voltage, its polarity, and membrane composition modulate VDAC currents. Experiments with VDAC-1 mutants identified amino acids that regulate the gating process. However, the mechanisms for how these factors regulate VDAC-1, and which changes they trigger in the channel, are still unknown. In this study, molecular dynamics simulations and single-channel experiments of VDAC-1 show agreement for the current-voltage relationships of an "open" channel and they also show several subconducting transient states that are more cation selective in the simulations. We observed voltage-dependent asymmetric distortions of the VDAC-1 barrel and the displacement of particular charged amino acids. We constructed conformational models of the protein voltage response and the pore changes that consistently explain the protein conformations observed at opposite voltage polarities, either in phosphatidylethanolamine or phosphatidylcholine membranes. The submicrosecond VDAC-1 voltage response shows intrinsic structural changes that explain the role of key gating amino acids and support some of the current gating hypotheses. These voltage-dependent protein changes include asymmetric barrel distortion, its interaction with the membrane, and significant displacement of N-α amino acids.
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Affiliation(s)
- Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany.
| | - Conrad Weichbrodt
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany
| | - Licia Paltrinieri
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Ingo Mey
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany
| | - Saskia Villinger
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Karin Giller
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Adam Lange
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Markus Zweckstetter
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany; Department of Neurology, University Medical Center, University of Goettingen, Goettingen, Germany
| | - Christian Griesinger
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Stefan Becker
- NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany
| | - Claudia Steinem
- Institute of Organic and Biomolecular Chemistry, University of Goettingen, Goettingen, Germany.
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany.
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16
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Revisiting trends on mitochondrial mega-channels for the import of proteins and nucleic acids. J Bioenerg Biomembr 2016; 49:75-99. [DOI: 10.1007/s10863-016-9662-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/25/2016] [Indexed: 12/14/2022]
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17
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The N-terminus of VDAC: Structure, mutational analysis, and a potential role in regulating barrel shape. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1350-61. [PMID: 26997586 DOI: 10.1016/j.bbamem.2016.03.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/12/2016] [Accepted: 03/17/2016] [Indexed: 01/24/2023]
Abstract
A novel feature of the voltage-dependent anion channel (VDAC, mitochondrial porin), is the barrel, comprising an odd number of β-strands and closed by parallel strands. Recent research has focused on the N-terminal segment, which in the available structures, resides in the lumen and is not part of the barrel. In this review, the structural data obtained from vertebrate VDAC are integrated with those from VDAC in artificial bilayers, emphasizing the array of native and tagged versions of VDAC used. The data are discussed with respect to a recent gating model (Zachariae et al. (2012) Structure 20:1-10), in which the N-terminus acts not as a gate on a stable barrel, but rather stabilizes the barrel, preventing its shift into a partially collapsed, low-conductance, closed state. Additionally, the role of the N-terminus in VDAC oligomerization, apoptosis through interactions with hexokinase and its interaction with ATP are discussed briefly.
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18
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Li Y, Zhang L, Qu T, Li L, Zhang G. Characterization of Oyster Voltage-Dependent Anion Channel 2 (VDAC2) Suggests Its Involvement in Apoptosis and Host Defense. PLoS One 2016; 11:e0146049. [PMID: 26727366 PMCID: PMC4700975 DOI: 10.1371/journal.pone.0146049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 12/11/2015] [Indexed: 01/03/2023] Open
Abstract
Genomic and transcriptomic studies have revealed a sophisticated and powerful apoptosis regulation network in oyster, highlighting its adaptation to sessile life in a highly stressful intertidal environment. However, the functional molecular basis of apoptosis remains largely unexplored in oysters. In this study, we focused on a representative apoptotic gene encoding voltage-dependent anion channel 2 (VDAC2), a porin that abounds at the mitochondrial outer membrane. This is the first report on the identification and characterization of a VDAC gene in the Pacific oyster, Crassostrea gigas (CgVDAC2). The full length of CgVDAC2 was 1,738 bp with an open reading frame of 843 bp that encoded a protein of 281 amino acids. A four-element eukaryotic porin signature motif, a conserved ATP binding motif, and a VKAKV-like sequence were identified in the predicted CgVDAC2. Expression pattern analysis in different tissues and developmental stages as well as upon infection by ostreid herpesvirus 1 revealed the energy supply-related and immunity-related expression of CgVDAC2. CgVDAC2 was co-localized with mitochondria when it was transiently transfected into HeLa cells. Overexpression of CgVDAC2 in HEK293T cells suppressed the UV irradiation-induced apoptosis by inhibiting the pro-apoptotic function of CgBak. RNA interference induced reduction in CgVDAC2 expression showed a promoted apoptosis level upon UV light irradiation in hemocytes. The yeast two-hybrid system and co-immunoprecipitation assay indicated a direct interaction between CgVDAC2 and the pro-apoptotic protein CgBak. This study revealed the function of VDAC2 in oyster and provided new insights into its involvement in apoptosis modulation and host defense in mollusks.
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Affiliation(s)
- Yingxiang Li
- University of Chinese Academy of Sciences, Beijing, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Linlin Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Tao Qu
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Li
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (LL); (GZ)
| | - Guofan Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (LL); (GZ)
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19
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Suzuki T, Yamaguchi H, Kikusato M, Hashizume O, Nagatoishi S, Matsuo A, Sato T, Kudo T, Matsuhashi T, Murayama K, Ohba Y, Watanabe S, Kanno SI, Minaki D, Saigusa D, Shinbo H, Mori N, Yuri A, Yokoro M, Mishima E, Shima H, Akiyama Y, Takeuchi Y, Kikuchi K, Toyohara T, Suzuki C, Ichimura T, Anzai JI, Kohzuki M, Mano N, Kure S, Yanagisawa T, Tomioka Y, Toyomizu M, Tsumoto K, Nakada K, Bonventre JV, Ito S, Osaka H, Hayashi KI, Abe T. Mitochonic Acid 5 Binds Mitochondria and Ameliorates Renal Tubular and Cardiac Myocyte Damage. J Am Soc Nephrol 2015; 27:1925-32. [PMID: 26609120 DOI: 10.1681/asn.2015060623] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 09/24/2015] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial dysfunction causes increased oxidative stress and depletion of ATP, which are involved in the etiology of a variety of renal diseases, such as CKD, AKI, and steroid-resistant nephrotic syndrome. Antioxidant therapies are being investigated, but clinical outcomes have yet to be determined. Recently, we reported that a newly synthesized indole derivative, mitochonic acid 5 (MA-5), increases cellular ATP level and survival of fibroblasts from patients with mitochondrial disease. MA-5 modulates mitochondrial ATP synthesis independently of oxidative phosphorylation and the electron transport chain. Here, we further investigated the mechanism of action for MA-5. Administration of MA-5 to an ischemia-reperfusion injury model and a cisplatin-induced nephropathy model improved renal function. In in vitro bioenergetic studies, MA-5 facilitated ATP production and reduced the level of mitochondrial reactive oxygen species (ROS) without affecting activity of mitochondrial complexes I-IV. Additional assays revealed that MA-5 targets the mitochondrial protein mitofilin at the crista junction of the inner membrane. In Hep3B cells, overexpression of mitofilin increased the basal ATP level, and treatment with MA-5 amplified this effect. In a unique mitochondrial disease model (Mitomice with mitochondrial DNA deletion that mimics typical human mitochondrial disease phenotype), MA-5 improved the reduced cardiac and renal mitochondrial respiration and seemed to prolong survival, although statistical analysis of survival times could not be conducted. These results suggest that MA-5 functions in a manner differing from that of antioxidant therapy and could be a novel therapeutic drug for the treatment of cardiac and renal diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Takehiro Suzuki
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and Renal Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hiroaki Yamaguchi
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Motoi Kikusato
- Animal Nutrition, Life Sciences, Graduate School of Agricultural Science
| | - Osamu Hashizume
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Akihiro Matsuo
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | | | - Tai Kudo
- Primetech Co. Ltd., Tokyo, Japan
| | | | | | - Yuki Ohba
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Shun Watanabe
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Shin-Ichiro Kanno
- Division of Dynamic Proteome in Cancer and Aging, Institute of Development, Aging and Cancer
| | | | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | | | - Akinori Yuri
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Miyuki Yokoro
- Department of Food Sciences and Nutrition, School of Human Environmental Sciences, Mukogawa Women's University, Nishinomiya, Japan
| | - Eikan Mishima
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Hisato Shima
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | | | - Yoichi Takeuchi
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Koichi Kikuchi
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Chitose Suzuki
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Takaharu Ichimura
- Renal Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | | | | | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Masaaki Toyomizu
- Animal Nutrition, Life Sciences, Graduate School of Agricultural Science
| | - Kohei Tsumoto
- Department of Bioengineering, University of Tokyo, Tokyo, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Joseph V Bonventre
- Renal Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Sadayoshi Ito
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and
| | - Hitoshi Osaka
- Division of Pediatrics, Jichi Medical University, Tochigi, Japan; and
| | - Ken-Ichi Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama, Japan
| | - Takaaki Abe
- Divisions of Nephrology, Endocrinology, and Vascular Medicine and Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan;
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20
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Phosphorylation, nitrosation and plasminogen K3 modulation make VDAC-1 lucid as part of the extrinsic apoptotic pathway—Resulting thesis: Native VDAC-1 indispensible for finalisation of its 3D structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1410-6. [DOI: 10.1016/j.bbamem.2015.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 02/17/2015] [Accepted: 02/25/2015] [Indexed: 02/06/2023]
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21
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Krammer EM, Vu GT, Homblé F, Prévost M. Dual mechanism of ion permeation through VDAC revealed with inorganic phosphate ions and phosphate metabolites. PLoS One 2015; 10:e0121746. [PMID: 25860993 PMCID: PMC4393092 DOI: 10.1371/journal.pone.0121746] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/03/2015] [Indexed: 11/19/2022] Open
Abstract
In the exchange of metabolites and ions between the mitochondrion and the cytosol, the voltage-dependent anion channel (VDAC) is a key element, as it forms the major transport pathway for these compounds through the mitochondrial outer membrane. Numerous experimental studies have promoted the idea that VDAC acts as a regulator of essential mitochondrial functions. In this study, using a combination of molecular dynamics simulations, free-energy calculations, and electrophysiological measurements, we investigated the transport of ions through VDAC, with a focus on phosphate ions and metabolites. We showed that selectivity of VDAC towards small anions including monovalent phosphates arises from short-lived interactions with positively charged residues scattered throughout the pore. In dramatic contrast, permeation of divalent phosphate ions and phosphate metabolites (AMP and ATP) involves binding sites along a specific translocation pathway. This permeation mechanism offers an explanation for the decrease in VDAC conductance measured in the presence of ATP or AMP at physiological salt concentration. The binding sites occur at similar locations for the divalent phosphate ions, AMP and ATP, and contain identical basic residues. ATP features a marked affinity for a central region of the pore lined by two lysines and one arginine of the N-terminal helix. This cluster of residues together with a few other basic amino acids forms a "charged brush" which facilitates the passage of the anionic metabolites through the pore. All of this reveals that VDAC controls the transport of the inorganic phosphates and phosphate metabolites studied here through two different mechanisms.
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Affiliation(s)
- Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Giang Thi Vu
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles (ULB), Brussels, Belgium
- * E-mail: (MP)
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22
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Gattin Z, Schneider R, Laukat Y, Giller K, Maier E, Zweckstetter M, Griesinger C, Benz R, Becker S, Lange A. Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2. JOURNAL OF BIOMOLECULAR NMR 2015; 61:311-20. [PMID: 25399320 PMCID: PMC5653203 DOI: 10.1007/s10858-014-9876-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/11/2014] [Indexed: 05/22/2023]
Abstract
The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles.
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Affiliation(s)
- Zrinka Gattin
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Max Planck Institute for Dynamics and Selforganisation, Am Fassberg 17, 37077 Göttingen, Germany
| | - Robert Schneider
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Bât. C9, 59655 Villeneuve d'Ascq, France
| | - Yvonne Laukat
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elke Maier
- Lehrstuhl für Biotechnologie, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Markus Zweckstetter
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Deutsches Zentrum für neurodegenerative Erkrankungen (DZNE), Göttingen, Germany
- Center for the Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany
| | - Christian Griesinger
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Roland Benz
- Lehrstuhl für Biotechnologie, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefan Becker
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstr. 110, 10115 Berlin, Germany
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23
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Monaco G, Decrock E, Arbel N, van Vliet AR, La Rovere RM, De Smedt H, Parys JB, Agostinis P, Leybaert L, Shoshan-Barmatz V, Bultynck G. The BH4 domain of anti-apoptotic Bcl-XL, but not that of the related Bcl-2, limits the voltage-dependent anion channel 1 (VDAC1)-mediated transfer of pro-apoptotic Ca2+ signals to mitochondria. J Biol Chem 2015; 290:9150-61. [PMID: 25681439 DOI: 10.1074/jbc.m114.622514] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Indexed: 01/01/2023] Open
Abstract
Excessive Ca(2+) fluxes from the endoplasmic reticulum to the mitochondria result in apoptotic cell death. Bcl-2 and Bcl-XL proteins exert part of their anti-apoptotic function by directly targeting Ca(2+)-transport systems, like the endoplasmic reticulum-localized inositol 1,4,5-trisphosphate receptors (IP3Rs) and the voltage-dependent anion channel 1 (VDAC1) at the outer mitochondrial membranes. We previously demonstrated that the Bcl-2 homology 4 (BH4) domain of Bcl-2 protects against Ca(2+)-dependent apoptosis by binding and inhibiting IP3Rs, although the BH4 domain of Bcl-XL was protective independently of binding IP3Rs. Here, we report that in contrast to the BH4 domain of Bcl-2, the BH4 domain of Bcl-XL binds and inhibits VDAC1. In intact cells, delivery of the BH4-Bcl-XL peptide via electroporation limits agonist-induced mitochondrial Ca(2+) uptake and protects against staurosporine-induced apoptosis, in line with the results obtained with VDAC1(-/-) cells. Moreover, the delivery of the N-terminal domain of VDAC1 as a synthetic peptide (VDAC1-NP) abolishes the ability of BH4-Bcl-XL to suppress mitochondrial Ca(2+) uptake and to protect against apoptosis. Importantly, VDAC1-NP did not affect the ability of BH4-Bcl-2 to suppress agonist-induced Ca(2+) release in the cytosol or to prevent apoptosis, as done instead by an IP3R-derived peptide. In conclusion, our data indicate that the BH4 domain of Bcl-XL, but not that of Bcl-2, selectively targets VDAC1 and inhibits apoptosis by decreasing VDAC1-mediated Ca(2+) uptake into the mitochondria.
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Affiliation(s)
- Giovanni Monaco
- From the Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, and
| | - Elke Decrock
- the Physiology Group, Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Nir Arbel
- the Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Alexander R van Vliet
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Rita M La Rovere
- From the Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, and the Laboratory of Cellular Physiology, Department of Neuroscience Imaging and Clinical Sciences, Faculty of Pharmacy, "G. D'annunzio" University, 66013 Chieti, Italy
| | - Humbert De Smedt
- From the Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, and
| | - Jan B Parys
- From the Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, and
| | - Patrizia Agostinis
- Laboratory of Cell Death Research and Therapy, Department of Cellular and Molecular Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Luc Leybaert
- the Physiology Group, Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Varda Shoshan-Barmatz
- the Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, and
| | - Geert Bultynck
- From the Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, and
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24
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Eddy MT, Andreas L, Teijido O, Su Y, Clark L, Noskov SY, Wagner G, Rostovtseva TK, Griffin RG. Magic angle spinning nuclear magnetic resonance characterization of voltage-dependent anion channel gating in two-dimensional lipid crystalline bilayers. Biochemistry 2015; 54:994-1005. [PMID: 25545271 PMCID: PMC4318587 DOI: 10.1021/bi501260r] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The N-terminus of the voltage-dependent
anion channel (VDAC) has
been proposed to contain the mechanistically important gating helices
that modulate channel opening and closing. In this study, we utilize
magic angle spinning nuclear magnetic resonance (MAS NMR) to determine
the location and structure of the N-terminus for functional channels
in lipid bilayers by measuring long-range 13C–13C distances between residues in the N-terminus and other
domains of VDAC reconstituted into DMPC lipid bilayers. Our structural
studies show that the distance between A14 Cβ in
the N-terminal helix and S193 Cβ is ∼4–6
Å. Furthermore, VDAC phosphorylation by a mitochondrial kinase
at residue S193 has been claimed to delay mitochondrial cell death
by causing a conformational change that closes the channel, and a
VDAC-Ser193Glu mutant has been reported to show properties very similar
to those of phosphorylated VDAC in a cellular context. We expressed
VDAC-S193E and reconstituted it into DMPC lipid bilayers. Two-dimensional 13C–13C correlation experiments showed chemical
shift perturbations for residues located in the N-terminus, indicating
possible structural perturbations to that region. However, electrophysiological
data recorded on VDAC-S193E showed that channel characteristics were
identical to those of wild type samples, indicating that phosphorylation
of S193 does not directly affect channel gating. The combination of
NMR and electrophysiological results allows us to discuss the validity
of proposed gating models.
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Affiliation(s)
- Matthew T Eddy
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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25
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Salinas T, El Farouk-Ameqrane S, Ubrig E, Sauter C, Duchêne AM, Maréchal-Drouard L. Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs. Nucleic Acids Res 2014; 42:9937-48. [PMID: 25114051 PMCID: PMC4150812 DOI: 10.1093/nar/gku728] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In plants, the voltage-dependent anion-selective channel (VDAC) is a major component of a pathway involved in transfer RNA (tRNA) translocation through the mitochondrial outer membrane. However, the way in which VDAC proteins interact with tRNAs is still unknown. Potato mitochondria contain two major mitochondrial VDAC proteins, VDAC34 and VDAC36. These two proteins, composed of a N-terminal α-helix and of 19 β-strands forming a β-barrel structure, share 75% sequence identity. Here, using both northwestern and gel shift experiments, we report that these two proteins interact differentially with nucleic acids. VDAC34 binds more efficiently with tRNAs or other nucleic acids than VDAC36. To further identify specific features and critical amino acids required for tRNA binding, 21 VDAC34 mutants were constructed and analyzed by northwestern. This allowed us to show that the β-barrel structure of VDAC34 and the first 50 amino acids that contain the α-helix are essential for RNA binding. Altogether the work shows that during evolution, plant mitochondrial VDAC proteins have diverged so as to interact differentially with nucleic acids, and this may reflect their involvement in various specialized biological functions.
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Affiliation(s)
- Thalia Salinas
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Samira El Farouk-Ameqrane
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Elodie Ubrig
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Claude Sauter
- Institut de Biologie Moléculaire et Cellulaire, UPR 9002 CNRS, associated with Strasbourg University, 15 rue René Descartes 67084 Strasbourg cedex, France
| | - Anne-Marie Duchêne
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
| | - Laurence Maréchal-Drouard
- Institut de Biologie Moléculaire des Plantes, UPR 2357 CNRS, associated with Strasbourg University, 12 rue du Général Zimmer 67084 Strasbourg cedex, France
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26
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Choudhary OP, Paz A, Adelman JL, Colletier JP, Abramson J, Grabe M. Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nat Struct Mol Biol 2014; 21:626-32. [PMID: 24908397 PMCID: PMC4157756 DOI: 10.1038/nsmb.2841] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 05/14/2014] [Indexed: 01/02/2023]
Abstract
The voltage-dependent anion channel (VDAC) mediates the flow of metabolites and ions across the outer mitochondrial membrane of all eukaryotic cells. The open channel passes millions of ATP molecules per second, whereas the closed state exhibits no detectable ATP flux. High-resolution structures of VDAC1 revealed a 19-stranded β-barrel with an α-helix partially occupying the central pore. To understand ATP permeation through VDAC, we solved the crystal structure of mouse VDAC1 (mVDAC1) in the presence of ATP, revealing a low-affinity binding site. Guided by these coordinates, we initiated hundreds of molecular dynamics simulations to construct a Markov state model of ATP permeation. These simulations indicate that ATP flows through VDAC through multiple pathways, in agreement with our structural data and experimentally determined physiological rates.
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Affiliation(s)
- Om P Choudhary
- 1] Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, USA. [2]
| | - Aviv Paz
- 1] Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA. [2]
| | - Joshua L Adelman
- 1] Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. [2]
| | - Jacques-Philippe Colletier
- 1] Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France. [2] Centre National de la Recherche Scientifique, Institut de Biologie Structurale, Grenoble, France. [3] Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Direction des Sciences du Vivant, Institut de Biologie Structurale, Grenoble, France. [4]
| | - Jeff Abramson
- 1] Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA. [2] Institute for Stem Cell Biology and Regenerative Medicine, National Centre for Biological Sciences-Tata Institute of Fundamental Research, Bangalore, India
| | - Michael Grabe
- 1] Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA. [2] Cardiovascular Research Institute, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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