1
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Dong Y, Wang J, Grewer C. Transient kinetics reveal the mechanism of competitive inhibition of the neutral amino acid transporter ASCT2. J Biol Chem 2024; 300:107382. [PMID: 38763337 PMCID: PMC11193019 DOI: 10.1016/j.jbc.2024.107382] [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: 01/10/2024] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 05/21/2024] Open
Abstract
ASCT2 (alanine serine cysteine transporter 2), a member of the solute carrier 1 family, mediates Na+-dependent exchange of small neutral amino acids across cell membranes. ASCT2 was shown to be highly expressed in tumor cells, making it a promising target for anticancer therapies. In this study, we explored the binding mechanism of the high-affinity competitive inhibitor L-cis hydroxyproline biphenyl ester (Lc-BPE) with ASCT2, using electrophysiological and rapid kinetic methods. Our investigations reveal that Lc-BPE binding requires one or two Na+ ions initially bound to the apo-transporter with high affinity, with Na1 site occupancy being more critical for inhibitor binding. In contrast to the amino acid substrate bound form, the final, third Na+ ion cannot bind, due to distortion of its binding site (Na2), thus preventing the formation of a translocation-competent complex. Based on the rapid kinetic analysis, the application of Lc-BPE generated outward transient currents, indicating that despite its net neutral nature, the binding of Lc-BPE in ASCT2 is weakly electrogenic, most likely because of asymmetric charge distribution within the amino acid moiety of the inhibitor. The preincubation with Lc-BPE also led to a decrease of the turnover rate of substrate exchange and a delay in the activation of substrate-induced anion current, indicating relatively slow Lc-BPE dissociation kinetics. Overall, our results provide new insight into the mechanism of binding of a prototypical competitive inhibitor to the ASCT transporters.
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Affiliation(s)
- Yang Dong
- Department of Chemistry, Binghamton University, Binghamton, New York, USA
| | - Jiali Wang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA
| | - Christof Grewer
- Department of Chemistry, Binghamton University, Binghamton, New York, USA.
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2
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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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3
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Ngo VA, Queralt-Martín M, Khan F, Bergdoll L, Abramson J, Bezrukov SM, Rostovtseva TK, Hoogerheide DP, Noskov SY. The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating. J Am Chem Soc 2022; 144:14564-14577. [PMID: 35925797 DOI: 10.1021/jacs.2c03316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The voltage-dependent anion channel (VDAC) is a β-barrel channel of the mitochondrial outer membrane (MOM) that passively transports ions, metabolites, polypeptides, and single-stranded DNA. VDAC responds to a transmembrane potential by "gating," i.e. transitioning to one of a variety of low-conducting states of unknown structure. The gated state results in nearly complete suppression of multivalent mitochondrial metabolite (such as ATP and ADP) transport, while enhancing calcium transport. Voltage gating is a universal property of β-barrel channels, but VDAC gating is anomalously sensitive to transmembrane potential. Here, we show that a single residue in the pore interior, K12, is responsible for most of VDAC's voltage sensitivity. Using the analysis of over 40 μs of atomistic molecular dynamics (MD) simulations, we explore correlations between motions of charged residues inside the VDAC pore and geometric deformations of the β-barrel. Residue K12 is bistable; its motions between two widely separated positions along the pore axis enhance the fluctuations of the β-barrel and augment the likelihood of gating. Single channel electrophysiology of various K12 mutants reveals a dramatic reduction of the voltage-induced gating transitions. The crystal structure of the K12E mutant at a resolution of 2.6 Å indicates a similar architecture of the K12E mutant to the wild type; however, 60 μs of atomistic MD simulations using the K12E mutant show restricted motion of residue 12, due to enhanced connectivity with neighboring residues, and diminished amplitude of barrel motions. We conclude that β-barrel fluctuations, governed particularly by residue K12, drive VDAC gating transitions.
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Affiliation(s)
- Van A Ngo
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.,Advanced Computing for Life Sciences and Engineering, Computing and Computational Sciences, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
| | - María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States.,Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain
| | - Farha Khan
- Department of Physiology, University of California, Los Angeles, California 90095, United States
| | - Lucie Bergdoll
- LISM UMR 7255, CNRS and Aix-Marseille University, Marseille cedex 20, 13402, France
| | - Jeff Abramson
- Department of Physiology, University of California, Los Angeles, California 90095, United States
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sergei Yu Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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4
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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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5
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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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6
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Queralt-Martín M, Bergdoll L, Teijido O, Munshi N, Jacobs D, Kuszak AJ, Protchenko O, Reina S, Magrì A, De Pinto V, Bezrukov SM, Abramson J, Rostovtseva TK. A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology. J Gen Physiol 2021; 152:133600. [PMID: 31935282 PMCID: PMC7062508 DOI: 10.1085/jgp.201912501] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/20/2019] [Indexed: 01/30/2023] Open
Abstract
Voltage-dependent anion channel (VDAC) is the major pathway for the transport of ions and metabolites across the mitochondrial outer membrane. Among the three known mammalian VDAC isoforms, VDAC3 is the least characterized, but unique functional roles have been proposed in cellular and animal models. Yet, a high-sequence similarity between VDAC1 and VDAC3 is indicative of a similar pore-forming structure. Here, we conclusively show that VDAC3 forms stable, highly conductive voltage-gated channels that, much like VDAC1, are weakly anion selective and facilitate metabolite exchange, but exhibit unique properties when interacting with the cytosolic proteins α-synuclein and tubulin. These two proteins are known to be potent regulators of VDAC1 and induce similar characteristic blockages (on the millisecond time scale) of VDAC3, but with 10- to 100-fold reduced on-rates and altered α-synuclein blocking times, indicative of an isoform-specific function. Through cysteine scanning mutagenesis, we found that VDAC3's cysteine residues regulate its interaction with α-synuclein, demonstrating VDAC3-unique functional properties and further highlighting a general molecular mechanism for VDAC isoform-specific regulation of mitochondrial bioenergetics.
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Affiliation(s)
- María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Oscar Teijido
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Nabill Munshi
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Daniel Jacobs
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Adam J Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Olga Protchenko
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Simona Reina
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Andrea Magrì
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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7
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Saidani H, Léonetti M, Kmita H, Homblé F. The Open State Selectivity of the Bean Seed VDAC Depends on Stigmasterol and Ion Concentration. Int J Mol Sci 2021; 22:ijms22063034. [PMID: 33809742 PMCID: PMC8002290 DOI: 10.3390/ijms22063034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) is the major pathway for metabolites and ions transport through the mitochondrial outer membrane. It can regulate the flow of solutes by switching to a low conductance state correlated with a selectivity reversal, or by a selectivity inversion of its open state. The later one was observed in non-plant VDACs and is poorly characterized. We aim at investigating the selectivity inversion of the open state using plant VDAC purified from Phaseolus coccineus (PcVDAC) to evaluate its physiological role. Our main findings are: (1) The VDAC selectivity inversion of the open state occurs in PcVDAC, (2) Ion concentration and stigmasterol affect the occurrence of the open state selectivity inversion and stigmasterol appears to interact directly with PcVDAC. Interestingly, electrophysiological data concerning the selectivity inversion of the PcVDAC open state suggests that the phenomenon probably does not have a significant physiological effect in vivo.
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Affiliation(s)
- Hayet Saidani
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 206/2, B-1050 Bruxelles, Belgium;
- Laboratory of Functional Neurophysiology and Pathology, Research Unit, UR/11ES09, Department of Biological Sciences, Faculty of Science of Tunis, University Tunis El Manar, 1068 Tunis, Tunisia
| | - Marc Léonetti
- Université de. Grenoble Alpes, CNRS, LRP, 38000 Grenoble, France;
| | - Hanna Kmita
- Department of Bioenergetics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland;
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles (ULB), Boulevard du Triomphe CP 206/2, B-1050 Bruxelles, Belgium;
- Correspondence: ; Tel.: +32-2-650-5383
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8
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Outer membrane protein evolution. Curr Opin Struct Biol 2021; 68:122-128. [PMID: 33493965 DOI: 10.1016/j.sbi.2021.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 01/02/2021] [Indexed: 01/31/2023]
Abstract
Outer membrane proteins have remarkably homogeneous structure. They are all up down β-barrels. Up down barrels themselves are composed of repeated sets of β-hairpins. The consistency of the usage of the β-hairpin throughout the outer membrane milieu allows for interrogation of the evolution of these repetitive structures. Here we describe recent investigations of outer membrane protein evolution and how evolutionary precepts have been used for novel outer membrane protein design.
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9
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Sander P, Gudermann T, Schredelseker J. A Calcium Guard in the Outer Membrane: Is VDAC a Regulated Gatekeeper of Mitochondrial Calcium Uptake? Int J Mol Sci 2021; 22:ijms22020946. [PMID: 33477936 PMCID: PMC7833399 DOI: 10.3390/ijms22020946] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 12/15/2022] Open
Abstract
Already in the early 1960s, researchers noted the potential of mitochondria to take up large amounts of Ca2+. However, the physiological role and the molecular identity of the mitochondrial Ca2+ uptake mechanisms remained elusive for a long time. The identification of the individual components of the mitochondrial calcium uniporter complex (MCUC) in the inner mitochondrial membrane in 2011 started a new era of research on mitochondrial Ca2+ uptake. Today, many studies investigate mitochondrial Ca2+ uptake with a strong focus on function, regulation, and localization of the MCUC. However, on its way into mitochondria Ca2+ has to pass two membranes, and the first barrier before even reaching the MCUC is the outer mitochondrial membrane (OMM). The common opinion is that the OMM is freely permeable to Ca2+. This idea is supported by the presence of a high density of voltage-dependent anion channels (VDACs) in the OMM, forming large Ca2+ permeable pores. However, several reports challenge this idea and describe VDAC as a regulated Ca2+ channel. In line with this idea is the notion that its Ca2+ selectivity depends on the open state of the channel, and its gating behavior can be modified by interaction with partner proteins, metabolites, or small synthetic molecules. Furthermore, mitochondrial Ca2+ uptake is controlled by the localization of VDAC through scaffolding proteins, which anchor VDAC to ER/SR calcium release channels. This review will discuss the possibility that VDAC serves as a physiological regulator of mitochondrial Ca2+ uptake in the OMM.
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Affiliation(s)
- Paulina Sander
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany; (P.S.); (T.G.)
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany; (P.S.); (T.G.)
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
| | - Johann Schredelseker
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, LMU Munich, 80336 Munich, Germany; (P.S.); (T.G.)
- Deutsches Zentrum für Herz-Kreislauf-Forschung, Partner Site Munich Heart Alliance, Munich, Germany
- Correspondence: ; Tel.: +49-(0)89-2180-73831
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10
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Wilting F, Kopp R, Gurnev PA, Schedel A, Dupper NJ, Kwon O, Nicke A, Gudermann T, Schredelseker J. The antiarrhythmic compound efsevin directly modulates voltage-dependent anion channel 2 by binding to its inner wall and enhancing mitochondrial Ca 2+ uptake. Br J Pharmacol 2020; 177:2947-2958. [PMID: 32059260 PMCID: PMC7279994 DOI: 10.1111/bph.15022] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND PURPOSE The synthetic compound efsevin was recently identified to suppress arrhythmogenesis in models of cardiac arrhythmia, making it a promising candidate for antiarrhythmic therapy. Its activity was shown to be dependent on the voltage-dependent anion channel 2 (VDAC2) in the outer mitochondrial membrane. Here, we investigated the molecular mechanism of the efsevin-VDAC2 interaction. EXPERIMENTAL APPROACH To evaluate the functional interaction of efsevin and VDAC2, we measured currents through recombinant VDAC2 in planar lipid bilayers. Using molecular ligand-protein docking and mutational analysis, we identified the efsevin binding site on VDAC2. Finally, physiological consequences of the efsevin-induced modulation of VDAC2 were analysed in HL-1 cardiomyocytes. KEY RESULTS In lipid bilayers, efsevin reduced VDAC2 conductance and shifted the channel's open probability towards less anion-selective closed states. Efsevin binds to a binding pocket formed by the inner channel wall and the pore-lining N-terminal α-helix. Exchange of amino acids N207, K236 and N238 within this pocket for alanines abolished the channel's efsevin-responsiveness. Upon heterologous expression in HL-1 cardiomyocytes, both channels, wild-type VDAC2 and the efsevin-insensitive VDAC2AAA restored mitochondrial Ca2+ uptake, but only wild-type VDAC2 was sensitive to efsevin. CONCLUSION AND IMPLICATIONS In summary, our data indicate a direct interaction of efsevin with VDAC2 inside the channel pore that leads to modified gating and results in enhanced SR-mitochondria Ca2+ transfer. This study sheds new light on the function of VDAC2 and provides a basis for structure-aided chemical optimization of efsevin.
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Affiliation(s)
- Fabiola Wilting
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
| | - Robin Kopp
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
| | - Philip A. Gurnev
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthBethesdaMaryland
| | - Anna Schedel
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
| | - Nathan J. Dupper
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia
| | - Ohyun Kwon
- Department of Chemistry and BiochemistryUniversity of California Los AngelesLos AngelesCalifornia
| | - Annette Nicke
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
| | - Thomas Gudermann
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
- Deutsches Zentrum für Herz‐Kreislauf‐Forschung (DZHK)Partner Site Munich Heart Alliance (MHA)MunichGermany
| | - Johann Schredelseker
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of MedicineLMU MunichMunichGermany
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11
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Kanwar P, Samtani H, Sanyal SK, Srivastava AK, Suprasanna P, Pandey GK. VDAC and its interacting partners in plant and animal systems: an overview. Crit Rev Biotechnol 2020; 40:715-732. [PMID: 32338074 DOI: 10.1080/07388551.2020.1756214] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular trafficking between different subcellular compartments is the key for normal cellular functioning. Voltage-dependent anion channels (VDACs) are small-sized proteins present in the outer mitochondrial membrane, which mediate molecular trafficking between mitochondria and cytoplasm. The conductivity of VDAC is dependent on the transmembrane voltage, its oligomeric state and membrane lipids. VDAC acts as a convergence point to a diverse variety of mitochondrial functions as well as cell survival. This functional diversity is attained due to their interaction with a plethora of proteins inside the cell. Although, there are hints toward functional conservation/divergence between animals and plants; knowledge about the functional role of the VDACs in plants is still limited. We present here a comparative overview to provide an integrative picture of the interactions of VDAC with different proteins in both animals and plants. Also discussed are their physiological functions from the perspective of cellular movements, signal transduction, cellular fate, disease and development. This in-depth knowledge of the biological importance of VDAC and its interacting partner(s) will assist us to explore their function in the applied context in both plant and animal.
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Affiliation(s)
- Poonam Kanwar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Sibaji K Sanyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Ashish K Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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12
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Ponnalagu D, Singh H. Insights Into the Role of Mitochondrial Ion Channels in Inflammatory Response. Front Physiol 2020; 11:258. [PMID: 32327997 PMCID: PMC7160495 DOI: 10.3389/fphys.2020.00258] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/05/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are the source of many pro-inflammatory signals that cause the activation of the immune system and generate inflammatory responses. They are also potential targets of pro-inflammatory mediators, thus triggering a severe inflammatory response cycle. As mitochondria are a central hub for immune system activation, their dysfunction leads to many inflammatory disorders. Thus, strategies aiming at regulating mitochondrial dysfunction can be utilized as a therapeutic tool to cure inflammatory disorders. Two key factors that determine the structural and functional integrity of mitochondria are mitochondrial ion channels and transporters. They are not only important for maintaining the ionic homeostasis of the cell, but also play a role in regulating reactive oxygen species generation, ATP production, calcium homeostasis and apoptosis, which are common pro-inflammatory signals. The significance of the mitochondrial ion channels in inflammatory response is still not clearly understood and will need further investigation. In this article, we review the different mechanisms by which mitochondria can generate the inflammatory response as well as highlight how mitochondrial ion channels modulate these mechanisms and impact the inflammatory processes.
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Affiliation(s)
- Devasena Ponnalagu
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH, United States
| | - Harpreet Singh
- Department of Physiology and Cell Biology, Davis Heart and Lung Research Institute, The Ohio State University, Wexner Medical Center, Columbus, OH, United States
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13
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Xie D, Audi SH, Dash RK. A size-modified poisson-boltzmann ion channel model in a solvent of multiple ionic species: Application to voltage-dependent anion channel. J Comput Chem 2020; 41:218-230. [PMID: 31845398 PMCID: PMC8189662 DOI: 10.1002/jcc.26091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/30/2019] [Accepted: 09/24/2019] [Indexed: 12/30/2022]
Abstract
We present a new size-modified Poisson-Boltzmann ion channel (SMPBIC) model and use it to calculate the electrostatic potential, ionic concentrations, and electrostatic solvation free energy for a voltage-dependent anion channel (VDAC) on a biological membrane in a solution mixture of multiple ionic species. In particular, the new SMPBIC model adopts a membrane surface charge density and a natural Neumann boundary condition to reflect the charge effect of the membrane on the electrostatics of VDAC. To avoid the singularity difficulties caused by the atomic charges of VDAC, the new SMPBIC model is split into three submodels such that the solution of one of the submodels is obtained analytically and contains all the singularity points of the SMPBIC model. The other two submodels are then solved numerically much more efficiently than the original SMPBIC model. As an application of this SMPBIC submodel partitioning scheme, we derive a new formula for computing the electrostatic solvation free energy. Numerical results for a human VDAC isoform 1 (hVDAC1) in three different salt solutions, each with up to five different ionic species, confirm the significant effects of membrane surface charges on both the electrostatics and ionic concentrations. The results also show that the new SMPBIC model can describe well the anion selectivity property of hVDAC1, and that the new electrostatic solvation free energy formula can significantly improve the accuracy of the currently used formula. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Dexuan Xie
- Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, 53201
| | - Said H Audi
- Department of Biomedical Engineering, Marquette University, Milwaukee, Wisconsin, 53233
| | - Ranjan K Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, 53226
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14
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Lopes-Rodrigues M, Matagne A, Zanuy D, Alemán C, Perpète EA, Michaux C. Structural and functional characterization of Solanum tuberosum VDAC36. Proteins 2019; 88:729-739. [PMID: 31833115 DOI: 10.1002/prot.25861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/26/2019] [Accepted: 12/06/2019] [Indexed: 11/05/2022]
Abstract
As it forms water-filled channel in the mitochondria outer membrane and diffuses essential metabolites such as NADH and ATP, the voltage-dependent anion channel (VDAC) protein family plays a central role in all eukaryotic cells. In comparison with their mammalian homologues, little is known about the structural and functional properties of plant VDACs. In the present contribution, one of the two VDACs isoforms of Solanum tuberosum, stVDAC36, has been successfully overexpressed and refolded by an in-house method, as demonstrated by the information on its secondary and tertiary structure gathered from circular dichroism and intrinsic fluorescence. Cross-linking and molecular modeling studies have evidenced the presence of dimers and tetramers, and they suggest the formation of an intermolecular disulfide bond between two stVDAC36 monomers. The pore-forming activity was also assessed by liposome swelling assays, indicating a typical pore diameter between 2.0 and 2.7 nm. Finally, insights about the ATP binding inside the pore are given by docking studies and electrostatic calculations.
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Affiliation(s)
- Maximilien Lopes-Rodrigues
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - André Matagne
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines (CIP), Université de Liège, Liège, Belgium
| | - David Zanuy
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, Barcelona, Spain.,Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, Eduard Maristany, Barcelona, Spain
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Namur, Belgium.,Namur Institute of Structured Matter, University of Namur, Namur, Belgium.,Institute of Life-Earth-Environment, University of Namur, Namur, Belgium
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15
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Reif MM, Fischer M, Fredriksson K, Hagn F, Zacharias M. The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding. J Mol Biol 2019; 431:223-243. [DOI: 10.1016/j.jmb.2018.09.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/11/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022]
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16
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Hoogerheide DP, Noskov SY, Kuszak AJ, Buchanan SK, Rostovtseva TK, Nanda H. Structure of voltage-dependent anion channel-tethered bilayer lipid membranes determined using neutron reflectivity. Acta Crystallogr D Struct Biol 2018; 74:1219-1232. [PMID: 30605136 PMCID: PMC6317592 DOI: 10.1107/s2059798318011749] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/20/2018] [Indexed: 01/05/2023] Open
Abstract
Neutron reflectivity (NR) has emerged as a powerful technique to study the structure and behavior of membrane proteins at planar lipid interfaces. Integral membrane proteins (IMPs) remain a significant challenge for NR owing to the difficulty of forming complete bilayers with sufficient protein density for scattering techniques. One strategy to achieve high protein density on a solid substrate is the capture of detergent-stabilized, affinity-tagged IMPs on a nitrilotriacetic acid (NTA)-functionalized self-assembled monolayer (SAM), followed by reconstitution into the lipids of interest. Such protein-tethered bilayer lipid membranes (ptBLMs) have the notable advantage of a uniform IMP orientation on the substrate. Here, NR is used to provide a structural characterization of the ptBLM process from formation of the SAM to capture of the detergent-stabilized IMP and lipid reconstitution. The mitochondrial outer-membrane voltage-dependent anion channel (VDAC), which controls the exchange of bioenergetic metabolites between mitochondria and the cytosol, was used as a model β-barrel IMP. Molecular dynamics simulations were used for comparison with the experimental results and to inform the parameters of the physical models describing the NR data. The detailed structure of the SAM is shown to depend on the density of the NTA chelating groups. The relative content of detergent and protein in surface-immobilized, detergent-stabilized VDAC is measured, while the reconstituted lipid bilayer is shown to be complete to within a few percent, using the known atomic structure of VDAC. Finally, excess lipid above the reconstituted bilayer, which is of consequence for more indirect structural and functional studies, is shown to be present.
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Affiliation(s)
- David P. Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
| | - Sergei Yu. Noskov
- Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Adam J. Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tatiana K. Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirsh Nanda
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20878, USA
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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17
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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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18
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Manzo G, Serra I, Magrí A, Casu M, De Pinto V, Ceccarelli M, Scorciapino MA. Folded Structure and Membrane Affinity of the N-Terminal Domain of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion-Selective Channel. ACS OMEGA 2018; 3:11415-11425. [PMID: 30320261 PMCID: PMC6173511 DOI: 10.1021/acsomega.8b01536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
Voltage-dependent anion-selective channels (VDACs) are primarily located in the mitochondrial outer membrane (MOM). They are essential for the regulation of ion and metabolite exchanges. In particular, their role in energy-related nucleotide exchange has many implications in apoptosis, cancer, and neurodegenerative diseases. It has been proposed that VDACs' functions are regulated by mobility of the N-terminal helical domain, which is bound to the inner wall of the main β-barrel domain but exists in equilibrium between the bound-folded and the unbound-unfolded state. When the N-terminal domain detaches from the channel's wall and eventually leaves the lumen, it can either stay exposed to the cytosolic environment or interact with the outer leaflet of the MOM; then, it may also interact with other protein partners. In humans, three different VDAC isoforms are expressed at different tissue-specific levels with evidence of distinct roles. Although the N-terminal domains share high sequence similarity, important differences do exist, with the functionality of the entire protein mostly attributed to them. In this work, the three-dimensional structure and membrane affinity of the three isolated hVDAC N-terminal peptides have been compared through Fourier-transform infrared and NMR spectroscopy in combination with molecular dynamics simulations, and measurement of the surface pressure of lipid monolayers. Although peptides were studied as isolated from the β-barrel domain, the observed differences are relevant for those whole protein's functions in which a protein-protein interaction is mediated by the N-terminal domain.
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Affiliation(s)
- Giorgia Manzo
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Ilaria Serra
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Andrea Magrí
- Department of Biomedicine
and Biotechnology, Section of Biology and Genetics, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Mariano Casu
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Vito De Pinto
- Department of Biomedicine
and Biotechnology, Section of Biology and Genetics, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Matteo Ceccarelli
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
| | - Mariano Andrea Scorciapino
- Department
of Chemical and Geological Sciences, Cittadella Universitaria di Monserrato, Department of Physics,
Cittadella Universitaria di Monserrato, and Department
of Biomedical Sciences, Biochemistry Unit, Cittadella Universitaria
di Monserrato, University of Cagliari, S.P. 8 km 0.700, 09042 Monserrato, Cagliari, Italy
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19
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Caterino M, Ruoppolo M, Mandola A, Costanzo M, Orrù S, Imperlini E. Protein-protein interaction networks as a new perspective to evaluate distinct functional roles of voltage-dependent anion channel isoforms. MOLECULAR BIOSYSTEMS 2018; 13:2466-2476. [PMID: 29028058 DOI: 10.1039/c7mb00434f] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Voltage-dependent anion channels (VDACs) are a family of three mitochondrial porins and the most abundant integral membrane proteins of the mitochondrial outer membrane (MOM). VDACs are known to be involved in metabolite/ion transport across the MOM and in many cellular processes ranging from mitochondria-mediated apoptosis to the control of energy metabolism, by interacting with cytosolic, mitochondrial and cytoskeletal proteins and other membrane channels. Despite redundancy and compensatory mechanisms among VDAC isoforms, they display not only different channel properties and protein expression levels, but also distinct protein partners. Here, we review the known protein interactions for each VDAC isoform in order to shed light on their peculiar roles in physiological and pathological conditions. As proteins associated with the MOM, VDAC opening/closure as a metabolic checkpoint is regulated by protein-protein interactions, and is of pharmacological interest in pathological conditions such as cancer. The interactions involving VDAC1 have been characterized more in depth than those involving VDAC2 and VDAC3. Nevertheless, the so far explored VDAC-protein interactions for each isoform show that VDAC1 is mainly involved in the maintenance of cellular homeostasis and in pro-apoptotic processes, whereas VDAC2 displays an anti-apoptotic role. Despite there being limited information on VDAC3, this isoform could contribute to mitochondrial protein quality control and act as a marker of oxidative status. In pathological conditions, namely neurodegenerative and cardiovascular diseases, both VDAC1 and VDAC2 establish abnormal interactions aimed to counteract the mitochondrial dysfunction which contributes to end-organ damage.
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Affiliation(s)
- Marianna Caterino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy
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20
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Association of the VDAC3 gene polymorphism with sperm count in Han-Chinese population with idiopathic male infertility. Oncotarget 2018; 8:45242-45248. [PMID: 28431403 PMCID: PMC5542182 DOI: 10.18632/oncotarget.16891] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/27/2017] [Indexed: 11/25/2022] Open
Abstract
Voltage-dependent anion channel (VDAC) is a multifunctional channel protein across the outer mitochondrial membrane of somatic cells and participates in many physiological and pathophysiological processes. Up to now, only a few studies, including our previous studies, showed that VDAC exists in mammalian spermatozoa and is involved in spermatogenesis and sperm functions. There is no report about VDAC genetic variants in germinal tissues or cells. To investigate the possible association between VDAC genetic variants and human sperm quality, we performed semen analysis and variant Genotyping of VDAC3 subtype (rs7004637, rs16891278 and rs6773) of 523 Han-Chinese males with idiopathic infertility respectively by computer assisted semen analysis (CASA) and single nucleotide polymorphism (SNP) Genotyping assay. No significant association was found between rs7004637 and rs6773 genotypes and semen quality. However, the AG genotype of rs16891278 showed a significantly lower sperm concentration compared with the AA genotype (P = 0.044). Our findings suggest that VDAC3 genetic variants may be associated with human sperm count.
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21
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Zeth K, Zachariae U. Ten Years of High Resolution Structural Research on the Voltage Dependent Anion Channel (VDAC)-Recent Developments and Future Directions. Front Physiol 2018; 9:108. [PMID: 29563878 PMCID: PMC5845903 DOI: 10.3389/fphys.2018.00108] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/02/2018] [Indexed: 12/20/2022] Open
Abstract
Mitochondria are evolutionarily related to Gram-negative bacteria and both comprise two membrane systems with strongly differing protein composition. The major protein in the outer membrane of mitochondria is the voltage-dependent anion channel (VDAC), which mediates signal transmission across the outer membrane but also the exchange of metabolites, most importantly ADP and ATP. More than 30 years after its discovery three identical high-resolution structures were determined in 2008. These structures show a 19-stranded anti-parallel beta-barrel with an N-terminal helix located inside. An odd number of beta-strands is also shared by Tom40, another member of the VDAC superfamily. This indicates that this superfamily is evolutionarily relatively young and that it has emerged in the context of mitochondrial evolution. New structural information obtained during the last decade on Tom40 can be used to cross-validate the structure of VDAC and vice versa. Interpretation of biochemical and biophysical studies on both protein channels now rests on a solid basis of structural data. Over the past 10 years, complementary structural and functional information on proteins of the VDAC superfamily has been collected from in-organello, in-vitro, and in silico studies. Most of these findings have confirmed the validity of the original structures. This short article briefly reviews the most important advances on the structure and function of VDAC superfamily members collected during the last decade and summarizes how they enhanced our understanding of the channel.
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Affiliation(s)
- Kornelius Zeth
- Department for Science and Environment, Roskilde University, Roskilde, Denmark
| | - Ulrich Zachariae
- School of Science and Engineering, University of Dundee, Dundee, United Kingdom.,School of Life Sciences, University of Dundee, Dundee, United Kingdom
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22
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Cao X, Cui Y, Zhang X, Lou J, Zhou J, Bei H, Wei R. Proteomic profile of human spermatozoa in healthy and asthenozoospermic individuals. Reprod Biol Endocrinol 2018; 16:16. [PMID: 29482568 PMCID: PMC5828484 DOI: 10.1186/s12958-018-0334-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/22/2018] [Indexed: 01/11/2023] Open
Abstract
Asthenozoospermia is considered as a common cause of male infertility and characterized by reduced sperm motility. However, the molecular mechanism that impairs sperm motility remains unknown in most cases. In the present review, we briefly reviewed the proteome of spermatozoa and seminal plasma in asthenozoospermia and considered post-translational modifications in spermatozoa of asthenozoospermia. The reduction of sperm motility in asthenozoospermic patients had been attributed to factors, for instance, energy metabolism dysfunction or structural defects in the sperm-tail protein components and the differential proteins potentially involved in sperm motility such as COX6B, ODF, TUBB2B were described. Comparative proteomic analysis open a window to discover the potential pathogenic mechanisms of asthenozoospermia and the biomarkers with clinical significance.
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Affiliation(s)
- Xiaodan Cao
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Yun Cui
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Xiaoxia Zhang
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Jiangtao Lou
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Jun Zhou
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Huafeng Bei
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China
| | - Renxiong Wei
- Department of Clinical Laboratory, Ningbo Municipal Hospital of Traditional Chinese Medicine, Ningbo, 315000, China.
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23
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Wang J, Albers T, Grewer C. Energy Landscape of the Substrate Translocation Equilibrium of Plasma-Membrane Glutamate Transporters. J Phys Chem B 2017; 122:28-39. [PMID: 29218993 DOI: 10.1021/acs.jpcb.7b09059] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glutamate transporters maintain a large glutamate concentration gradient across synaptic membranes and are, thus, critical for functioning of the excitatory synapse. Mammalian glutamate transporters concentrate glutamate inside cells through energetic coupling of glutamate flux to the transmembrane concentration gradient of Na+. Structural models based on an archeal homologue, GltPh, suggest an elevator-like carrier mechanism. However, the energetic determinants of this carrier-based movement are not well understood. Although electrostatics play an important role in governing these energetics, their implication on transport dynamics has not been studied. Here, we combine a pre-steady-state kinetic analysis of the translocation equilibrium with electrostatic computations to gain insight into the energetics of the translocation process. Our results show the biphasic nature of translocation, consistent with the existence of an intermediate on the translocation pathway. In the absence of voltage, the equilibrium is shifted to the outward-facing configuration. Electrostatic computations confirm the intermediate state and show that the elevator-like movement is energetically feasible in the presence of bound Na+ ions, whereas a substrate-hopping model is energetically prohibitive. Our results highlight the critical contribution of charge compensation to transport and add to results from previous molecular dynamics simulations for improved understanding of the glutamate translocation process.
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Affiliation(s)
- Jiali Wang
- Department of Chemistry, Binghamton University , Binghamton, New York 13902, United States
| | - Thomas Albers
- Department of Chemistry, Binghamton University , Binghamton, New York 13902, United States
| | - Christof Grewer
- Department of Chemistry, Binghamton University , Binghamton, New York 13902, United States
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24
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Chen D. Fractional Poisson-Nernst-Planck Model for Ion Channels I: Basic Formulations and Algorithms. Bull Math Biol 2017; 79:2696-2726. [PMID: 28940114 DOI: 10.1007/s11538-017-0349-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/15/2017] [Indexed: 11/28/2022]
Abstract
In this work, we propose a fractional Poisson-Nernst-Planck model to describe ion permeation in gated ion channels. Due to the intrinsic conformational changes, crowdedness in narrow channel pores, binding and trapping introduced by functioning units of channel proteins, ionic transport in the channel exhibits a power-law-like anomalous diffusion dynamics. We start from continuous-time random walk model for a single ion and use a long-tailed density distribution function for the particle jump waiting time, to derive the fractional Fokker-Planck equation. Then, it is generalized to the macroscopic fractional Poisson-Nernst-Planck model for ionic concentrations. Necessary computational algorithms are designed to implement numerical simulations for the proposed model, and the dynamics of gating current is investigated. Numerical simulations show that the fractional PNP model provides a more qualitatively reasonable match to the profile of gating currents from experimental observations. Meanwhile, the proposed model motivates new challenges in terms of mathematical modeling and computations.
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Affiliation(s)
- Duan Chen
- Department of Mathematics and Statistics, University of North Carolina at Charlotte, Charlotte, NC, USA.
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25
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DNA methylation and histone deacetylation regulating insulin sensitivity due to chronic cold exposure. Cryobiology 2017; 74:36-42. [DOI: 10.1016/j.cryobiol.2016.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/01/2016] [Accepted: 12/13/2016] [Indexed: 11/18/2022]
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26
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Noskov SY, Rostovtseva TK, Chamberlin AC, Teijido O, Jiang W, Bezrukov SM. Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC). BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1858:1778-90. [PMID: 26940625 PMCID: PMC4877207 DOI: 10.1016/j.bbamem.2016.02.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/04/2023]
Abstract
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane provides a controlled pathway for respiratory metabolites in and out of the mitochondria. In spite of the wealth of experimental data from structural, biochemical, and biophysical investigations, the exact mechanisms governing selective ion and metabolite transport, especially the role of titratable charged residues and interactions with soluble cytosolic proteins, remain hotly debated in the field. The computational advances hold a promise to provide a much sought-after solution to many of the scientific disputes around solute and ion transport through VDAC and hence, across the mitochondrial outer membrane. In this review, we examine how Molecular Dynamics, Free Energy, and Brownian Dynamics simulations of the large β-barrel channel, VDAC, advanced our understanding. We will provide a short overview of non-conventional techniques and also discuss examples of how the modeling excursions into VDAC biophysics prospectively aid experimental efforts. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Sergei Yu Noskov
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, 2500 University Drive N.W., Calgary, Alberta T2N1N4, Canada.
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | - Oscar Teijido
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; Department of Medical Epigenetics, Institute of Medical Sciences and Genomic Medicine, EuroEspes Sta. Marta de Babío S/N, 15165 Bergondo, A Coruña, Spain
| | - Wei Jiang
- Leadership Computing Facility, Argonne National Laboratory, 9700S Cass Avenue, Lemont, IL 60439, USA
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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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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28
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Ge L, Villinger S, Mari SA, Giller K, Griesinger C, Becker S, Müller DJ, Zweckstetter M. Molecular Plasticity of the Human Voltage-Dependent Anion Channel Embedded Into a Membrane. Structure 2016; 24:585-594. [PMID: 27021164 PMCID: PMC5654509 DOI: 10.1016/j.str.2016.02.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 12/28/2022]
Abstract
The voltage-dependent anion channel (VDAC) regulates the flux of metabolites and ions across the outer mitochondrial membrane. Regulation of ion flow involves conformational transitions in VDAC, but the nature of these changes has not been resolved to date. By combining single-molecule force spectroscopy with nuclear magnetic resonance spectroscopy we show that the β barrel of human VDAC embedded into a membrane is highly flexible. Its mechanical flexibility exceeds by up to one order of magnitude that determined for β strands of other membrane proteins and is largest in the N-terminal part of the β barrel. Interaction with Ca(2+), a key regulator of metabolism and apoptosis, considerably decreases the barrel's conformational variability and kinetic free energy in the membrane. The combined data suggest that physiological VDAC function depends on the molecular plasticity of its channel.
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Affiliation(s)
- Lin Ge
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Saskia Villinger
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Karin Giller
- Department of NMR-based Structural Biology, 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
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Strasse 3a, 37075 Göttingen, Germany; Department of Neurology, University Medical Center Göttingen, University of Göttingen, Am Waldweg 33, 37073 Göttingen, Germany.
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29
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Tanui R, Tao Z, Silverstein N, Kanner B, Grewer C. Electrogenic Steps Associated with Substrate Binding to the Neuronal Glutamate Transporter EAAC1. J Biol Chem 2016; 291:11852-64. [PMID: 27044739 DOI: 10.1074/jbc.m116.722470] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Indexed: 12/13/2022] Open
Abstract
Glutamate transporters actively take up glutamate into the cell, driven by the co-transport of sodium ions down their transmembrane concentration gradient. It was proposed that glutamate binds to its binding site and is subsequently transported across the membrane in the negatively charged form. With the glutamate binding site being located partially within the membrane domain, the possibility has to be considered that glutamate binding is dependent on the transmembrane potential and, thus, is electrogenic. Experiments presented in this report test this possibility. Rapid application of glutamate to the wild-type glutamate transporter subtype EAAC1 (excitatory amino acid carrier 1) through photo-release from caged glutamate generated a transient inward current, as expected for the electrogenic inward movement of co-transported Na(+) In contrast, glutamate application to a transporter with the mutation A334E induced transient outward current, consistent with movement of negatively charged glutamate into its binding site within the dielectric of the membrane. These results are in agreement with electrostatic calculations, predicting a valence for glutamate binding of -0.27. Control experiments further validate and rule out other possible explanations for the transient outward current. Electrogenic glutamate binding can be isolated in the mutant glutamate transporter because reactions, such as glutamate translocation and/or Na(+) binding to the glutamate-bound state, are inhibited by the A334E substitution. Electrogenic glutamate binding has to be considered together with other voltage-dependent partial reactions to cooperatively determine the voltage dependence of steady-state glutamate uptake and glutamate buffering at the synapse.
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Affiliation(s)
- Rose Tanui
- From the Department of Chemistry Binghamton University, Binghamton, New York 13902 and
| | - Zhen Tao
- From the Department of Chemistry Binghamton University, Binghamton, New York 13902 and
| | - Nechama Silverstein
- the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Baruch Kanner
- the Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Christof Grewer
- From the Department of Chemistry Binghamton University, Binghamton, New York 13902 and
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30
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Saidani H, Grobys D, Léonetti M, Kmita H, Homblé F. Towards understanding of plant mitochondrial VDAC proteins: an overview of bean ( Phaseolus) VDAC proteins. AIMS BIOPHYSICS 2016. [DOI: 10.3934/biophy.2017.1.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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31
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Guardiani C, Scorciapino MA, Amodeo GF, Grdadolnik J, Pappalardo G, De Pinto V, Ceccarelli M, Casu M. The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities. Biochemistry 2015; 54:5646-56. [DOI: 10.1021/acs.biochem.5b00469] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Carlo Guardiani
- Department
of Physics, University of Cagliari, 09042 Monserrato, Italy
| | - Mariano Andrea Scorciapino
- Department
of Biomedical Sciences, Biochemistry Unit, University of Cagliari, 09042 Monserrato, Italy
- Istituto
Officina dei Materiali del Consiglio Nazionale delle Ricerche (IOM-CNR), UOS, Cagliari, Italy
| | | | | | | | - Vito De Pinto
- Department
of Biological, Geological and Environmental Sciences, Section of Molecular
Biology, University of Catania, and National Institute for Biostructures and Biosystems, Section of Catania, Catania, Italy
| | - Matteo Ceccarelli
- Department
of Physics, University of Cagliari, 09042 Monserrato, Italy
- Istituto
Officina dei Materiali del Consiglio Nazionale delle Ricerche (IOM-CNR), UOS, Cagliari, Italy
| | - Mariano Casu
- Department
of Chemical and Geological Sciences, University of Cagliari, 09042 Monserrato, Italy
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32
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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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33
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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
![]()
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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34
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Tewari D, Ahmed T, Chirasani VR, Singh PK, Maji SK, Senapati S, Bera AK. Modulation of the mitochondrial voltage dependent anion channel (VDAC) by curcumin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:151-8. [PMID: 25459681 DOI: 10.1016/j.bbamem.2014.10.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/06/2014] [Accepted: 10/13/2014] [Indexed: 01/30/2023]
Abstract
Voltage dependent anion channel (VDAC) of mitochondria plays a crucial role in apoptosis. Human VDAC-1, reconstituted in planar lipid bilayer showed reduced conductance when treated with curcumin. Curcumin interacts with residues in the α helical N-terminus of VDAC and in the channel wall, as revealed by molecular docking, followed by mutational analysis. N-terminus mimicking peptide showed conformational changes in circular dichroism, upon curcumin treatment. We propose that the interaction of curcumin with amino acids in N-terminus and in channel wall fixes the α helix in closed conformation. This restricts its movement which is required for the opening of the channel.
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Affiliation(s)
- Debanjan Tewari
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - Tofayel Ahmed
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - Venkat R Chirasani
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - Pradeep K Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjib Senapati
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - Amal Kanti Bera
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences Building, Indian Institute of Technology Madras, Chennai 600036, India.
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35
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36
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Maldonado EN, Lemasters JJ. ATP/ADP ratio, the missed connection between mitochondria and the Warburg effect. Mitochondrion 2014; 19 Pt A:78-84. [PMID: 25229666 DOI: 10.1016/j.mito.2014.09.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/08/2014] [Accepted: 09/08/2014] [Indexed: 02/06/2023]
Abstract
Non-proliferating cells generate the bulk of cellular ATP by fully oxidizing respiratory substrates in mitochondria. Respiratory substrates cross the mitochondrial outer membrane through only one channel, the voltage dependent anion channel (VDAC). Once in the matrix, respiratory substrates are oxidized in the tricarboxylic acid cycle to generate mostly NADH that is further oxidized in the respiratory chain to generate a proton motive force comprised mainly of membrane potential (ΔΨ) to synthesize ATP. Mitochondrial ΔΨ then drives the release of ATP(4-) from the matrix in exchange for ADP(3-) in the cytosol via the adenine nucleotide translocator (ANT) located in the mitochondrial inner membrane. Thus, mitochondrial function in non-proliferating cells drives a high cytosolic ATP/ADP ratio, essential to inhibit glycolysis. By contrast, the bioenergetics of the Warburg phenotype of proliferating cells is characterized by enhanced aerobic glycolysis and the suppression of mitochondrial metabolism. Suppressed mitochondrial function leads to lower production of mitochondrial ATP and hence lower cytosolic ATP/ADP ratios that favor enhanced glycolysis. Thus, the cytosolic ATP/ADP ratio is a key feature that determines if cell metabolism is predominantly oxidative or glycolytic. Here, we describe two novel mechanisms to explain the suppression of mitochondrial metabolism in cancer cells: the relative closure of VDAC by free tubulin and the inactivation of ANT. Both mechanisms contribute to low ATP/ADP ratios that activate glycolysis.
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Affiliation(s)
- Eduardo N Maldonado
- Center for Cell Death, Injury & Regeneration, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States
| | - John J Lemasters
- Center for Cell Death, Injury & Regeneration, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Drug Discovery & Biomedical Sciences, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States; Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia.
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37
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Amodeo GF, Scorciapino MA, Messina A, De Pinto V, Ceccarelli M. Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel. PLoS One 2014; 9:e103879. [PMID: 25084457 PMCID: PMC4146382 DOI: 10.1371/journal.pone.0103879] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/02/2014] [Indexed: 11/18/2022] Open
Abstract
Voltage Dependent Anion-selective Channels (VDACs) are pore-forming proteins located in the outer mitochondrial membrane. They are responsible for the access of ions and energetic metabolites into the inner membrane transport systems. Three VDAC isoforms exist in mammalian, but their specific role is unknown. In this work we have performed extensive (overall ∼5 µs) Molecular Dynamics (MD) simulations of the human VDAC isoforms to detect structural and conformational variations among them, possibly related to specific functional roles of these proteins. Secondary structure analysis of the N-terminal domain shows a high similarity among the three human isoforms of VDAC but with a different plasticity. In particular, the N-terminal domain of the hVDAC1 is characterized by a higher plasticity, with a ∼20% occurrence for the 'unstructured' conformation throughout the folded segment, while hVDAC2, containing a peculiar extension of 11 amino acids at the N-terminal end, presents an additional 310-helical folded portion comprising residues 10' to 3, adhering to the barrel wall. The N-terminal sequences of hVDAC isoforms are predicted to have a low flexibility, with possible consequences in the dynamics of the human VDACs. Clear differences were found between hVDAC1 and hVDAC3 against hVDAC2: a significantly modified dynamics with possible important consequence on the voltage-gating mechanism. Charge distribution inside and at the mouth of the pore is responsible for a different preferential localization of ions with opposite charge and provide a valuable rationale for hVDAC1 and hVDAC3 having a Cl-/K+ selectivity ratio of 1.8, whereas hVDAC2 of 1.4. Our conclusion is that hVDAC isoforms, despite sharing a similar scaffold, have modified working features and a biological work is now requested to give evidence to the described dissimilarities.
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Affiliation(s)
| | - Mariano Andrea Scorciapino
- Department of Physics, University of Cagliari, Cagliari, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Cagliari, Italy
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Catania, Italy
- National Institute for Biomembranes and Biosystems, Catania, Italy
| | - Vito De Pinto
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Catania, Italy
- National Institute for Biomembranes and Biosystems, Catania, Italy
| | - Matteo Ceccarelli
- Department of Physics, University of Cagliari, Cagliari, Italy
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche, Cagliari, Italy
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38
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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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39
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Abstract
The field of mitochondrial ion channels has recently seen substantial progress, including the molecular identification of some of the channels. An integrative approach using genetics, electrophysiology, pharmacology, and cell biology to clarify the roles of these channels has thus become possible. It is by now clear that many of these channels are important for energy supply by the mitochondria and have a major impact on the fate of the entire cell as well. The purpose of this review is to provide an up-to-date overview of the electrophysiological properties, molecular identity, and pathophysiological functions of the mitochondrial ion channels studied so far and to highlight possible therapeutic perspectives based on current information.
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40
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Schredelseker J, Paz A, López CJ, Altenbach C, Leung CS, Drexler MK, Chen JN, Hubbell WL, Abramson J. High resolution structure and double electron-electron resonance of the zebrafish voltage-dependent anion channel 2 reveal an oligomeric population. J Biol Chem 2014; 289:12566-77. [PMID: 24627492 DOI: 10.1074/jbc.m113.497438] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In recent years, there has been a vast increase in structural and functional understanding of VDAC1, but VDAC2 and -3 have been understudied despite having many unique phenotypes. One reason for the paucity of structural and biochemical characterization of the VDAC2 and -3 isoforms stems from the inability of obtaining purified, functional protein. Here we demonstrate the expression, isolation, and basic characterization of zebrafish VDAC2 (zfVDAC2). Further, we resolved the structure of zfVDAC2 at 2.8 Å resolution, revealing a crystallographic dimer. The dimer orientation was confirmed in solution by double electron-electron resonance spectroscopy and by cross-linking experiments disclosing a dimer population of ∼20% in lauryldimethine amine oxide detergent micelles, whereas in lipidic bicelles a higher population of dimeric and higher order oligomers species were observed. The present study allows for a more accurate structural comparison between VDAC2 and its better-studied counterpart VDAC1.
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41
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Laghaei R, Kowallis W, Evans DG, Coalson RD. Calculation of Iron Transport through Human H-chain Ferritin. J Phys Chem A 2014; 118:7442-53. [DOI: 10.1021/jp500198u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rozita Laghaei
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - William Kowallis
- Department
of Chemistry, Carlow University, Pittsburgh, Pennsylvania 15213, United States
| | - Deborah G. Evans
- The
Nanoscience and Microsystems Program and the Department of Chemistry
and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131-0001, United States
| | - Rob D. Coalson
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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42
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Zhou HX. Theoretical frameworks for multiscale modeling and simulation. Curr Opin Struct Biol 2014; 25:67-76. [PMID: 24492203 DOI: 10.1016/j.sbi.2014.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 12/25/2013] [Accepted: 01/10/2014] [Indexed: 02/08/2023]
Abstract
Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.
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Affiliation(s)
- Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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Noskov SY, Rostovtseva TK, Bezrukov SM. ATP transport through VDAC and the VDAC-tubulin complex probed by equilibrium and nonequilibrium MD simulations. Biochemistry 2013; 52:9246-56. [PMID: 24245503 PMCID: PMC7259721 DOI: 10.1021/bi4011495] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane, serves as a principal pathway for ATP, ADP, and other respiratory substrates across this membrane. Using umbrella-sampling simulations, we established the thermodynamic and kinetic components governing ATP transport across the VDAC1 channel. We found that there are several low-affinity binding sites for ATP along the translocation pathway and that the main barrier for ATP transport is located around the center of the channel and is formed predominantly by residues in the N-terminus. The binding affinity of ATP to an open channel was found to be in the millimolar to micromolar range. However, we show that this weak binding increases the ATP translocation probability by about 10-fold compared with the VDAC pore in which attractive interactions were artificially removed. Recently, it was found that free dimeric tubulin induces a highly efficient, reversible blockage of VDAC reconstituted into planar lipid membranes. It was proposed that by blocking VDAC permeability for ATP/ADP and other mitochondrial respiratory substrates tubulin controls mitochondrial respiration. Using the Rosetta protein-protein docking algorithm, we established a tentative structure of the VDAC-tubulin complex. An extensive set of equilibrium and nonequilibrium (under applied electric field) molecular dynamics (MD) simulations was used to establish the conductance of the open and blocked channel. It was found that the presence of the unstructured C-terminal tail of tubulin in the VDAC pore decreases its conductance by more than 40% and switches its selectivity from anionic to cationic. The subsequent 1D potential of mean force (PMF) computations for the VDAC-tubulin complex show that the state renders ATP transport virtually impossible. A number of residues pivotal for tubulin binding to the channel were identified that help to clarify the molecular details of VDAC-tubulin interaction and to provide new insight into the mechanism of the control of mitochondria respiration by VDAC.
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Affiliation(s)
- Sergei Yu. Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Tatiana K. Rostovtseva
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sergey M. Bezrukov
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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Wei GW. Multiscale Multiphysics and Multidomain Models I: Basic Theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013; 12:10.1142/S021963361341006X. [PMID: 25382892 PMCID: PMC4220694 DOI: 10.1142/s021963361341006x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA Department of Biochemistry and Molecular Biology Michigan State University, MI 48824, USA
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Zander CB, Albers T, Grewer C. Voltage-dependent processes in the electroneutral amino acid exchanger ASCT2. ACTA ACUST UNITED AC 2013; 141:659-72. [PMID: 23669717 PMCID: PMC3664696 DOI: 10.1085/jgp.201210948] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Neutral amino acid exchange by the alanine serine cysteine transporter (ASCT)2 was reported to be electroneutral and coupled to the cotransport of one Na+ ion. The cotransported sodium ion carries positive charge. Therefore, it is possible that amino acid exchange is voltage dependent. However, little information is available on the electrical properties of the ASCT2 amino acid transport process. Here, we have used a combination of experimental and computational approaches to determine the details of the amino acid exchange mechanism of ASCT2. The [Na+] dependence of ASCT2-associated currents indicates that the Na+/amino acid stoichiometry is at least 2:1, with at least one sodium ion binding to the amino acid–free apo form of the transporter. When the substrate and two Na+ ions are bound, the valence of the transport domain is +0.81. Consistently, voltage steps applied to ASCT2 in the fully loaded configuration elicit transient currents that decay on a millisecond time scale. Alanine concentration jumps at the extracellular side of the membrane are followed by inwardly directed transient currents, indicative of translocation of net positive charge during exchange. Molecular dynamics simulations are consistent with these results and point to a sequential binding process in which one or two modulatory Na+ ions bind with high affinity to the empty transporter, followed by binding of the amino acid substrate and the subsequent binding of a final Na+ ion. Overall, our results are consistent with voltage-dependent amino acid exchange occurring on a millisecond time scale, the kinetics of which we predict with simulations. Despite some differences, transport mechanism and interaction with Na+ appear to be highly conserved between ASCT2 and the other members of the solute carrier 1 family, which transport acidic amino acids.
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Affiliation(s)
- Catherine B Zander
- Department of Chemistry, Binghamton University, Binghamton, NY 13902, USA
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Krammer EM, Homblé F, Prévost M. Molecular origin of VDAC selectivity towards inorganic ions: a combined molecular and Brownian dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:1284-92. [PMID: 23313453 DOI: 10.1016/j.bbamem.2012.12.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 12/14/2012] [Accepted: 12/31/2012] [Indexed: 11/15/2022]
Abstract
The voltage-dependent anion channel (VDAC) serves as the major pore for metabolites and electrolytes in the outer mitochondrial membrane. To refine our understanding of ion permeation through this channel we performed an extensive Brownian (BD) and molecular dynamics (MD) study on the mouse VDAC isoform 1 wild-type and mutants (K20E, D30K, K61E, E158K and K252E). The selectivity and the conductance of the wild-type and of the variant channels computed from the BD trajectories are in agreement with experimental data. The calculated selectivity is shown to be very sensitive to slight conformational changes which may have some bearing on the variability of the selectivity values measured on the VDAC open state. The MD and BD free energy profiles of the ion permeation suggest that the pore region comprising the N-terminal helix and the barrel band encircling it predominantly controls the ion transport across the channel. The overall 12μs BD and 0.9μs MD trajectories of the mouse VDAC isoform 1 wild-type and mutants feature no distinct pathways for ion diffusion and no long-lived ion-protein interactions. The dependence of ion distribution in the wild-type channel with the salt concentration can be explained by an ionic screening of the permanent charges of the protein arising from the pore. Altogether these results bolster the role of electrostatic features of the pore as the main determinant of VDAC selectivity towards inorganic anions.
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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), Boulevard du Triomphe CP 206/2, B-1050 Brussels, Belgium
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47
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Mwaura J, Tao Z, James H, Albers T, Schwartz A, Grewer C. Protonation state of a conserved acidic amino acid involved in Na(+) binding to the glutamate transporter EAAC1. ACS Chem Neurosci 2012; 3:1073-83. [PMID: 23259042 DOI: 10.1021/cn300163p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 10/19/2012] [Indexed: 01/08/2023] Open
Abstract
Substrate transport by glutamate transporters is coupled to the co-transport of 3 Na(+) ions and counter-transport of 1 K(+) ion. The highly conserved Asp454, which may be negatively charged, is of interest as its side chain may coordinate cations and/or contribute to charge compensation. Mutation to the nonionizable Asn resulted in a transporter that no longer catalyzed forward transport. However, Na(+)/glutamate exchange was still functional, as demonstrated by the presence of transient currents following rapid substrate application and voltage jumps. While the kinetics of Na(+)/glutamate exchange were slowed, the apparent valence (z) of the charge moved in EAAC1 D454N (0.71) was similar to that of EAAC1 WT (0.64). Valences calculated using the Poisson-Boltzmann equation were close to the experimental values for EAAC1 D454N (0.55), and with D454 protonated (0.45). In addition, pK(a) calculations performed for the bacterial homologue GltPh revealed a highly perturbed pK(a) (7.6 to >14) for D405 residue (analogous to D454), consistent with this site being protonated at physiological pH. In contrast to the D454N mutation, substitution to alanine resulted in a transporter that still bound glutamate, but could not translocate it. The results are consistent with molecular dynamics simulations, showing that the alanine but not the asparagine mutation resulted in defective Na(+) coordination. Our results raise the possibility that the protonated state of D454 supports transporter function.
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Affiliation(s)
- Juddy Mwaura
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
| | - Zhen Tao
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
| | - Herbert James
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
| | - Thomas Albers
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
| | - Alexander Schwartz
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
| | - Christof Grewer
- Department of Chemistry, Binghamton University, Binghamton, New York 13902,
United States
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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49
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Shoshan-Barmatz V, Mizrachi D. VDAC1: from structure to cancer therapy. Front Oncol 2012; 2:164. [PMID: 23233904 PMCID: PMC3516065 DOI: 10.3389/fonc.2012.00164] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 10/24/2012] [Indexed: 12/14/2022] Open
Abstract
Here, we review current evidence pointing to the function of VDAC1 in cell life and death, and highlight these functions in relation to cancer. Found at the outer mitochondrial membrane, VDAC1 assumes a crucial position in the cell, controlling the metabolic cross-talk between mitochondria and the rest of the cell. Moreover, its location at the boundary between the mitochondria and the cytosol enables VDAC1 to interact with proteins that mediate and regulate the integration of mitochondrial functions with other cellular activities. As a metabolite transporter, VDAC1 contributes to the metabolic phenotype of cancer cells. This is reflected by VDAC1 over-expression in many cancer types, and by inhibition of tumor development upon silencing VDAC1 expression. Along with regulating cellular energy production and metabolism, VDAC1 is also a key protein in mitochondria-mediated apoptosis, participating in the release of apoptotic proteins and interacting with anti-apoptotic proteins. The involvement of VDAC1 in the release of apoptotic proteins located in the inter-membranal space is discussed, as is VDAC1 oligomerization as an important step in apoptosis induction. VDAC also serves as an anchor point for mitochondria-interacting proteins, some of which are also highly expressed in many cancers, such as hexokinase (HK), Bcl2, and Bcl-xL. By binding to VDAC, HK provides both metabolic benefit and apoptosis-suppressive capacity that offers the cell a proliferative advantage and increases its resistance to chemotherapy. VDAC1-based peptides that bind specifically to HK, Bcl2, or Bcl-xL abolished the cell’s abilities to bypass the apoptotic pathway. Moreover, these peptides promote cell death in a panel of genetically characterized cell lines derived from different human cancers. These and other functions point to VDAC1 as a rational target for the development of a new generation of therapeutics.
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Affiliation(s)
- Varda Shoshan-Barmatz
- Department of Life Sciences, Ben-Gurion University of the Negev Beer-Sheva, Israel ; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev Beer-Sheva, Israel
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Mertins B, Psakis G, Grosse W, Back KC, Salisowski A, Reiss P, Koert U, Essen LO. Flexibility of the N-terminal mVDAC1 segment controls the channel's gating behavior. PLoS One 2012; 7:e47938. [PMID: 23110136 PMCID: PMC3479125 DOI: 10.1371/journal.pone.0047938] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/25/2012] [Indexed: 11/26/2022] Open
Abstract
Since the solution of the molecular structures of members of the voltage dependent anion channels (VDACs), the N-terminal α-helix has been the main focus of attention, since its strategic location, in combination with its putative conformational flexibility, could define or control the channel’s gating characteristics. Through engineering of two double-cysteine mVDAC1 variants we achieved fixing of the N-terminal segment at the bottom and midpoint of the pore. Whilst cross-linking at the midpoint resulted in the channel remaining constitutively open, cross-linking at the base resulted in an “asymmetric” gating behavior, with closure only at one electric field´s orientation depending on the channel’s orientation in the lipid bilayer. Additionally, and while the native channel adopts several well-defined closed states (S1 and S2), the cross-linked variants showed upon closure a clear preference for the S2 state. With native-channel characteristics restored following reduction of the cysteines, it is evident that the conformational flexibility of the N-terminal segment plays indeed a major part in the control of the channel’s gating behavior.
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Affiliation(s)
- Barbara Mertins
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Georgios Psakis
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Wolfgang Grosse
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | | | | | - Philipp Reiss
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Ulrich Koert
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, Marburg, Germany
- * E-mail:
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