51
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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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52
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Clémençon B, Fine M, Hediger MA. Conservation of the oligomeric state of native VDAC1 in detergent micelles. Biochimie 2016; 127:163-72. [PMID: 27238246 DOI: 10.1016/j.biochi.2016.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
The voltage-dependent anion-selective channel (VDAC) is an intrinsic β-barrel membrane protein located within the mitochondrial outer membrane where it serves as a pore, connecting the mitochondria to the cytosol. The high-resolution structures of both the human and murine VDACs have been resolved by X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) in 2008. However, the structural data are not completely in line with the findings that were obtained after decades of research on biochemical and functional analysis of VDAC. This discrepancy may be related to the fact that structural biology studies of membrane proteins reveal specific static conformations that may not necessarily represent the physiological state. For example, overexpression of membrane proteins in bacterial inclusion bodies or simply the extraction from the native lipid environment using harsh purification methods (i.e. chaotropic agents) can disturb the physiological conformations and the supramolecular assemblies. To address these potential issues, we have developed a method, allowing rapid one step purification of endogenous VDAC expressed in the native mitochondrial membrane without overexpression of recombinant protein or usage of harsh chaotropic extraction procedures. Using the Saccharomyces cerevisiae isoform 1 of VDAC as a model, this method yields efficient purification, preserving VDAC in a more physiological, native state following extraction from mitochondria. Single particle analysis using transmission electron microscopy (TEM) demonstrated conservation of oligomeric assembly after purification. Maintenance of the native state was evaluated using functional assessment that involves an ATP-binding assay by micro-scale thermophoresis (MST). Using this approach, we were able to determine for the first time the apparent KD for ATP of 1.2 mM.
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Affiliation(s)
- Benjamin Clémençon
- Institute of Biochemistry and Molecular Medicine (IBMM), National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland.
| | - Michael Fine
- Institute of Biochemistry and Molecular Medicine (IBMM), National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine (IBMM), National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland.
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53
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Raschle T, Rios Flores P, Opitz C, Müller DJ, Hiller S. Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509910] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Raschle
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Perla Rios Flores
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Christian Opitz
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Sebastian Hiller
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
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54
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Raschle T, Rios Flores P, Opitz C, Müller DJ, Hiller S. Monitoring Backbone Hydrogen‐Bond Formation in β‐Barrel Membrane Protein Folding. Angew Chem Int Ed Engl 2016; 55:5952-5. [DOI: 10.1002/anie.201509910] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/16/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Raschle
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Perla Rios Flores
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Christian Opitz
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
| | - Daniel J. Müller
- Department of Biosystems Science and Engineering Eidgenössische Technische Hochschule Zürich Mattenstrasse 26 4058 Basel Switzerland
| | - Sebastian Hiller
- Biozentrum University of Basel Klingelbergstrasse 70 4056 Basel Switzerland
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55
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Wang F, Qiang Y, Zhu L, Jiang Y, Wang Y, Shao X, Yin L, Chen J, Chen Z. MicroRNA-7 downregulates the oncogene VDAC1 to influence hepatocellular carcinoma proliferation and metastasis. Tumour Biol 2016; 37:10235-46. [PMID: 26831666 DOI: 10.1007/s13277-016-4836-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/11/2016] [Indexed: 11/30/2022] Open
Abstract
Recent studies have been shown that voltage-dependent anion channel 1 (VDAC1) plays an important role in carcinogenesis. However, its molecular biological function in hepatocellular carcinoma (HCC) has not been entirely clarified. This study investigated the expression of VDAC1 in HCC and its prognostic value for HCC patients. Furthermore, we also identify the relevant VDAC1 direct target. Western blot, real-time quantitative PCR (qRT-PCR), and immunohistochemical (IHC) staining were performed to detect the expression of VDAC1 in HCC. Furthermore, the relationship between the VDAC1 level and clinicopathological features and prognostic values was explored. The effects of VDAC1 on HCC cell proliferation, migration, and invasion were also investigated in vitro. Predicted target gene of VDAC1 was determined by dual-luciferase reporter assay, qRT-PCR, and Western blot analyses. Our results revealed elevated VDAC1 messenger RNA (mRNA) (P = 0.0020) and protein (P = 0.0035) expression in tumor tissue samples compared with paired adjacent non-tumorous tissue samples. High VDAC1 expression was correlated with distant metastasis (P = 0.025), differentiation (P = 0.002), and advanced tumor stage (P = 0.004) in HCC patients. Kaplan-Meier survival analysis demonstrated that high expression of VDAC1 was significantly correlated with a poor prognosis for HCC patients (P < 0.001). The multivariate analysis revealed that VDAC1 expression was an independent prognostic factor of the overall survival rate of HCC patients. Furthermore, knockdown of VDAC1 inhibits HCC cell proliferation, migration, and invasion in vitro. Moreover, further study revealed that miR-7 was a putative target of VDAC1. Our study suggested that miR-7 suppressed the expression of VDAC1. VDAC1 plays an important role in tumor progression and may be used as a potential role in the prognosis of HCC patients.
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Affiliation(s)
- Feiran Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Yong Qiang
- Department of General Surgery, The First People's Hospital of Jingmen, Dongbao District, Jingmen, Hubei, 448000, People's Republic of China
| | - Lirong Zhu
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Yasu Jiang
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Yinda Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Xian Shao
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Lei Yin
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China
| | - Jiahui Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Zhong Chen
- Department of General Surgery, Affiliated Hospital of Nantong University, Xi Si Road, Nantong, Jiangsu Province, 226001, People's Republic of China. .,Department of Hepatobiliary Surgery, Affiliated Hospital of Nantong University and Research Institute of Hepatobiliary Surgery of Nantong University, 20 Xisi Road, Nantong, Jiangsu, 226001, People's Republic of China.
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56
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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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57
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Schuler MH, Di Bartolomeo F, Böttinger L, Horvath SE, Wenz LS, Daum G, Becker T. Phosphatidylcholine affects the role of the sorting and assembly machinery in the biogenesis of mitochondrial β-barrel proteins. J Biol Chem 2015; 290:26523-32. [PMID: 26385920 DOI: 10.1074/jbc.m115.687921] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 11/06/2022] Open
Abstract
Two protein translocases drive the import of β-barrel precursor proteins into the mitochondrial outer membrane: The translocase of the outer membrane (TOM complex) promotes transport of the precursor to the intermembrane space, whereas the sorting and assembly machinery (SAM complex) mediates subsequent folding of the β-barrel and its integration into the target membrane. The non-bilayer-forming phospholipids phosphatidylethanolamine (PE) and cardiolipin (CL) are required for the biogenesis of β-barrel proteins. Whether bilayer-forming phospholipids such as phosphatidylcholine (PC), the most abundant phospholipid of the mitochondrial outer membrane, play a role in the import of β-barrel precursors is unclear. In this study, we show that PC is required for stability and function of the SAM complex during the biogenesis of β-barrel proteins. PC further promotes the SAM-dependent assembly of the TOM complex, indicating a general role of PC for the function of the SAM complex. In contrast to PE-deficient mitochondria precursor accumulation at the TOM complex is not affected by depletion of PC. We conclude that PC and PE affect the function of distinct protein translocases in mitochondrial β-barrel biogenesis.
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Affiliation(s)
- Max-Hinderk Schuler
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | | | - Lena Böttinger
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Lena-Sophie Wenz
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Günther Daum
- Institute for Biochemistry, Graz University of Technology, NaWi Graz, A-8010 Graz, Austria,
| | - Thomas Becker
- From the Institute for Biochemistry and Molecular Biology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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58
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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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59
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Xu HD, Su HJ, Zou WB, Liu SS, Yan WR, Wang QQ, Yuan LL, Chan SF, Yu XQ, He JG, Weng SP. Identification of mud crab reovirus VP12 and its interaction with the voltage-dependent anion-selective channel protein of mud crab Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2015; 44:224-231. [PMID: 25542377 DOI: 10.1016/j.fsi.2014.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/01/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
Mud crab reovirus (MCRV) is the causative agent of a severe disease in cultured mud crab (Scylla paramamosain), which has caused huge economic losses in China. MCRV is a double-stranded RNA virus with 12 genomic segments. In this paper, SDS-PAGE, mass spectrometry and Western blot analyses revealed that the VP12 protein encoded by S12 gene is a structural protein of MCRV. Immune electron microscopy assay indicated that MCRV VP12 is a component of MCRV outer shell capsid. Yeast two hybrid cDNA library of mud crab was constructed and mud crab voltage-dependent anion-selective channel (mcVDAC) was obtained by MCRV VP12 screening. The full length of mcVDAC was 1180 bp with an open reading frame (ORF) of 849 bp encoding a 282 amino acid protein. The mcVDAC had a constitutive expression pattern in different tissues of mud crab. The interaction between MCRV VP12 and mcVDAC was determined by co-immunoprecipitation assay. The results of this study have provided an insight on the mechanisms of MCRV infection and the interactions between the virus and mud crab.
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Affiliation(s)
- Hai-Dong Xu
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Hong-Jun Su
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Wei-Bin Zou
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Shan-Shan Liu
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Wen-Rui Yan
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Qian-Qian Wang
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Li-Li Yuan
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Siuming Francis Chan
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong, People's Republic of China
| | - Xiao-Qiang Yu
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Jian-Guo He
- MOE Key Laboratory of Aquatic Product Safety / State Key Laboratory for Biocontrol, School of Marine Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China; School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China
| | - Shao-Ping Weng
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road West, Guangzhou, Guangdong, People's Republic of China.
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60
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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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61
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Gupta R, Ghosh S. Phosphorylation of voltage-dependent anion channel by c-Jun N-terminal Kinase-3 leads to closure of the channel. Biochem Biophys Res Commun 2015; 459:100-6. [PMID: 25721670 DOI: 10.1016/j.bbrc.2015.02.077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 02/15/2015] [Indexed: 01/30/2023]
Abstract
Stress activated c-Jun N-terminal Kinase-3 (JNK3) has been reported to act on mitochondrion to promote neuronal cell death. Phosphorylation of mitochondrial Voltage-Dependent Anion Channel (VDAC) plays an important role in mitochondria-mediated cell death. Keeping these in view phosphorylation of rat brain VDAC by JNK3 has been studied in vitro. Pro Q Diamond phospho-protein staining experiment demonstrates VDAC is phosphorylated by JNK3. Bilayer electrophysiological experiments show that single-channel conductance of VDAC phosphorylated by JNK3 is significantly lower than that of the native VDAC at a membrane potential. The opening probability of VDAC undergoes massive reduction due to phosphorylation by JNK3. These indicate closure of VDAC due to phosphorylation by JNK3. Treatment of phosphorylated VDAC with alkaline phosphatase reversed the VDAC functional activity as shown by single-channel current and opening probability. The physiological consequence of closure of VDAC as a result of phosphorylation has been attributed to JNK3 dependent mitochondria-mediated apoptosis.
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Affiliation(s)
- Rajeev Gupta
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Subhendu Ghosh
- Department of Biophysics, University of Delhi South Campus, New Delhi, India.
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62
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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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63
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Prasad M, Kaur J, Pawlak KJ, Bose M, Whittal RM, Bose HS. Mitochondria-associated endoplasmic reticulum membrane (MAM) regulates steroidogenic activity via steroidogenic acute regulatory protein (StAR)-voltage-dependent anion channel 2 (VDAC2) interaction. J Biol Chem 2014; 290:2604-16. [PMID: 25505173 DOI: 10.1074/jbc.m114.605808] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Steroid hormones are essential for carbohydrate metabolism, stress management, and reproduction and are synthesized from cholesterol in mitochondria of adrenal glands and gonads/ovaries. In acute stress or hormonal stimulation, steroidogenic acute regulatory protein (StAR) transports substrate cholesterol into the mitochondria for steroidogenesis by an unknown mechanism. Here, we report for the first time that StAR interacts with voltage-dependent anion channel 2 (VDAC2) at the mitochondria-associated endoplasmic reticulum membrane (MAM) prior to its translocation to the mitochondrial matrix. In the MAM, StAR interacts with mitochondrial proteins Tom22 and VDAC2. However, Tom22 knockdown by siRNA had no effect on pregnenolone synthesis. In the absence of VDAC2, StAR was expressed but not processed into the mitochondria as a mature 30-kDa protein. VDAC2 interacted with StAR via its C-terminal 20 amino acids and N-terminal amino acids 221-229, regulating the mitochondrial processing of StAR into the mature protein. In the absence of VDAC2, StAR could not enter the mitochondria or interact with MAM-associated proteins, and therefore steroidogenesis was inhibited. Furthermore, the N terminus was not essential for StAR activity, and the N-terminal deletion mutant continued to interact with VDAC2. The endoplasmic reticulum-targeting prolactin signal sequence did not affect StAR association with the MAM and thus its mitochondrial targeting. Therefore, VDAC2 controls StAR processing and activity, and MAM is thus a central location for initiating mitochondrial steroidogenesis.
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Affiliation(s)
- Manoj Prasad
- From the Mercer University School of Medicine, Savannah, Georgia 31404
| | - Jasmeet Kaur
- From the Mercer University School of Medicine, Savannah, Georgia 31404
| | - Kevin J Pawlak
- From the Mercer University School of Medicine, Savannah, Georgia 31404
| | - Mahuya Bose
- Center of Excellence for Health Regeneration Biotechnology, Florida Biologix, University of Florida, Alachua, Florida 32615, Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida 32610
| | - Randy M Whittal
- Department of Chemistry, University of Alberta, Alberta T6G2G2, Canada, and
| | - Himangshu S Bose
- From the Mercer University School of Medicine, Savannah, Georgia 31404, Anderson Cancer Institute, Memorial University Medical Center, Savannah, Georgia 31404
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64
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Mitochondrial cholesterol: mechanisms of import and effects on mitochondrial function. J Bioenerg Biomembr 2014; 48:137-51. [PMID: 25425472 DOI: 10.1007/s10863-014-9592-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/14/2014] [Indexed: 12/23/2022]
Abstract
Mitochondria require cholesterol for biogenesis and membrane maintenance, and for the synthesis of steroids, oxysterols and hepatic bile acids. Multiple pathways mediate the transport of cholesterol from different subcellular pools to mitochondria. In steroidogenic cells, the steroidogenic acute regulatory protein (StAR) interacts with a mitochondrial protein complex to mediate cholesterol delivery to the inner mitochondrial membrane for conversion to pregnenolone. In non-steroidogenic cells, several members of a protein family defined by the presence of a StAR-related lipid transfer (START) domain play key roles in the delivery of cholesterol to mitochondrial membranes. Subdomains of the endoplasmic reticulum (ER), termed mitochondria-associated ER membranes (MAM), form membrane contact sites with mitochondria and may contribute to the transport of ER cholesterol to mitochondria, either independently or in conjunction with lipid-transfer proteins. Model systems of mitochondria enriched with cholesterol in vitro and mitochondria isolated from cells with (patho)physiological mitochondrial cholesterol accumulation clearly demonstrate that mitochondrial cholesterol levels affect mitochondrial function. Increased mitochondrial cholesterol levels have been observed in several diseases, including cancer, ischemia, steatohepatitis and neurodegenerative diseases, and influence disease pathology. Hence, a deeper understanding of the mechanisms maintaining mitochondrial cholesterol homeostasis may reveal additional targets for therapeutic intervention. Here we give a brief overview of mitochondrial cholesterol import in steroidogenic cells, and then focus on cholesterol trafficking pathways that deliver cholesterol to mitochondrial membranes in non-steroidogenic cells. We also briefly discuss the consequences of increased mitochondrial cholesterol levels on mitochondrial function and their potential role in disease pathology.
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Shoshan-Barmatz V, Ben-Hail D, Admoni L, Krelin Y, Tripathi SS. The mitochondrial voltage-dependent anion channel 1 in tumor cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:2547-75. [PMID: 25448878 DOI: 10.1016/j.bbamem.2014.10.040] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/20/2014] [Accepted: 10/24/2014] [Indexed: 02/06/2023]
Abstract
VDAC1 is found at the crossroads of metabolic and survival pathways. VDAC1 controls metabolic cross-talk between mitochondria and the rest of the cell by allowing the influx and efflux of metabolites, ions, nucleotides, Ca2+ and more. The location of VDAC1 at the outer mitochondrial membrane also enables its interaction with proteins that mediate and regulate the integration of mitochondrial functions with cellular activities. As a transporter of metabolites, VDAC1 contributes to the metabolic phenotype of cancer cells. Indeed, this protein is over-expressed in many cancer types, and silencing of VDAC1 expression induces an inhibition of tumor development. At the same time, along with regulating cellular energy production and metabolism, VDAC1 is involved in the process of mitochondria-mediated apoptosis by mediating the release of apoptotic proteins and interacting with anti-apoptotic proteins. The engagement of VDAC1 in the release of apoptotic proteins located in the inter-membranal space involves VDAC1 oligomerization that mediates the release of cytochrome c and AIF to the cytosol, subsequently leading to apoptotic cell death. Apoptosis can also be regulated by VDAC1, serving as an anchor point for mitochondria-interacting proteins, such as hexokinase (HK), Bcl2 and Bcl-xL, some of which are also highly expressed in many cancers. By binding to VDAC1, HK provides both a metabolic benefit and apoptosis-suppressive capacity that offer the cell a proliferative advantage and increase its resistance to chemotherapy. Thus, these and other functions point to VDAC1 as an excellent target for impairing the re-programed metabolism of cancer cells and their ability to evade apoptosis. Here, we review current evidence pointing to the function of VDAC1 in cell life and death, and highlight these functions in relation to both cancer development and therapy. In addressing the recently solved 3D structures of VDAC1, this review will point to structure-function relationships of VDAC as critical for deciphering how this channel can perform such a variety of roles, all of which are important for cell life and death. Finally, this review will also provide insight into VDAC function in Ca2+ homeostasis, protection against oxidative stress, regulation of apoptosis and involvement in several diseases, as well as its role in the action of different drugs. We will discuss the use of VDAC1-based strategies to attack the altered metabolism and apoptosis of cancer cells. These strategies include specific siRNA able to impair energy and metabolic homeostasis, leading to arrested cancer cell growth and tumor development, as well VDAC1-based peptides that interact with anti-apoptotic proteins to induce apoptosis, thereby overcoming the resistance of cancer cell to chemotherapy. Finally, small molecules targeting VDAC1 can induce apoptosis. VDAC1 can thus be considered as standing at the crossroads between mitochondrial metabolite transport and apoptosis and hence represents an emerging cancer drug target. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.
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Affiliation(s)
- Varda Shoshan-Barmatz
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Danya Ben-Hail
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Lee Admoni
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yakov Krelin
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shambhoo Sharan Tripathi
- Department of Life Sciences, and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Nikiforova AB, Saris NEL, Kruglov AG. External mitochondrial NADH-dependent reductase of redox cyclers: VDAC1 or Cyb5R3? Free Radic Biol Med 2014; 74:74-84. [PMID: 24945955 DOI: 10.1016/j.freeradbiomed.2014.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 06/06/2014] [Accepted: 06/10/2014] [Indexed: 11/19/2022]
Abstract
It was reported that VDAC1 possesses an NADH oxidoreductase activity and plays an important role in the activation of xenobiotics in the outer mitochondrial membrane. In the present work, we evaluated the participation of VDAC1 and Cyb5R3 in the NADH-dependent activation of various redox cyclers in mitochondria. We show that external NADH oxidoreductase caused the redox cycling of menadione ≫ lucigenin>nitrofurantoin. Paraquat was predominantly activated by internal mitochondria oxidoreductases. An increase in the ionic strength stimulated and suppressed the redox cycling of negatively and positively charged acceptors, as was expected for the Cyb5R3-mediated reduction. Antibodies against Cyb5R3 but not VDAC substantially inhibited the NADH-related oxidoreductase activities. The specific VDAC blockers G3139 and erastin, separately or in combination, in concentrations sufficient for the inhibition of substrate transport, exhibited minimal effects on the redox cycler-dependent NADH oxidation, ROS generation, and reduction of exogenous cytochrome c. In contrast, Cyb5R3 inhibitors (6-propyl-2-thiouracil, p-chloromercuriobenzoate, quercetin, mersalyl, and ebselen) showed similar patterns of inhibition of ROS generation and cytochrome c reduction. The analysis of the spectra of the endogenous cytochromes b5 and c in the presence of nitrofurantoin and the inhibitors of VDAC and Cyb5R3 demonstrated that the redox cycler can transfer electrons from Cyb5R3 to endogenous cytochrome c. This caused the oxidation of outer membrane-bound cytochrome b5, which is in redox balance with Cyb5R3. The data obtained argue against VDAC1 and in favor of Cyb5R3 involvement in the activation of redox cyclers in the outer mitochondrial membrane.
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Affiliation(s)
- Anna B Nikiforova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Nils-Erik L Saris
- Department of Food and Environmental Sciences, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Alexey G Kruglov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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68
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Weiser BP, Salari R, Eckenhoff RG, Brannigan G. Computational investigation of cholesterol binding sites on mitochondrial VDAC. J Phys Chem B 2014; 118:9852-60. [PMID: 25080204 PMCID: PMC4141696 DOI: 10.1021/jp504516a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
mitochondrial voltage-dependent anion channel (VDAC) allows
passage of ions and metabolites across the mitochondrial outer membrane.
Cholesterol binds mammalian VDAC, and we investigated the effects
of binding to human VDAC1 with atomistic molecular dynamics simulations
that totaled 1.4 μs. We docked cholesterol to specific sites
on VDAC that were previously identified with NMR, and we tested the
reliability of multiple docking results in each site with simulations.
The most favorable binding modes were used to build a VDAC model with
cholesterol occupying five unique sites, and during multiple 100 ns
simulations, cholesterol stably and reproducibly remained bound to
the protein. For comparison, VDAC was simulated in systems with identical
components but with cholesterol initially unbound. The dynamics of
loops that connect adjacent β-strands were most affected by
bound cholesterol, with the averaged root-mean-square fluctuation
(RMSF) of multiple residues altered by 20–30%. Cholesterol
binding also stabilized charged residues inside the channel and localized
the surrounding electrostatic potentials. Despite this, ion diffusion
through the channel was not significantly affected by bound cholesterol,
as evidenced by multi-ion potential of mean force measurements. Although
we observed modest effects of cholesterol on the open channel, our
model will be particularly useful in experiments that investigate
how cholesterol affects VDAC function under applied electrochemical
forces and also how other ligands and proteins interact with the channel.
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Affiliation(s)
- Brian P Weiser
- Department of Anesthesiology and Critical Care and ‡Department of Pharmacology, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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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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70
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Tan J, Rouse SL, Li D, Pye VE, Vogeley L, Brinth AR, El Arnaout T, Whitney JC, Howell PL, Sansom MSP, Caffrey M. A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2054-68. [PMID: 25084326 PMCID: PMC4118822 DOI: 10.1107/s1399004714001850] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/26/2014] [Indexed: 11/11/2022]
Abstract
The exopolysaccharide alginate is an important component of biofilms produced by Pseudomonas aeruginosa, a major pathogen that contributes to the demise of cystic fibrosis patients. Alginate exits the cell via the outer membrane porin AlgE. X-ray structures of several AlgE crystal forms are reported here. Whilst all share a common β-barrel constitution, they differ in the degree to which loops L2 and T8 are ordered. L2 and T8 have been identified as an extracellular gate (E-gate) and a periplasmic gate (P-gate), respectively, that reside on either side of an alginate-selectivity pore located midway through AlgE. Passage of alginate across the membrane is proposed to be regulated by the sequential opening and closing of the two gates. In one crystal form, the selectivity pore contains a bound citrate. Because citrate mimics the uronate monomers of alginate, its location is taken to highlight a route through AlgE taken by alginate as it crosses the pore. Docking and molecular-dynamics simulations support and extend the proposed transport mechanism. Specifically, the P-gate and E-gate are flexible and move between open and closed states. Citrate can leave the selectivity pore bidirectionally. Alginate docks stably in a linear conformation through the open pore. To translate across the pore, a force is required that presumably is provided by the alginate-synthesis machinery. Accessing the open pore is facilitated by complex formation between AlgE and the periplasmic protein AlgK. Alginate can thread through a continuous pore in the complex, suggesting that AlgK pre-orients newly synthesized exopolysaccharide for delivery to AlgE.
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Affiliation(s)
- Jingquan Tan
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Sarah L. Rouse
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Dianfan Li
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Valerie E. Pye
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Lutz Vogeley
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Alette R. Brinth
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Toufic El Arnaout
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - John C. Whitney
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, England
| | - Martin Caffrey
- Schools of Medicine and Biochemistry and Immunology, Trinity College, Dublin, Ireland
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71
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Zeng F, Wu X, Qiu B, Wu F, Jiang L, Zhang G. Physiological and proteomic alterations in rice (Oryza sativa L.) seedlings under hexavalent chromium stress. PLANTA 2014; 240:291-308. [PMID: 24819712 DOI: 10.1007/s00425-014-2077-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 04/13/2014] [Indexed: 06/03/2023]
Abstract
Rice plants employ two strategies to cope with Cr toxicity: immobilizing Cr ions into cell walls to reduce its translocation and activating antioxidant defense to mitigate Cr-induced oxidative stress. The investigation aimed at understanding the physiological and proteomic responses of rice seedlings to hexavalent chromium (Cr(6+)) stress was conducted using two rice genotypes, which differ in Cr tolerance and accumulation. Cr toxicity (200 µM) heavily increased the accumulation of H2O2 and [Formula: see text], enhanced lipid peroxidation, decreased cell viability and consequently inhibited rice plant growth. Proteomic analyses suggest that the response of rice proteome to Cr stress is genotype- and Cr dosage-dependent and tissue specific. Sixty-four proteins, which show more than fourfold difference under either two Cr levels, have been successfully identified. They are involved in a range of cellular processes, including cell wall synthesis, energy production, primary metabolism, electron transport and detoxification. Two proteins related to cell wall structure, NAD-dependent epimerase/dehydratase and reversibly glycosylated polypeptide were greatly up-regulated by Cr stress. Their enhancements coupled with callose accumulation by Cr suggest that cell wall is an important barrier for rice plants to resist Cr stress. Some enzymes involved in antioxidant defense, such as ferredoxin-NADP reductase, NADP-isocitrate dehydrogenase, glyoxalase I (Gly I) and glutamine synthetase 1 (GS1) have also been identified in response to Cr stress. However, they were only detected in Cr-tolerant genotype, indicating the genotypic difference in the capacity of activating the defense system to fight against Cr-induced oxidative stress. Overall, two strategies in coping with Cr stress in rice plants can be hypothesized: (i) immobilizing Cr ions into cell walls to reduce its translocation and (ii) activating antioxidant defense to mitigate Cr-induced oxidative stress.
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Affiliation(s)
- Fanrong Zeng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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72
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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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73
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Lackey SWK, Taylor RD, Go NE, Wong A, Sherman EL, Nargang FE. Evidence supporting the 19 β-strand model for Tom40 from cysteine scanning and protease site accessibility studies. J Biol Chem 2014; 289:21640-50. [PMID: 24947507 DOI: 10.1074/jbc.m114.578765] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Most proteins found in mitochondria are translated in the cytosol and enter the organelle via the TOM complex (translocase of the outer mitochondrial membrane). Tom40 is the pore forming component of the complex. Although the three-dimensional structure of Tom40 has not been determined, the structure of porin, a related protein, has been shown to be a β-barrel containing 19 membrane spanning β-strands and an N-terminal α-helical region. The evolutionary relationship between the two proteins has allowed modeling of Tom40 into a similar structure by several laboratories. However, it has been suggested that the 19-strand porin structure does not represent the native form of the protein. If true, modeling of Tom40 based on the porin structure would also be invalid. We have used substituted cysteine accessibility mapping to identify several potential β-strands in the Tom40 protein in isolated mitochondria. These data, together with protease accessibility studies, support the 19 β-strand model for Tom40 with the C-terminal end of the protein localized to the intermembrane space.
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Affiliation(s)
- Sebastian W K Lackey
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Rebecca D Taylor
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Nancy E Go
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Annie Wong
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - E Laura Sherman
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Frank E Nargang
- From the Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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74
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Cysteine residues impact the stability and micelle interaction dynamics of the human mitochondrial β-barrel anion channel hVDAC-2. PLoS One 2014; 9:e92183. [PMID: 24642864 PMCID: PMC3967697 DOI: 10.1371/journal.pone.0092183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/20/2014] [Indexed: 01/06/2023] Open
Abstract
The anti-apoptotic 19-stranded transmembrane human voltage dependent anion channel isoform 2 (hVDAC-2) β-barrel stability is crucial for anion transport in mitochondria. The role of the unusually high number of cysteine residues in this isoform is poorly understood. Using a Cys-less construct of hVDAC-2, we haveinvestigated the contribution of cysteines to channel function, barrel stability and its influence on the strength of protein-micelle interactions. We observe that despite the overall preservation in barrel structure upon cysteine mutation, subtle local variations in the mode of interaction of the barrel with its refolded micellar environment arise, which may manifest itself in the channel activity of both the proteins.Fluorescence measurements of the Trp residues in hVDAC-2 point to possible differences in the association of the barrel with lauryldimethylamine oxide (LDAO) micelles. Upon replacement of cysteines in hVDAC-2, our data suggests greater barrel rigidity by way of intra-protein interactions. This, in turn, lowers the equilibrium barrel thermodynamic parameters in LDAOby perturbingthe stability of the protein-micelle complex. In addition to this, we also find a difference in the cooperativity of unfolding upon increasing the LDAO concentration, implying the importance of micelle concentration and micelle-protein ratios on the stability of this barrel. Our results indicate that the nine cysteine residues of hVDAC-2 are the key in establishing strong(er) barrel interactions with its environment and also impart additional malleability to the barrel scaffold.
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Kozuch J, Weichbrodt C, Millo D, Giller K, Becker S, Hildebrandt P, Steinem C. Voltage-dependent structural changes of the membrane-bound anion channel hVDAC1 probed by SEIRA and electrochemical impedance spectroscopy. Phys Chem Chem Phys 2014; 16:9546-55. [DOI: 10.1039/c4cp00167b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SEIRA spectroscopy provides insight into the potential-induced structural changes of the anion channel hVDAC1 embedded in the tethered bilayer lipid membrane.
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Affiliation(s)
- Jacek Kozuch
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin, Germany
| | - Conrad Weichbrodt
- Georg-August-Universität Göttingen
- Institut für Organische und Biomolekulare Chemie
- 37077 Göttingen, Germany
| | - Diego Millo
- Vrije Universiteit Amsterdam
- Biomolecular Spectroscopy/LaserLaB Amsterdam
- 1081 HV Amsterdam, The Netherlands
| | - Karin Giller
- Max-Planck Institut für Biophysikalische Chemie
- D-37077 Göttingen, Germany
| | - Stefan Becker
- Max-Planck Institut für Biophysikalische Chemie
- D-37077 Göttingen, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin
- Institut für Chemie
- D-10623 Berlin, Germany
| | - Claudia Steinem
- Georg-August-Universität Göttingen
- Institut für Organische und Biomolekulare Chemie
- 37077 Göttingen, Germany
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76
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Tomasello MF, Guarino F, Reina S, Messina A, De Pinto V. The voltage-dependent anion selective channel 1 (VDAC1) topography in the mitochondrial outer membrane as detected in intact cell. PLoS One 2013; 8:e81522. [PMID: 24324700 PMCID: PMC3855671 DOI: 10.1371/journal.pone.0081522] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022] Open
Abstract
Voltage-Dependent Anion selective Channel maintains the permeability of the outer mitochondrial membrane and is relevant in bioenergetic metabolism and apoptosis. The structure of the protein was shown to be a β-barrel formed by 19 strands. The topology or sideness of the pore has been predicted with various approaches but a general consensus was never reached. This is an important issue since VDAC is considered receptor of Hexokinase and Bcl-2. We fused at VDAC1 C-terminus two tags separated by a caspase cleavage site. Activation in cellulo of caspases was used to eventually separate the two reporters. This experiment did not require the isolation of mitochondria and limited the possibility of outer membrane rupture due to similar procedures. Our results show that the C-terminus end of VDAC faces the mitochondrial inter-membrane space.
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Affiliation(s)
- Marianna F. Tomasello
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, and National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy
| | - Francesca Guarino
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, and National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy
| | - Simona Reina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, and National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy
| | - Angela Messina
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, and National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, and National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy
- * E-mail:
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77
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Maurya SR, Mahalakshmi R. Modulation of human mitochondrial voltage-dependent anion channel 2 (hVDAC-2) structural stability by cysteine-assisted barrel-lipid interactions. J Biol Chem 2013; 288:25584-25592. [PMID: 23873934 DOI: 10.1074/jbc.m113.493692] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human mitochondrial voltage-dependent anion channel 2 (hVDAC-2), the most predominant isoform seen in brain mitochondria, is not only crucial for cell survival but is also implicated in Alzheimer disease. The abundance of cysteines in this isoform is particularly fascinating, as hVDAC-1 cysteines have no associated functional role. We report a detailed biophysical examination of a Cys-less mutant of hVDAC-2, and its behavioral comparison with the wild type protein. Our findings suggest that cysteine mutation results in the formation of a better barrel at the expense of weakened protein-lipid interactions. The wild type protein displays stronger lipid association, despite being less structured. A reversal in behavior of both proteins is observed in the case of chemical denaturation, with the Cys-less mutant exhibiting lowered unfolding free energies. In bicellar systems comprising 14-C phosphocholines, we observe that protein-lipid interactions are weakened in both constructs, resulting in barrel structure destabilization. Our biochemical and biophysical studies together reveal key structural roles for the cysteine residues. We find that minor conformational variations in local residues are sufficient to define the membrane protein dynamics in hVDAC-2. Such subtle sequence variations contribute to differential stability of VDACs and may have implications in their in vivo regulation and recycling.
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Affiliation(s)
- Svetlana Rajkumar Maurya
- From the Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- From the Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India.
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78
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Nuclear localization of the mitochondrial factor HIGD1A during metabolic stress. PLoS One 2013; 8:e62758. [PMID: 23646141 PMCID: PMC3639984 DOI: 10.1371/journal.pone.0062758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 03/25/2013] [Indexed: 12/14/2022] Open
Abstract
Cellular stress responses are frequently governed by the subcellular localization of critical effector proteins. Apoptosis-inducing Factor (AIF) or Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH), for example, can translocate from mitochondria to the nucleus, where they modulate apoptotic death pathways. Hypoxia-inducible gene domain 1A (HIGD1A) is a mitochondrial protein regulated by Hypoxia-inducible Factor-1α (HIF1α). Here we show that while HIGD1A resides in mitochondria during physiological hypoxia, severe metabolic stress, such as glucose starvation coupled with hypoxia, in addition to DNA damage induced by etoposide, triggers its nuclear accumulation. We show that nuclear localization of HIGD1A overlaps with that of AIF, and is dependent on the presence of BAX and BAK. Furthermore, we show that AIF and HIGD1A physically interact. Additionally, we demonstrate that nuclear HIGD1A is a potential marker of metabolic stress in vivo, frequently observed in diverse pathological states such as myocardial infarction, hypoxic-ischemic encephalopathy (HIE), and different types of cancer. In summary, we demonstrate a novel nuclear localization of HIGD1A that is commonly observed in human disease processes in vivo.
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79
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Thinnes FP. New findings concerning vertebrate porin II--on the relevance of glycine motifs of type-1 VDAC. Mol Genet Metab 2013; 108:212-24. [PMID: 23419876 DOI: 10.1016/j.ymgme.2013.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/15/2013] [Accepted: 01/16/2013] [Indexed: 10/27/2022]
Abstract
New findings concerning vertebrate porin part I was published in 1997, then summarizing early data and reflections regarding the molecular structure of vertebrate voltage-dependent anion-selective channels, VDAC/eukaryotic porin, and the extra-mitochondrial expression pattern of human type-1 VDAC. Meanwhile, endeavors of different laboratories confirmed and widened this beginning by encircling the function of the channels. Regarding the function of mitochondrial outer membrane-standing VDACs the channels are established parts of the intrinsic apoptotic pathway and thus therapeutic targets in studies on several diseases: cancer, Alzheimer's disease, Down Syndrome, Parkinson's disease, Amyotrophic Lateral Sclerosis, cystic fibrosis and malaria. Regarding cell membrane-integrated type-1 VDAC it has been documented by different approaches that this porin channel is engaged in cell volume regulation, trans-membrane electron transport and apoptosis. Furthermore, new data insinuate a bridging of extrinsic and intrinsic apoptotic pathways, putatively gaining relevance in Alzheimer research. Mammalian type-1 VDAC, a β-barrel, is basically built up by nineteen β-sheets connected by peptide stretches of varying lengths. The molecule also comprises an N-terminal stretch of some twenty amino acids which, according to biochemical data, traverses the channel lumen towards the cytosolic surface of outer mitochondrial membranes or the plasma lemma, respectively and works as voltage sensor in channel gating. In artificial lipid bilayers VDACs figure as anion or cation-channels, as VDACs are permeable to both cations and anions, with voltage shifts changing the relative permeability. Type-1 VDAC carries several motifs where glycine residues are in critical positions. Motifs of this type, on the on hand, are established nucleotide binding sites. On the other hand, the GxxxG motifs are also discussed as relevant peptide dimerization/aggregation/membrane perturbation motifs. Finally, GxxxG motifs bind cholesterol. Type-1 VDAC shows one such GxxxG motif at the proximal end of its N-terminal voltage sensor while amyloid Aβ peptides include three of them in series. Noteworthy, two additional may be modified versions, GxxxGxG and GxxGxxxG, are found on β-sheet 19 or 9, respectively. Recent data have allowed speculating that amyloid Aβ induces apoptosis via opening type-1 VDAC in cell membranes of hypo-metabolic neurons, a process most likely running over life time--as leaves fall from trees in the tropics--and ending in Alzheimer's disease whenever critical brain regions are affected. The expression of GxxxG motifs on either reactant under consideration is in line with this model of Alzheimer's disease pathogenesis, which clearly differs from the amyloid Aβ cascade theory, and which can, furthermore, be understood as a basic model for apoptosis induction. However, to assume randomly distributed interactions of body wide found amyloid Aβ peptides with the N-terminal voltage sensors of ubiquitously expressed cell membrane-standing human type-1 VDAC opens up a new view on Alzheimer's disease, which might even include a clue on systemic aspects of the disease. While elaborating this concept, my focus was at first only on the GxxxG motif at the proximal end of the N-terminal voltage sensor of type-1 VDAC. Here, I include a corresponding sequence stretch on the channel's β-sheet 19, too.
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80
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Deletion of β-strands 9 and 10 converts VDAC1 voltage-dependence in an asymmetrical process. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:793-805. [PMID: 23541892 DOI: 10.1016/j.bbabio.2013.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/06/2013] [Accepted: 03/18/2013] [Indexed: 11/21/2022]
Abstract
Voltage-dependent anion selective channel isoform1 maintains the permeability of the outer mitochondrial membrane. Its voltage-gating properties are relevant in bioenergetic metabolism and apoptosis. The N-terminal domain is suspected to be involved in voltage-gating, due to its peculiar localization. However this issue is still controversial. In this work we exchanged or deleted the β-strands that take contact with the N-terminal domain. The exchange of the whole hVDAC1 β-barrel with the homologous hVDAC3 β-barrel produces a chimeric protein that, in reconstituted systems, loses completely voltage-dependence. hVDAC3 β-barrel has most residues in common with hVDAC1, including V143 and L150 considered anchor points for the N-terminus. hVDAC1 mutants completely lacking either the β-strand 9 or both β-strands 9 and 10 were expressed, refolded and reconstituted in artificial bilayers. The mutants formed smaller pores. Molecular dynamics simulations of the mutant structure supported its ability to form smaller pores. The mutant lacking both β-strands 9 and 10 showed a new voltage-dependence feature resulting in a fully asymmetric behavior. These data indicate that a network of β-strands in the pore-walls, and not single residues, are required for voltage-gating in addition to the N-terminus.
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81
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Abstract
The outer membrane of Gram-negative bacteria contains a large number of channel-forming proteins, porins, for the uptake of small nutrient molecules. Neisseria gonorrhoeae PorBIA (PorB of serotype A) are associated with disseminating diseases and mediate a rapid bacterial invasion into host cells in a phosphate-sensitive manner. To gain insights into this structure-function relationship we analysed PorBIA by X-ray crystallography in the presence of phosphate and ATP. The structure of PorBIA in the complex solved at a resolution of 3.3 Å (1 Å=0.1 nm) displays a surplus of positive charges inside the channel. ATP ligand-binding in the channel is co-ordinated by the positively charged residues of the channel interior. These residues ligate the aromatic, sugar and pyrophosphate moieties of the ligand. Two phosphate ions were observed in the structure, one of which clamped by two arginine residues (Arg92 and Arg124) localized at the extraplasmic channel exit. A short β-bulge in β2-strand together with the long L3 loop narrow the barrel diameter significantly and further support substrate specificity through hydrogen bond interactions. Interestingly the structure also comprised a small peptide as a remnant of a periplasmic protein which physically links porin molecules to the peptidoglycan network. To test the importance of Arg92 on bacterial invasion the residue was mutated. In vivo assays of bacteria carrying a R92S mutation confirmed the importance of this residue for host-cell invasion. Furthermore systematic sequence and structure comparisons of PorBIA from Neisseriaceae indicated Arg92 to be unique in disseminating N. gonorrhoeae thereby possibly distinguishing invasion-promoting porins from other neisserial porins.
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82
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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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83
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Vinothkumar KR, Edwards PC, Standfuss J. Practical aspects in expression and purification of membrane proteins for structural analysis. Methods Mol Biol 2013; 955:17-30. [PMID: 23132053 DOI: 10.1007/978-1-62703-176-9_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A surge of membrane protein structures in the last few years can be attributed to advances in technologies starting at the level of genomes, to highly efficient expression systems, stabilizing conformational flexibility, automation of crystallization and data collection for screening large numbers of crystals and the microfocus beam lines at synchrotrons. The substantial medical importance of many membrane proteins provides a strong incentive to understand them at the molecular level. It is becoming obvious that the major bottleneck in many of the membrane projects is obtaining sufficient amount of stable functional proteins in a detergent micelle for structural studies. Naturally, large effort has been spent on optimizing and advancing multiple expression systems and purification strategies that have started to yield sufficient protein and structures. We describe in this chapter protocols to refold membrane proteins from inclusion bodies, purification from inner membranes of Escherichia coli and from mammalian cell lines.
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84
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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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85
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Rey M, Forest E, Pelosi L. Exploring the conformational dynamics of the bovine ADP/ATP carrier in mitochondria. Biochemistry 2012; 51:9727-35. [PMID: 23136955 DOI: 10.1021/bi300759x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mitochondrial ADP/ATP carrier catalyzes the transport of ADP and ATP across the mitochondrial inner membrane by switching between two different conformations. They can be blocked by two inhibitors: carboxyatractyloside (CATR) and bongkrekic acid (BA). Our understanding of the ADP/ATP transport process is largely based on analysis of structural differences between the individual inhibited states. The X-ray crystallographic three-dimensional structure of bovine ADP/ATP carrier isoform 1 (bAnc1p) complexed with CATR was determined, but the structure of the BA-carrier complex remains unknown. We recently investigated the conformational dynamics of bAnc1p in detergent solution using hydrogen/deuterium exchange and mass spectrometry (HDX-MS). This study shed light on some features of ADP/ATP translocation, but the mechanism itself and the organization of bAnc1p in the membrane required further investigation. This paper describes the first study of bAnc1p in the mitochondria on the whole-protein scale using HDX-MS. Membrane-embedded bAnc1p was deuterated and purified under HDX-MS-compatible conditions. Our results for the carrier in the mitochondrial inner membrane differed from those published for the carrier in a detergent solution. These differences were mainly in the upper half of the cavity that globally showed a limited H/D exchange whatever the complex analyzed and at the level of the matrix loops that were less accessible to the solvent in the BA-carrier complex than in the CATR-carrier complex. They are discussed with respect to published data for bAnc1p and have provided new insights into the conformation of the matrix loops of the bovine carrier in complex with BA in mitochondria.
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Affiliation(s)
- Martial Rey
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Direction des Sciences du Vivant (DSV), Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Laboratoire de Biologie à Grande Echelle (BGE), Grenoble F-38054, France
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86
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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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87
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Affiliation(s)
- Marco Colombini
- Department of Biology,
University of Maryland, College
Park, Maryland 20742, United States
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88
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Zachariae U, Schneider R, Briones R, Gattin Z, Demers JP, Giller K, Maier E, Zweckstetter M, Griesinger C, Becker S, Benz R, de Groot BL, Lange A. β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure 2012; 20:1540-9. [PMID: 22841291 PMCID: PMC5650048 DOI: 10.1016/j.str.2012.06.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 05/30/2012] [Accepted: 06/04/2012] [Indexed: 11/27/2022]
Abstract
The voltage-dependent anion channel (VDAC) is the major protein in the outer mitochondrial membrane, where it mediates transport of ATP and ADP. Changes in its permeability, induced by voltage or apoptosis-related proteins, have been implicated in apoptotic pathways. The three-dimensional structure of VDAC has recently been determined as a 19-stranded β-barrel with an in-lying N-terminal helix. However, its gating mechanism is still unclear. Using solid-state NMR spectroscopy, molecular dynamics simulations, and electrophysiology, we show that deletion of the rigid N-terminal helix sharply increases overall motion in VDAC's β-barrel, resulting in elliptic, semicollapsed barrel shapes. These states quantitatively reproduce conductance and selectivity of the closed VDAC conformation. Mutation of the N-terminal helix leads to a phenotype intermediate to the open and closed states. These data suggest that the N-terminal helix controls entry into elliptic β-barrel states which underlie VDAC closure. Our results also indicate that β-barrel channels are intrinsically flexible.
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Affiliation(s)
- Ulrich Zachariae
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- SUPA, School of Physics and Astronomy, The University of Edinburgh, King's Buildings, Edinburgh EH9 3JZ, UK
| | - Robert Schneider
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
- Protein Dynamics and Flexibility by NMR, Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, France
| | - Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Zrinka Gattin
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jean-Philippe Demers
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Karin Giller
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Elke Maier
- Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
| | - Markus Zweckstetter
- 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
| | - Roland Benz
- Rudolf Virchow Center, DFG Research Center for Experimental Biomedicine, University of Würzburg, Versbacher Str. 9, 97078 Würzburg, Germany
- School of Engineering and Science, Jacobs University Bremen, Campusring 1, 28759 Bremen, Germany
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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89
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Rostovtseva TK, Bezrukov SM. VDAC inhibition by tubulin and its physiological implications. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:1526-35. [PMID: 22100746 PMCID: PMC3302949 DOI: 10.1016/j.bbamem.2011.11.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/24/2011] [Accepted: 11/02/2011] [Indexed: 11/23/2022]
Abstract
Regulation of mitochondrial outer membrane (MOM) permeability has dual importance: in normal metabolite and energy exchange between mitochondria and cytoplasm, and thus in control of respiration, and in apoptosis by release of apoptogenic factors into the cytosol. However, the mechanism of this regulation involving the voltage-dependent anion channel (VDAC), the major channel of MOM, remains controversial. For example, one of the long-standing puzzles was that in permeabilized cells, adenine nucleotide translocase is less accessible to cytosolic ADP than in isolated mitochondria. Still another puzzle was that, according to channel-reconstitution experiments, voltage regulation of VDAC is limited to potentials exceeding 30mV, which are believed to be much too high for MOM. We have solved these puzzles and uncovered multiple new functional links by identifying a missing player in the regulation of VDAC and, hence, MOM permeability - the cytoskeletal protein tubulin. We have shown that, depending on VDAC phosphorylation state and applied voltage, nanomolar to micromolar concentrations of dimeric tubulin induce functionally important reversible blockage of VDAC reconstituted into planar phospholipid membranes. The voltage sensitivity of the blockage equilibrium is truly remarkable. It is described by an effective "gating charge" of more than ten elementary charges, thus making the blockage reaction as responsive to the applied voltage as the most voltage-sensitive channels of electrophysiology are. Analysis of the tubulin-blocked state demonstrated that although this state is still able to conduct small ions, it is impermeable to ATP and other multi-charged anions because of the reduced aperture and inversed selectivity. The findings, obtained in a channel reconstitution assay, were supported by experiments with isolated mitochondria and human hepatoma cells. Taken together, these results suggest a previously unknown mechanism of regulation of mitochondrial energetics, governed by VDAC interaction with tubulin at the mitochondria-cytosol interface. Immediate physiological implications include new insights into serine/threonine kinase signaling pathways, Ca(2+) homeostasis, and cytoskeleton/microtubule activity in health and disease, especially in the case of the highly dynamic microtubule network which is characteristic of cancerogenesis and cell proliferation. In the present review, we speculate how these findings may help to identify new mechanisms of mitochondria-associated action of chemotherapeutic microtubule-targeting drugs, and also to understand why and how cancer cells preferentially use inefficient glycolysis rather than oxidative phosphorylation (Warburg effect). This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Tatiana K Rostovtseva
- Laboratory of Physical and Structural Biology, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Bethesda, MD 20892, USA.
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90
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Protein profiling of keloidal scar tissue. Arch Dermatol Res 2012; 304:533-40. [DOI: 10.1007/s00403-012-1224-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 01/09/2023]
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91
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Brahimi-Horn MC, Ben-Hail D, Ilie M, Gounon P, Rouleau M, Hofman V, Doyen J, Mari B, Shoshan-Barmatz V, Hofman P, Pouysségur J, Mazure NM. Expression of a truncated active form of VDAC1 in lung cancer associates with hypoxic cell survival and correlates with progression to chemotherapy resistance. Cancer Res 2012; 72:2140-50. [PMID: 22389449 DOI: 10.1158/0008-5472.can-11-3940] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Resistance to chemotherapy-induced apoptosis of tumor cells represents a major hurdle to efficient cancer therapy. Although resistance is a characteristic of tumor cells that evolve in a low oxygen environment (hypoxia), the mechanisms involved remain elusive. We observed that mitochondria of certain hypoxic cells take on an enlarged appearance with reorganized cristae. In these cells, we found that a major mitochondrial protein regulating metabolism and apoptosis, the voltage-dependent anion channel 1 (VDAC1), was linked to chemoresistance when in a truncated (VDAC1-ΔC) but active form. The formation of truncated VDAC1, which had a similar channel activity and voltage dependency as full-length, was hypoxia-inducible factor-1 (HIF-1)-dependent and could be inhibited in the presence of the tetracycline antibiotics doxycycline and minocycline, known inhibitors of metalloproteases. Its formation was also reversible upon cell reoxygenation and associated with cell survival through binding to the antiapoptotic protein hexokinase. Hypoxic cells containing VDAC1-ΔC were less sensitive to staurosporine- and etoposide-induced cell death, and silencing of VDAC1-ΔC or treatment with the tetracycline antibiotics restored sensitivity. Clinically, VDAC1-ΔC was detected in tumor tissues of patients with lung adenocarcinomas and was found more frequently in large and late-stage tumors. Together, our findings show that via induction of VDAC1-ΔC, HIF-1 confers selective protection from apoptosis that allows maintenance of ATP and cell survival in hypoxia. VDAC1-ΔC may also hold promise as a biomarker for tumor progression in chemotherapy-resistant patients.
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Affiliation(s)
- M Christiane Brahimi-Horn
- Institute of Developmental Biology and Cancer Research, University of Nice, CNRS-UMR 6543, Centre Antoine Lacassagne, Nice, France
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92
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Colombini M. VDAC structure, selectivity, and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:1457-65. [PMID: 22240010 DOI: 10.1016/j.bbamem.2011.12.026] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 12/02/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
VDAC channels exist in the mitochondrial outer membrane of all eukaryotic organisms. Of the different isoforms present in one organism, it seems that one of these is the canonical VDAC whose properties and 3D structure are highly conserved. The fundamental role of these channels is to control the flux of metabolites between the cytosol and mitochondrial spaces. Based on many functional studies, the fundamental structure of the pore wall consists of one α helix and 13 β strands tilted at a 46° angle. This results in a pore with an estimated internal diameter of 2.5nm. This structure has not yet been resolved. The published 3D structure consists of 19 β strands and is different from the functional structure that forms voltage-gated channels. The selectivity of the channel is exquisite, being able to select for ATP over molecules of the same size and charge. Voltage gating involves two separate gating processes. The mechanism involves the translocation of a positively charged portion of the wall of the channel to the membrane surface resulting in a reduction in pore diameter and volume and an inversion in ion selectivity. This mechanism is consistent with experiments probing changes in selectivity, voltage gating, kinetics and energetics. Other published mechanisms are in conflict with experimental results. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Marco Colombini
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
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93
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Bay DC, Hafez M, Young MJ, Court DA. Phylogenetic and coevolutionary analysis of the β-barrel protein family comprised of mitochondrial porin (VDAC) and Tom40. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1502-19. [PMID: 22178864 DOI: 10.1016/j.bbamem.2011.11.027] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 11/14/2011] [Accepted: 11/22/2011] [Indexed: 12/21/2022]
Abstract
Beta-barrel proteins are the main transit points across the mitochondrial outer membrane. Mitochondrial porin, the voltage-dependent, anion-selective channel (VDAC), is responsible for the passage of small molecules between the mitochondrion and the cytosol. Through interactions with other mitochondrial and cellular proteins, it is involved in regulating organellar and cellular metabolism and likely contributes to mitochondrial structure. Tom40 is part of the translocase of the outer membrane, and acts as the channel for passage of preproteins during their import into the organelle. These proteins appear to share a common evolutionary origin and structure. In the current study, the evolutionary relationships between and within both proteins were investigated through phylogenetic analysis. The two groups have a common origin and have followed independent, complex evolutionary pathways, leading to the generation of paralogues in animals and plants. Structures of diverse representatives were modeled, revealing common themes rather than sites of high identity in both groups. Within each group, intramolecular coevolution was assessed, revealing a new set of sites potentially involved in structure-function relationships in these molecules. A weak link between Tom40 and proteins related to the mitochondrial distribution and morphology protein, Mdm10, was identified. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Denice C Bay
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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94
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Homblé F, Krammer EM, Prévost M. Plant VDAC: facts and speculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1486-501. [PMID: 22155681 DOI: 10.1016/j.bbamem.2011.11.028] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/12/2011] [Accepted: 11/22/2011] [Indexed: 01/01/2023]
Abstract
The voltage-dependent anion-selective channel (VDAC) is the most abundant protein in the mitochondrial outer membrane and the major transport pathway for a large variety of compounds ranging from ions to large polymeric molecules such as DNA and tRNA. Plant VDACs feature a secondary structure content and electrophysiological properties akin to those of VDACs from other organisms. They however undergo a specific regulation. The general importance of VDAC in plant physiology has only recently emerged. Besides their role in metabolite transport, plant VDACs are also involved in the programmed cell death triggered in response to biotic and abiotic stresses. Moreover, their colocalization in non-mitochondrial membranes suggests a diversity of function. This review summarizes our current understanding of the structure and function of plant VDACs. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Fabrice Homblé
- Structure et Fontion des Membranes Biologiques, Centre de Biologie Structurale et de Bioinformatique, Université Libre de Bruxelles, Boulevard du Triomphe CP, Brussels, Belgium.
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95
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Krammer EM, Homblé F, Prévost M. Concentration dependent ion selectivity in VDAC: a molecular dynamics simulation study. PLoS One 2011; 6:e27994. [PMID: 22164223 PMCID: PMC3229507 DOI: 10.1371/journal.pone.0027994] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 10/29/2011] [Indexed: 11/19/2022] Open
Abstract
The voltage-dependent anion channel (VDAC) forms the major pore in the outer mitochondrial membrane. Its high conducting open state features a moderate anion selectivity. There is some evidence indicating that the electrophysiological properties of VDAC vary with the salt concentration. Using a theoretical approach the molecular basis for this concentration dependence was investigated. Molecular dynamics simulations and continuum electrostatic calculations performed on the mouse VDAC1 isoform clearly demonstrate that the distribution of fixed charges in the channel creates an electric field, which determines the anion preference of VDAC at low salt concentration. Increasing the salt concentration in the bulk results in a higher concentration of ions in the VDAC wide pore. This event induces a large electrostatic screening of the charged residues promoting a less anion selective channel. Residues that are responsible for the electrostatic pattern of the channel were identified using the molecular dynamics trajectories. Some of these residues are found to be conserved suggesting that ion permeation between different VDAC species occurs through a common mechanism. This inference is buttressed by electrophysiological experiments performed on bean VDAC32 protein akin to mouse VDAC.
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Affiliation(s)
- Eva-Maria Krammer
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabrice Homblé
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
| | - Martine Prévost
- Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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96
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Abstract
We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca(2+) pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.
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Affiliation(s)
- Mei Hong
- Department of Chemistry, Iowa State University, Ames, 50011, USA.
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97
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Yu TY, Raschle T, Hiller S, Wagner G. Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:1562-9. [PMID: 22119777 DOI: 10.1016/j.bbamem.2011.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 10/27/2011] [Accepted: 11/07/2011] [Indexed: 10/24/2022]
Abstract
Three isoforms of the human voltage-dependent anion channel (VDAC), located in the outer mitochondrial membrane, are crucial regulators of mitochondrial function. Numerous studies have been carried out to elucidate biochemical properties, as well as the three-dimensional structure of VDAC-1. However, functional and structural studies of VDAC-2 and VDAC-3 at atomic resolution are still scarce. VDAC-2 is highly similar to VDAC-1 in amino acid sequence, but has substantially different biochemical functions and expression profiles. Here, we report the reconstitution of functional VDAC-2 in lauryldimethylamine-oxide (LDAO) detergent micelles and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer nanodiscs. We find that VDAC-2 is properly folded in both membrane-mimicking systems and that structural and functional characterization by solution NMR spectroscopy is feasible. This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Tsyr-Yan Yu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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98
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Chikando AC, Kettlewell S, Williams GS, Smith G, Lederer WJ. Ca2+ dynamics in the mitochondria - state of the art. J Mol Cell Cardiol 2011; 51:627-31. [PMID: 21864537 PMCID: PMC3814218 DOI: 10.1016/j.yjmcc.2011.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/05/2011] [Accepted: 08/06/2011] [Indexed: 01/24/2023]
Abstract
The importance of [Ca2+] in the mitochondrial matrix, [Ca2+]mito, had been proposed by early work of Carafoli and others [1 ], [2 ] and [3 ]. The key suggestion in the 1970s [4 ] was that regulatory [Ca2+]mito played a role in controlling the rate of activation of tricarboxylic acid cycle dehydrogenases, important in the regulation of ATP production by the electron transport chain (ETC) during oxidative phosphorylation. This view is now established [5 ] and [6 ] and the key questions currently debated are to what extent do the mitochondria acquire and release Ca2+, and what impact do mitochondria have on the dynamic Ca2+ signal in the cardiac ventricular myocyte [7 ]. Although investigations of Ca2+ dynamics in mitochondria have been problematic, disparate and inconclusive, they have also been both provocative and exciting. A recent special issue of this journal presented contrasting perspectives on the speed, extent and mechanisms of changes in [Ca2+]mito, and how these changes may influence cellular spatio-temporal [Ca2+]i dynamics [8 ]. An audio discussion is also available online [9 ]. The uncertain nature of the signaling pathways is noted in Table 1 (see below) which shows mitochondrial proteins and processes that are of current focus and which remain contentious. Each of the “items” listed is largely unsettled, or is a “work in progress”. There may be advocates for opposing positions noted or recent discoveries that must still be tested at multiple levels by diverse laboratories. Currently, the first item, the mitochondrial sodium/calcium exchanger (NCLX) [10 ], appears the most solid with respect to the molecular identification and physiological function, whereas, the recently described candidates of the mitochondrial Ca2+ uniporter (MCU) [11 ] and [12 ] still need to be verified and broadly examined by the scientific community.
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99
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Summers WAT, Wilkins JA, Dwivedi RC, Ezzati P, Court DA. Mitochondrial dysfunction resulting from the absence of mitochondrial porin in Neurospora crassa. Mitochondrion 2011; 12:220-9. [PMID: 21946565 DOI: 10.1016/j.mito.2011.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 09/01/2011] [Accepted: 09/09/2011] [Indexed: 12/20/2022]
Abstract
Porin, the voltage-dependent anion-selective channel (VDAC) in the mitochondrial outer membrane, contributes to metabolism and apoptosis. VDAC function was investigated in Neurospora, an obligate aerobe with a single porin. Porinless strains are viable, with cold-sensitive growth, cytochrome deficiencies and overexpression of alternative oxidase. iTRAQ labeling of mitochondria from a porinless strain and its progenitor revealed a small group of proteins with altered expression levels in the mutant organelles. Porinless Neurospora appears to compensate not by inducing alternative pores, but by altering electron flow and nucleotide metabolism. Transcriptional and post-transcriptional mechanisms contribute to the response, reflecting the extent of porin influence.
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Affiliation(s)
- William A T Summers
- Department of Microbiology, University of Manitoba, 301 Buller Building, Winnipeg, MB, Canada R3T 2N2.
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100
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Lee KI, Rui H, Pastor RW, Im W. Brownian dynamics simulations of ion transport through the VDAC. Biophys J 2011; 100:611-619. [PMID: 21281575 PMCID: PMC3030170 DOI: 10.1016/j.bpj.2010.12.3708] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 12/02/2010] [Accepted: 12/13/2010] [Indexed: 10/18/2022] Open
Abstract
It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.
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Affiliation(s)
- Kyu Il Lee
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Huan Rui
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Wonpil Im
- Center for Bioinformatics, University of Kansas, Lawrence, Kansas; Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas.
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