[1] | Colombini M (1980) Structure and mode of action of a voltage dependent anion-selective channel (VDAC) located in the outer mitochondrial membrane. Ann N Y Acad Sci 341: 552–563.
|
[2] | Shoshan-Barmatz V, De Pinto V, Zweckstetter M, Raviv Z, Keinan N, et al. (2010) VDAC, a multi-functional mitochondrial protein regulating cell life and death. Mol Aspects Med 31: 227–285. S0098-2997(10)00021-X [pii];10.1016/j.mam.2010.03.002 [doi].
|
[3] | Young MJ, Bay DC, Hausner G, Court DA (2007) The evolutionary history of mitochondrial porins. BMC Evol Biol 7: 31. 1471-2148-7-31 [pii];10.1186/1471-2148-7-31 [doi].
|
[4] | Wandrey M, Trevaskis B, Brewin N, Udvardi MK (2004) Molecular and cell biology of a family of voltage-dependent anion channel porins in Lotus japonicus. Plant Physiol 134: 182–193.
|
[5] | Tateda C, Watanabe K, Kusano T, Takahashi Y (2011) Molecular and genetic characterization of the gene family encoding the voltage-dependent anion channel in Arabidopsis. J Exp Bot 62: 4773–4783. err113 [pii];10.1093/jxb/err113 [doi].
|
[6] | De Pinto V, Messina A (2004) Gene Family Expression and Multitopological Localization of Eukaryotic Porin/Voltage Dependent Anion-Selective Channel (VDAC): Intracellular Trafficking and Alternative Splicing. Bacterial and Eukaryotic Porins. pp. 309–337. Wiley-VCH Verlag GmbH & Co. KGaA.
|
[7] | Benz R (1994) Permeation of hydrophilic solutes through mitochondrial outer membranes: review on mitochondrial porins. Biochim Biophys Acta 1197: 167–196. 0304-4157(94)90004-3 [pii].
|
[8] | Colombini M (1989) Voltage gating in the mitochondrial channel, VDAC. J Membr Biol 111: 103–111.
|
[9] | Abrecht H, Wattiez R, Ruysschaert JM, Homble F (2000) Purification and characterization of two voltage-dependent anion channel isoforms from plant seeds. Plant Physiol 124: 1181–1190.
|
[10] | Colombini M (2004) VDAC: the channel at the interface between mitochondria and the cytosol. Mol Cell Biochem 256–257: 107–115.
|
[11] | Hodge T, Colombini M (1997) Regulation of metabolite flux through voltage-gating of VDAC channels. J Membr Biol 157: 271–279.
|
[12] | Roos N, Benz R, Brdiczka D (1982) Identification and characterization of the pore-forming protein in the outer membrane of rat liver mitochondria. Biochim Biophys Acta 686: 204–214.
|
[13] | Troll H, Malchow D, Müller-Taubenberger A, Humbel B, Lottspeich F, et al. (1992) Purification, functional characterization, and cDNA sequencing of mitochondrial porin from Dictyostelium discoideum. J Biol Chem 267: 21072–21079.
|
[14] | Zambrowicz EB, Colombini M (1993) Zero-current potentials in a large membrane channel: a simple theory accounts for complex behavior. Biophys J 65: 1093–1100. S0006-3495(93)81148-2 [pii];10.1016/S0006-3495(93)81148-2 [doi].
|
[15] | Ludwig O, Krause J, Hay R, Benz R (1988) Purification and characterization of the pore forming protein of yeast mitochondrial outer membrane. Eur Biophys J 15: 269–276.
|
[16] | Freitag H, Neupert W, Benz R (1982) Purification and characterisation of a pore protein of the outer mitochondrial membrane from Neurospora crassa. Eur J Biochem 123: 629–636.
|
[17] | Hiller S, Garces RG, Malia TJ, Orekhov VY, Colombini M, et al. (2008) Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 321: 1206–1210. 321/5893/1206 [pii];10.1126/science.1161302 [doi].
|
[18] | Bayrhuber M, Meins T, Habeck M, Becker S, Giller K, et al. (2008) Structure of the human voltage-dependent anion channel. Proc Natl Acad Sci U S A 105: 15370–15375. 0808115105 [pii];10.1073/pnas.0808115105 [doi].
|
[19] | Ujwal R, Cascio D, Colletier JP, Faham S, Zhang J, et al. (2008) The crystal structure of mouse VDAC1 at 2.3 ? resolution reveals mechanistic insights into metabolite gating. Proc Natl Acad Sci U S A 105: 17742–17747. 0809634105 [pii];10.1073/pnas.0809634105 [doi].
|
[20] | Koebnik R, Locher KP, Van GP (2000) Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol 37: 239–253. mmi1983 [pii].
|
[21] | Colombini M (2009) The published 3D structure of the VDAC channel: native or not? Trends Biochem Sci 34: 382–389. S0968-0004(09)00118-2 [pii];10.1016/j.tibs.2009.05.001 [doi].
|
[22] | Raschle T, Hiller S, Yu TY, Rice AJ, Walz T, et al. (2009) Structural and functional characterization of the integral membrane protein VDAC-1 in lipid bilayer nanodiscs. J Am Chem Soc 131: 17777–17779. 10.1021/ja907918r [doi].
|
[23] | Hiller S, Abramson J, Mannella C, Wagner G, Zeth K (2010) The 3D structures of VDAC represent a native conformation. Trends Biochem Sci 35: 514–521. S0968-0004(10)00049-6 [pii];10.1016/j.tibs.2010.03.005 [doi].
|
[24] | Shanmugavadivu B, Apell HJ, Meins T, Zeth K, Kleinschmidt JH (2007) Correct folding of the beta-barrel of the human membrane protein VDAC requires a lipid bilayer. J Mol Biol 368: 66–78. S0022-2836(07)00130-1 [pii];10.1016/j.jmb.2007.01.066 [doi].
|
[25] | Guo XW, Smith PR, Cognon B, D'Arcangelis D, Dolginova E, et al. (1995) Molecular design of the voltage-dependent, anion-selective channel in the mitochondrial outer membrane. J Struct Biol 114: 41–59. S1047-8477(85)71004-0 [pii];10.1006/jsbi.1995.1004 [doi].
|
[26] | Mannella CA (1998) Conformational changes in the mitochondrial channel protein, VDAC, and their functional implications. J Struct Biol 121: 207–218. S1047-8477(97)93954-X [pii];10.1006/jsbi.1997.3954 [doi].
|
[27] | Shao L, Kinnally KW, Mannella CA (1996) Circular dichroism studies of the mitochondrial channel, VDAC, from Neurospora crassa. Biophys J 71: 778–786. S0006-3495(96)79277-9 [pii];10.1016/S0006-3495(96)79277-9 [doi].
|
[28] | Koppel DA, Kinnally KW, Masters P, Forte M, Blachly-Dyson E, et al. (1998) Bacterial expression and characterization of the mitochondrial outer membrane channel. Effects of N-terminal modifications. J Biol Chem 273: 13794–13800.
|
[29] | Choudhary OP, Ujwal R, Kowallis W, Coalson R, Abramson J, et al. (2010) The electrostatics of VDAC: implications for selectivity and gating. J Mol Biol 396: 580–592. S0022-2836(09)01476-4 [pii];10.1016/j.jmb.2009.12.006 [doi].
|
[30] | Lee KI, Rui H, Pastor RW, Im W (2011) Brownian dynamics simulations of ion transport through the VDAC. Biophys J 100: 611–619. S0006-3495(10)05252-5 [pii];10.1016/j.bpj.2010.12.3708 [doi].
|
[31] | Rui H, Lee KI, Pastor RW, Im W (2011) Molecular dynamics studies of ion permeation in VDAC. Biophys J 100: 602–610. S0006-3495(10)05255-0 [pii];10.1016/j.bpj.2010.12.3711 [doi].
|
[32] | De Pinto V, Prezioso G, Thinnes F, Link TA, Palmieri F (1991) Peptide-specific antibodies and proteases as probes of the transmembrane topology of the bovine heart mitochondrial porin. Biochemistry 30: 10191–10200.
|
[33] | Al Bitar F, Roosens N, Smeyers M, Vauterin M, van Boxtel J, et al. (2003) Sequence analysis, transcriptional and posttranscriptional regulation of the rice vdac family. Biochimica et Biophysica Acta-Gene Structure and Expression 1625: 43–51.
|
[34] | Schneider R, Etzkorn M, Giller K, Daebel V, Eisfeld J, et al. (2010) The native conformation of the human VDAC1 N terminus. Angew Chem Int Ed Engl 49: 1882–1885. 10.1002/anie.200906241 [doi].
|
[35] | Summers WA, Court DA (2010) Origami in outer membrane mimetics: correlating the first detailed images of refolded VDAC with over 20 years of biochemical data. Biochem Cell Biol 88: 425–438. o09-115 [pii];10.1139/o09-115 [doi].
|
[36] | Villinger S, Briones R, Giller K, Zachariae U, Lange A, et al. (2010) Functional dynamics in the voltage-dependent anion channel. Proc Natl Acad Sci U S A 107: 22546–22551. 1012310108 [pii];10.1073/pnas.1012310108 [doi].
|
[37] | Mlayeh L, Chatkaew S, Leonetti M, Homble F (2010) Modulation of plant mitochondrial VDAC by phytosterols. Biophys J 99: 2097–2106. S0006-3495(10)00984-7 [pii];10.1016/j.bpj.2010.07.067 [doi].
|
[38] | Cortese JD, Voglino AL, Hackenbrock CR (1991) Ionic strength of the intermembrane space of intact mitochondria as estimated with fluorescein-BSA delivered by low pH fusion. J Cell Biol 113: 1331–1340.
|
[39] | Peng S, Blachly-Dyson E, Forte M, Colombini M (1992) Large scale rearrangement of protein domains is associated with voltage gating of the VDAC channel. Biophys J 62: 123–131. S0006-3495(92)81799-X [pii];10.1016/S0006-3495(92)81799-X [doi].
|
[40] | Alcaraz A, Nestorovich EM, Aguilella-Arzo M, Aguilella VM, Bezrukov SM (2004) Salting out the ionic selectivity of a wide channel: the asymmetry of OmpF. Biophys J 87: 943–957. 10.1529/biophysj.104/043414 [doi];S0006-3495(04)73578-X [pii].
|
[41] | Alcaraz A, Nestorovich EM, Lopez ML, Garcia-Gimenez E, Bezrukov SM, et al. (2009) Diffusion, exclusion, and specific binding in a large channel: a study of OmpF selectivity inversion. Biophys J 96: 56–66. S0006-3495(08)00032-5 [pii];10.1016/j.bpj.2008.09.024 [doi].
|
[42] | Kobayashi Y, Nakae T (1985) The mechanism of ion selectivity of OmpF-porin pores of Escherichia coli. Eur J Biochem 151: 231–236.
|
[43] | Im W, Roux B (2002) Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J Mol Biol 322: 851–869. S0022283602007787 [pii].
|
[44] | Im W, Roux B (2002) Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J Mol Biol 319: 1177–1197. 10.1016/S0022-2836(02)00380-7 [doi];S0022-2836(02)00380-7 [pii].
|
[45] | Karshikoff A, Spassov V, Cowan SW, Ladenstein R, Schirmer T (1994) Electrostatic properties of two porin channels from Escherichia coli. J Mol Biol 240: 372–384. S0022-2836(84)71451-3 [pii];10.1006/jmbi.1994.1451 [doi].
|
[46] | Schirmer T, Phale PS (1999) Brownian dynamics simulation of ion flow through porin channels. J Mol Biol 294: 1159–1167. 10.1006/jmbi.1999.3326 [doi];S0022-2836(99)93326-0 [pii].
|
[47] | Lopez ML, Aguilella-Arzo M, Aguilella VM, Alcaraz A (2009) Ion selectivity of a biological channel at high concentration ratio: insights on small ion diffusion and binding. J Phys Chem B 113: 8745–8751. 10.1021/jp902267g [doi].
|
[48] | Garcia-Gimenez E, Alcaraz A, Aguilella VM (2010) Overcharging below the nanoscale: multivalent cations reverse the ion selectivity of a biological channel. Phys Rev E Stat Nonlin Soft Matter Phys 81: 021912.
|
[49] | Corry B (2004) Theoretical conformation of the closed and open states of the acetylcholine receptor channel. Biochim Biophys Acta 1663: 2–5. 10.1016/j.bbamem.2004.02.006 [doi];S000527360400063X [pii].
|
[50] | Jogini V, Roux B (2005) Electrostatics of the intracellular vestibule of K+ channels. J Mol Biol 354: 272–288. S0022-2836(05)01096-X [pii];10.1016/j.jmb.2005.09.031 [doi].
|
[51] | Tai K, Haider S, Grottesi A, Sansom MS (2009) Ion channel gates: comparative analysis of energy barriers. Eur Biophys J 38: 347–354. 10.1007/s00249-008-0377-x [doi].
|
[52] | Blachly-Dyson E, Peng S, Colombini M, Forte M (1990) Selectivity changes in site-directed mutants of the VDAC ion channel: structural implications. Science 247: 1233–1236.
|
[53] | De Pinto V, Ludwig O, Krause J, Benz R, Palmieri F (1987) Porin pores of mitochondrial outer membranes from high and low eukaryotic cells: biochemical and biophysical characterization. Biochim Biophys Acta 894: 109–119. 0005-2728(87)90180-0 [pii].
|
[54] | Smack DP, Colombini M (1985) Voltage-dependent channels found in the membrane fraction of corn mitochondria. Plant Physiol 79: 1094–1097.
|
[55] | Abrecht H, Goormaghtigh E, Ruysschaert JM, Homble F (2000) Structure and orientation of two voltage-dependent anion-selective channel isoforms - An attenuated total reflection Fourier-transform infrared spectroscopy study. J Biol Chem 275: 40992–40999.
|
[56] | Smeyers M, Léonetti M, Goormaghtigh E, Homblé F (2003) Chapter 15 Structure and function of plant membrane ion channels reconstituted in planar lipid bilayers. In: Tien HT, editor. Membrane Science and Technology - Planar Lipid Bilayers (BLMs) and Their Applications. Elsevier. pp. 449–478.
|
[57] | Liu MY, Colombini M (1992) Regulation of mitochondrial respiration by controlling the permeability of the outer membrane through the mitochondrial channel, VDAC. Biochim Biophys Acta 1098: 255–260.
|
[58] | 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: 13593–13599.
|
[59] | Ramirez P, Mafe S, Aguilella VM, Alcaraz A (2003) Synthetic nanopores with fixed charges: an electrodiffusion model for ionic transport. Phys Rev E Stat Nonlin Soft Matter Phys 68: 011910.
|
[60] | Bas DC, Rogers DM, Jensen JH (2008) Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 73: 765–783. 10.1002/prot.22102 [doi].
|
[61] | De Pinto V, al Jamal JA, Palmieri F (1993) Location of the dicyclohexylcarbodiimide-reactive glutamate residue in the bovine heart mitochondrial porin. J Biol Chem 268: 12977–12982.
|
[62] | Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29: 1859–1865. 10.1002/jcc.20945 [doi].
|
[63] | Feller SE, Mac Kerell DA Jr (2000) An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids. J Phys Chem B 104: 7510–7515.
|
[64] | MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, et al. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins. J Phys Chem B 102: 3586–3616.
|
[65] | Mackerell AD Jr, Feig M, Brooks CL III (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25: 1400–1415. 10.1002/jcc.20065 [doi].
|
[66] | Henin J, Shinoda W, Klein ML (2008) United-atom acyl chains for CHARMM phospholipids. J Phys Chem B 112: 7008–7015. 10.1021/jp800687p [doi].
|
[67] | Philipps JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. Journal of Computational Chemistry. J Comput Chem 26: 1781–1802.
|
[68] | 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: 10089–100894.
|
[69] | Tuckerman M, Berne BR, Martyna GJ (1992) Reversible multiple time scale molecular dynamics. J Chem Phys 97: 1990–1999.
|
[70] | Andersen HC (1983) Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. J Comput Phys 52: 24–34.
|
[71] | Lomize MA, Lomize AL, Pogozheva ID, Mosberg HI (2006) OPM: orientations of proteins in membranes database. Bioinformatics 22: 623–625. btk023 [pii];10.1093/bioinformatics/btk023 [doi].
|
[72] | Holst M, Saied F (1993) Multigrid solution of the Poisson—Boltzmann equation. J Comput Chem 14: 105–113.
|
[73] | Marrink S-J, Berendsen HJC (1994) Simulation of water transport through a lipid membrane. J Phys Chem 98: 4155–4168.
|
[74] | Egwolf B, Luo Y, Walters DE, Roux B (2010) Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter. II. Multi-ion effects studied with grand canonical Monte Carlo/Brownian dynamics simulations. J Phys Chem B 114: 2901–2909. 10.1021/jp906791b [doi].
|
[75] | Wang Y, Cohen J, Boron WF, Schulten K, Tajkhorshid E (2007) Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics. J Struct Biol 157: 534–544. S1047-8477(06)00378-9 [pii];10.1016/j.jsb.2006.11.008 [doi].
|
[76] | Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33–38. 0263785596000185 [pii].
|
[77] | Levine BG, Stone JE, Kohlmeyer A (2011) Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming. J Comput Phys 230: 3556–3569. 10.1016/j.jcp.2011.01.048 [doi].
|
[78] | Ohtaki H, Radnai T (1993) Structure and dynamics of hydrated ions. Chem Rev 93: 1157–1204.
|
[79] | Degrève L, da Silva FLB (1999) Large ionic clusters in concentrated aqueous NaCl solution. J Chem Phys 111: 5150–5157.
|
[80] | 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.
|
[81] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410. 10.1006/jmbi.1990.9999 [doi];S0022-2836(05)80360-2 [pii].
|
[82] | Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, et al. (2007) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35: D5–12. gkl1031 [pii];10.1093/nar/gkl1031 [doi].
|
[83] | Aksimentiev A, Schulten K (2005) Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys J 88: 3745–3761. S0006-3495(05)73429-9 [pii];10.1529/biophysj.104.058727 [doi].
|