Skip to main content
SpringerLink
Log in

Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to study the structure of the human VDAC isoform 2 in a lipid bilayer environment. We find that the structure of hVDAC2 is similar to the structure of hVDAC1, in line with recent investigations on zfVDAC2. However, hVDAC2 appears to exhibit an increased conformational heterogeneity compared to hVDAC1 which is reflected in broader solid-state NMR spectra and less defined electrophysiological profiles.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Anflous K, Armstrong DD, Craigen WJ (2001) Altered mitochondrial sensitivity for ADP and maintenance of creatine-stimulated respiration in oxidative striated muscles from VDAC1-deficient mice. J Biol Chem 276:1954–1960. doi:10.1074/jbc.M006587200

    Article  Google Scholar 

  • Bauer AJ, Gieschler S, Lemberg KM et al (2011) Functional model of metabolite gating by human voltage-dependent anion channel 2. Biochemistry 50:3408–3410. doi:10.1021/bi2003247

    Article  Google Scholar 

  • Bayrhuber M, Meins T, Habeck M et al (2008) Structure of the human voltage-dependent anion channel. Proc Natl Acad Sci USA 105:15370–15375. doi:10.1073/pnas.0808115105

    Article  ADS  Google Scholar 

  • Benz R (1994) Permeation of hydrophilic solutes through mitochondrial outer membranes: review on mitochondrial porins. Biochim Biophys Acta 1197:167–196

    Article  Google Scholar 

  • Benz R, Janko K, Boos W, Läuger P (1978) Formation of large, ion-permeable membrane channels by the matrix protein (porin) of Escherichia coli. Biochim Biophys Acta (BBA) 511:305–319

    Article  Google Scholar 

  • Benz R, Schmid A, Hancock R (1985) Ion selectivity of gram-negative bacterial porins. J Bacteriol 162:722–727

    Google Scholar 

  • Berendsen HJC, Postma JPM, van Gunsteren WF et al (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684. doi:10.1063/1.448118

    Article  ADS  Google Scholar 

  • Berger O, Edholm O, Jähnig F (1997) Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys J 72:2002–2013. doi:10.1016/S0006-3495(97)78845-3

    Article  Google Scholar 

  • Blachly-Dyson E, Song J (1997) Multicopy suppressors of phenotypes resulting from the absence of yeast VDAC encode a VDAC-like protein. Mol Cell Biochem 17:5727–5738

    Google Scholar 

  • Blachly-Dyson E, Zambronicz EB, Yu WH et al (1993) Cloning and functional expression in yeast of two human isoforms of the outer mitochondrial membrane channel, the voltage-dependent anion channel. J Biol Chem 268:1835–1841

    Google Scholar 

  • Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126:014101. doi:10.1063/1.2408420

    Article  ADS  Google Scholar 

  • Cheng EHY, Sheiko TV, Fisher JK et al (2003) VDAC2 inhibits BAK activation and mitochondrial apoptosis. Science 301:513–517. doi:10.1126/science.1083995

    Article  ADS  Google Scholar 

  • Choudhary OP, Paz A, Adelman JL et al (2014) Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1. Nat Struct Mol Biol 21:626–632. doi:10.1038/nsmb.2841

    Article  Google Scholar 

  • Colombini M (1980) Pore Size and Properties of Channels from Mitoehondria Isolated from Neurospora crassa. J MembrBiol 53:79–84

    Google Scholar 

  • Colombini M (2004) VDAC: the channel at the interface between mitochondria and the cytosol. Mol Cell Biochem 256–257:107–115

    Article  Google Scholar 

  • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J Chem Phys 98:10089. doi:10.1063/1.464397

    Article  ADS  Google Scholar 

  • Daura X, Gademann K, Jaun B et al (1999) Peptide folding: when simulation meets experiment. Angew Chem Int Ed Engl 38:236–240. doi:10.1002/(SICI)1521-3773(19990115)38:1/2<236:AID-ANIE236>3.0.CO;2-M

    Article  Google Scholar 

  • De Pinto V, Tomasello F, Messina A et al (2007) Determination of the conformation of the human VDAC1 N-terminal peptide, a protein moiety essential for the functional properties of the pore. ChemBioChem 8:744–756. doi:10.1002/cbic.200700009

    Article  Google Scholar 

  • Engelhardt H, Meins T, Poynor M et al (2007) High-level expression, refolding and probing the natural fold of the human voltage-dependent anion channel isoforms I and II. J Membr Biol 216:93–105. doi:10.1007/s00232-007-9038-8

    Article  Google Scholar 

  • Feenstra KA, Hess B, Berendsen HJC (1999) Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J Comput Chem 20:786–798. doi:10.1002/(SICI)1096-987X(199906)20:8<786:AID-JCC5>3.0.CO;2-B

    Article  Google Scholar 

  • Fung BM, Khitrina K, Ermolaev K (2000) An improved broadband decoupling sequence for liquid crystals and solids. J Magn Reson 142:97–101. doi:10.1006/jmre.1999.1896

    Article  ADS  Google Scholar 

  • Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463:AID-JCC4>3.0.CO;2-H

    Article  Google Scholar 

  • Hess B, Uppsala S, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation, pp 435–447

  • Hiller S, Garces RG, Malia TJ et al (2008) Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321:1206–1210. doi:10.1126/science.1161302

    Article  ADS  Google Scholar 

  • Jorgensen W (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225–11236

    Article  Google Scholar 

  • Jorgensen WL, Madura JD (1983) Solvation and conformation of methanol in water. J Am Chem Soc 105:1407–1413

    Article  Google Scholar 

  • Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577–2637. doi:10.1002/bip.360221211

    Article  Google Scholar 

  • Krammer E-M, Homblé F, Prévost M (2011) Concentration dependent ion selectivity in VDAC: a molecular dynamics simulation study. PLoS ONE 6:e27994. doi:10.1371/journal.pone.0027994

    Article  ADS  Google Scholar 

  • Lindén M, Gellerfors P (1983) Hydrodynamic properties of porin isolated from outer membranes of rat liver mitochondria. Biochim Biophys Acta 736:125–129

    Article  Google Scholar 

  • Miyamoto S, Kollman P (1992) Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J Comput Chem 13:952–962. doi:10.1002/jcc.540130805

    Article  Google Scholar 

  • Naghdi S, Varnai P, Hunyady L, Hajnoczky G (2012) The isoform specific N terminus of VDAC2 is dispensable for tBid induced cytochrome C release. Biophys J 102:437a. doi:10.1016/j.bpj.2011.11.2391

    Article  Google Scholar 

  • Popp B, Court DA, Benz R, Neupert W, Lill R (1996) The role of the N and C termini of recombinant Neurospora mitochondrial porin in channel formation and voltage-dependent gating. J Biol Chem 271:13593–13899

    Article  Google Scholar 

  • Reina S, Palermo V, Guarnera A et al (2010) Swapping of the N-terminus of VDAC1 with VDAC3 restores full activity of the channel and confers anti-aging features to the cell. FEBS Lett 584:2837–2844. doi:10.1016/j.febslet.2010.04.066

    Article  Google Scholar 

  • Rostovtseva T, Colombini M (1997) VDAC channels mediate and gate the flow of ATP: implications for the regulation of mitochondrial function. Biophys J 72:1954–1962. doi:10.1016/S0006-3495(97)78841-6

    Article  Google Scholar 

  • Rui H, Lee KI, Pastor RW, Im W (2011) Molecular dynamics studies of ion permeation in VDAC. Biophys J 100:602–610. doi:10.1016/j.bpj.2010.12.3711

    Article  Google Scholar 

  • Runke G, Maier E, Summers W et al (2006) Deletion variants of Neurospora mitochondrial porin: electrophysiological and spectroscopic analysis. Biophys J 90:3155–3164. doi:10.1529/biophysj.105.072520

    Article  Google Scholar 

  • Šali A, Blundell T (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234:779–815

    Article  Google Scholar 

  • Sampson MJ, Lovell RS, Craigen WJ (1996) Isolation, characterization, and mapping of two mouse mitochondrial voltage-dependent anion channel isoforms. Genomics 33:283–288. doi:10.1006/geno.1996.0193

    Article  Google Scholar 

  • Sampson MJ, Lovell RS, Craigen WJ (1997) The Murine voltage-dependent anion channel gene family. J Biol Chem 272:18966–18973

    Article  Google Scholar 

  • Sampson MJ, Decker WK, Beaudet AL et al (2001) Immotile sperm and infertility in mice lacking mitochondrial voltage-dependent anion channel type 3. J Biol Chem 276:39206–39212. doi:10.1074/jbc.M104724200

    Article  Google Scholar 

  • Schein SJ, Colombini M, Finkelstein A (1976) Reconstitution in planar lipid bilayers of a voltage-dependent anion-selective channel obtained from paramecium mitochondria. J Membr Biol 30:99–120

    Article  Google Scholar 

  • Schneider R, Etzkorn M, Giller K et al (2010) The native conformation of the human VDAC1 N terminus. Angew Chem Int Ed Engl 49:1882–1885. doi:10.1002/anie.200906241

    Article  Google Scholar 

  • Schredelseker J, Paz A, López CJ et al (2014) High resolution structure and double electron–electron resonance of the zebrafish voltage-dependent anion channel 2 reveal an oligomeric population. J Biol Chem 289:12566–12577. doi:10.1074/jbc.M113.497438

    Article  Google Scholar 

  • Smack DP, Colombini M (2014) Voltage-dependent channels found in the membrane fraction of corn mitochondria. 1985:1094–1097

  • Sorgato MC, Moran O (1993) Channels in mitochondrial membranes: knowns, unknowns, and prospects for the future. Crit Rev Biochem Mol Biol 28:127–171

    Article  Google Scholar 

  • Teijido O, Rappaport SM, Chamberlin A et al (2014) Acidification affects voltage-dependent anion channel functioning asymmetrically: role of salt bridges. J Biol Chem. doi:10.1074/jbc.M114.576314

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  Google Scholar 

  • Ujwal R, Cascio D, Colletier J-P et al (2008) The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating. Proc Natl Acad Sci USA 105:17742–17747. doi:10.1073/pnas.0809634105

    Article  ADS  Google Scholar 

  • Villinger S, Briones R, Giller K et al (2010) Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci USA 107:22546–22551. doi:10.1073/pnas.1012310108

    Article  ADS  Google Scholar 

  • Villinger S, Giller K, Bayrhuber M (2014) Nucleotide interactions of the human voltage-dependent anion channel. J Biol Chem 289:13397–13406. doi:10.1074/jbc.M113.524173

    Article  Google Scholar 

  • Wang J, Wolf RM, Caldwell JW et al (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174. doi:10.1002/jcc.20035

    Article  Google Scholar 

  • Xu X, Decker W, Sampson M (1999) Mouse VDAC isoforms expressed in yeast: channel properties and their roles in mitochondrial outer membrane permeability. J Membr Biol 170:89–102

    Article  Google Scholar 

  • Yagoda N, von Rechenberg M, Zaganjor E et al (2007) RAS-RAF-MEK-dependent oxidative cell death involving voltage-dependent anion channels. Nature 447:864–868. doi:10.1038/nature05859

    Article  ADS  Google Scholar 

  • Yamagata H, Shimizu S, Nishida Y et al (2009) Requirement of voltage-dependent anion channel 2 for pro-apoptotic activity of Bax. Oncogene 28:3563–3572. doi:10.1038/onc.2009.213

    Article  Google Scholar 

  • Yu T-Y, Raschle T, Hiller S, Wagner G (2012) Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. Biochim Biophys Acta 1818:1562–1569. doi:10.1016/j.bbamem.2011.11.012

    Article  Google Scholar 

  • Zachariae U, Schneider R, Briones R et al (2012) β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure 20:1540–1549. doi:10.1016/j.str.2012.06.015

    Article  Google Scholar 

Download references

Acknowledgments

We thank B. Angerstein for expert technical assistance and R. Briones for help in the initial stages of the project concerning GROMACS. This work was supported by the Max Planck Society, the Leibniz-Institut für Molekulare Pharmakologie, the ERC (grant agreement number 282008 to M.Z.), the DFG (Collaborative research center 803 to A.L., C.G., and M.Z. and Emmy Noether Fellowship to A.L.) and by a Marie Curie fellowship within the 7th EU Framework Program to Z.G.

Author information

Authors and Affiliations

  1. Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany

    Zrinka Gattin, Robert Schneider, Yvonne Laukat, Karin Giller, Markus Zweckstetter, Christian Griesinger, Stefan Becker & Adam Lange

  2. Max Planck Institute for Dynamics and Selforganisation, Am Fassberg 17, 37077, Göttingen, Germany

    Zrinka Gattin

  3. Unité de Glycobiologie Structurale et Fonctionnelle, Université des Sciences et Technologies de Lille, Bât. C9, 59655, Villeneuve d’Ascq, France

    Robert Schneider

  4. Lehrstuhl für Biotechnologie, Theodor-Boveri-Institut (Biozentrum) der Universität Würzburg, Am Hubland, 97074, Würzburg, Germany

    Elke Maier & Roland Benz

  5. Deutsches Zentrum für neurodegenerative Erkrankungen (DZNE), Göttingen, Germany

    Markus Zweckstetter

  6. Center for the Molecular Physiology of the Brain, University Medical Center, 37073, Göttingen, Germany

    Markus Zweckstetter

  7. School of Engineering and Science, Jacobs University Bremen, Campusring 1, 28759, Bremen, Germany

    Roland Benz

  8. Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany

    Adam Lange

  9. Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstr. 110, 10115, Berlin, Germany

    Adam Lange

Authors
  1. Zrinka Gattin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert Schneider
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yvonne Laukat
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Karin Giller
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Elke Maier
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Markus Zweckstetter
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Christian Griesinger
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Roland Benz
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Stefan Becker
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Adam Lange
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Adam Lange.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gattin, Z., Schneider, R., Laukat, Y. et al. Solid-state NMR, electrophysiology and molecular dynamics characterization of human VDAC2. J Biomol NMR 61, 311–320 (2015). https://doi.org/10.1007/s10858-014-9876-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-014-9876-5

Keywords

Search

Navigation