The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities(462 views) Guardiani C, Scorciapino MA, Amodeo GF, Grdadolnik J, Pappalardo G, De Pinto V, Ceccarelli M, Casu M
Department of Physics, University of Cagliari , 09042 Monserrato, Italy., 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., Department of Chemical and Geological Sciences, University of Cagliari , 09042 Monserrato, Italy., National Institute of Chemistry , Ljubljana, Slovenia., CNR Institute of Biostructures and Bioimaging , Catania, Italy., 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.,
References: Benz, R., Permeation of hydrophilic solutes through mitochondrial outer membranes: Review on mitochondrial porins (1994) Biochim. Biophys. Acta, Rev. Biomembr., 1197, pp. 167-19
Colombini, M., VDAC: The channel at the interface between mitochondria and the cytosol (2004) Mol. Cell. Biochem., 256-257, pp. 107-115
Shoshan-Barmatz, V., De Pinto, V., Zweckstetter, M., Raviv, Z., Keinan, N., Arbel, N., VDAC, a multi-functional mitochondrial protein regulating cell life and death (2010) Mol. Aspects Med., 31, pp. 227-285
Rostovtseva, T., Colombini, M., VDAC channels mediate and gate the flow of ATP: Implications for the regulation of mitochondrial function (1997) Biophys. J., 72, pp. 1954-1962
Beutner, G., Ruck, A., Riede, B., Brdiczka, D., Complexes between hexokinase, mitochondrial porin and adenylate translocator in brain: Regulation of hexokinase, oxidative phosphorylation and permeability transition pore (1997) Biochem. Soc. Trans., 25, pp. 151-157
Cheng, E.H.Y., Sheiko, T.V., Fisher, J.K., Craigen, W.J., Korsmeyer, S.J., VDAC2 inhibits BAK activation and mitochondrial apoptosis (2003) Science, 301, pp. 513-517
Tomasello, F.M., Messina, A., Lartigue, L., Schembri, L., Medina, C., Reina, S., Thoraval, D., De Giorgi, F., Outer membrane VDAC1 controls permeability transition of the inner mitochondrial membrane in cellulo during stress-induced apoptosis (2009) Cell Res., 19, pp. 1363-1376
Maldonado, E.N., Lemasters, J.J., Warburg revisited: Regulation of mitochondrial metabolism by voltage-dependent anion channels in cancer cells (2012) J. Pharmacol. Exp. Ther., 342, pp. 637-641
Messina, A., Reina, S., Guarino, F., De Pinto, V., VDAC isoforms in mammals (2012) Biochim. Biophys. Acta, Biomembr., 1818, pp. 1466-1476
De Pinto, V., Guarino, F., Guarnera, A., Messina, A., Reina, S., Tomasello, F.M., Palermo, V., Mazzoni, C., Characterization of human VDAC isoforms: A peculiar function for VDAC3? (2010) Biochim. Biophys. Acta, Bioenerg., 1797, pp. 1268-1275
Hiller, S., Garces, R.G., Malia, T.J., Orekhov, V.Y., Colombini, M., Wagner, G., Solution structure of the integral human membrane protein VDAC-1 in detergent micelles (2008) Science, 321, pp. 1206-1210
Ujwal, R., Cascio, D., Colletier, J.-P., Faham, S., Zhang, J., Toro, L., Ping, P., Abramson, J., The crystal structure of mouse VDAC1 at 2.3 A resolution reveals mechanistic insights into metabolite gating (2008) Proc. Natl. Acad. Sci. U. S. A., 105, pp. 17742-17747
Bayrhuber, M., Meins, T., Habeck, M., Becker, S., Giller, K., Villinger, S., Vonrhein, C., Zeth, K., Structure of the human voltage-dependent anion channel (2008) Proc. Natl. Acad. Sci. U. S. A., 105, pp. 15370-15375
Schredelseker, J., Paz, A., López, C.J., Altenbach, C., Leung, C.S., Drexler, M.K., Chen, J.-N., Abramson, J., High resolution structure and double electron-electron resonance of the zebrafish voltage-dependent anion channel 2 reveal an oligomeric population (2014) J. Biol. Chem., 289, pp. 12566-12577
Tomasello, F.M., Guarino, F., Reina, S., Messina, A., De Pinto, V., The voltage-dependent anion selective channel 1 (VDAC1) topography in the mitochondrion outer membrane as detected in intact cell (2013) PLoS One, 8, p. 81522
Teijido, O., Ujwal, R., Hillerdal, C.-O., Kullman, L., Rostovtseva, T.K., Abramson, J., Affixing N-terminal α-helix to the wall of the voltage-dependent anion channel does not prevent its voltage gating (2012) J. Biol. Chem., 287, pp. 11437-11445
Zachariae, U., Schneider, R., Briones, R., Gattin, Z., Demers, J., Giller, K., Maier, E., Lange, A., B-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel (2012) Structure, 20, pp. 1540-1549
Rui, H., Lee, K.I., Pastor, R.W., Im, W., Molecular dynamics studies of ion permeation in VDAC (2011) Biophys. J., 100, pp. 602-610
Choudhary, O.P., Ujwal, R., Kowallis, W., Coalson, R., Abramson, J., Grabe, M., The electrostatics of VDAC: Implications for selectivity and gating (2010) J. Mol. Biol., 396, pp. 580-592
Song, J., Midson, C., Blachly-Dyson, E., Forte, M., Colombini, M., The sensor regions of VDAC are translocated from within the membrane to the surface during the gating processes (1998) Biophys. J., 74, pp. 2926-2944
Mannella, C.A., Conformational changes in the mitochondrial channel protein, VDAC, and their functional implications (1998) J. Struct. Biol., 121, pp. 207-218
Abu-Hamad, S., Arbel, N., Calo, D., Arzoine, L., Israelson, A., Keinan, N., Ben-Romano, R., Shoshan-Barmatz, V., The VDAC1 N-terminus is essential both for apoptosis and the protective effect of anti-apoptotic proteins (2009) J. Cell Sci., 122, pp. 1906-1916
Kelly, S.M., Price, N.C., The use of circular dichroism in the investigation of protein structure and function (2000) Curr. Protein Pept. Sci., 1, pp. 349-384
Cavanagh, J., Fairbrother, W.J., Palmer, A.G., III, Rance, M., Skelton, N.J., (2007) Protein NMR Spectroscopy: Principles and Practice, , 2 nd ed. Elsevier Academic Press, Oxford, U.K
Ogg, R., Kingsley, P., Taylor, J., WET, a T1- and B1-Insensitive Water-Suppression Method for in Vivo Localized 1H NMR Spectroscopy (1994) J. Magn. Reson., Ser. B, 104, pp. 1-10
Smallcombe, S., Patt, S.L., Keifer, P., WET solvent suppression and its applications to LC NMR and high-resolution NMR spectroscopy (1995) J. Magn. Reson., Ser. A, 117, pp. 295-303
Shen, Y., Delaglio, F., Cornilescu, G., Bax, A., TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts (2009) J. Biomol. NMR, 44, pp. 213-223
Grantham, R., Amino acid difference formula to help explain protein evolution (1974) Science, 185, pp. 862-864
Muñoz, V., Serrano, L., Elucidating the folding problem of helical peptides using empirical parameters (1994) Nat. Struct. Biol., 1, pp. 399-409
Lacroix, E., Viguera, A.R., Serrano, L., Elucidating the folding problem of alpha-helices: Local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters (1998) J. Mol. Biol., 284, pp. 173-191
Case, D.A., Babin, V., Berryman, J.T., Betz, R.M., Cai, Q., Cerutti, D.S., Cheatham, T.E., III, Kollman, P.A., (2012) AMBER 14, , University of California, San Francisco
Fukunishi, H., Watanabe, O., Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction (2002) J. Chem. Phys., 116, pp. 9058-9067
Kannan, S., Zacharias, M., Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential (2007) Proteins: Struct., Funct., Genet., 66, pp. 697-706
Sugita, Y., Okamoto, Y., Replica-exchange molecular dynamics method for protein folding (1999) Chem. Phys. Lett., 314, pp. 141-151
Bergonzo, C., Henriksen, N.M., Roe, D.R., Swails, J.M., Roitberg, A.E., Cheatham, T.E., Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide (2014) J. Chem. Theory Comput., 10, pp. 492-499
Kabsch, W., Sander, C., Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features (1983) Biopolymers, 22, pp. 2577-2637
Sreerama, N., Woody, R.W., A self-consistent method for the analysis of protein secondary structure from circular dichroism (1993) Anal. Biochem., 209, pp. 32-44
Greenfield, N.J., Fasman, G.D., Computed circular dichroism spectra for the evaluation of protein conformation (1969) Biochemistry, 8, pp. 4108-4116
Barth, A., Infrared spectroscopy of proteins (2007) Biochim. Biophys. Acta, Bioenerg., 1767, pp. 1073-1101
Wishart, D.S., Sykes, B.D., Richards, F.M., Relationship between nuclear magnetic resonance chemical shift and protein secondary structure (1991) J. Mol. Biol., 222, pp. 311-333
De Pinto, V., Tomasello, F., Messina, A., Guarino, F., Benz, R., La Mendola, D., Magrì, A., Pappalardo, G., Determination of the conformation of the human VDAC1 N-terminal peptide, a protein moiety essential for the functional properties of the pore (2007) ChemBioChem, 8, pp. 744-756
Strandberg, E., Ulrich, A.S., NMR methods for studying membrane-active antimicrobial peptides (2004) Concepts Magn. Reson., Part A, 23, pp. 89-120
Manzo, G., Sanna, R., Casu, M., Mignogna, G., Mangoni, M.L., Rinaldi, A.C., Scorciapino, M.A., Toward an improved structural model of the frog-skin antimicrobial peptide esculentin-1b(1-18) (2012) Biopolymers, 97, pp. 873-881
Scorciapino, M.A., Pirri, G., Vargiu, A.V., Ruggerone, P., Giuliani, A., Casu, M., Buerck, J., Rinaldi, A.C., A novel dendrimeric peptide with antimicrobial properties: Structure-function analysis of SB056 (2012) Biophys. J., 102, pp. 1039-1048
Crevenna, A.H., Naredi-Rainer, N., Lamb, D.C., Wedlich-Söldner, R., Dzubiella, J., Effects of Hofmeister Ions on the α-Helical Structure of Proteins (2012) Biophys. J., 102, pp. 907-915
Dolinsky, T.J., Nielsen, J.E., McCammon, J.A., Baker, N.A., PDB2PQR: An automated pipeline for the setup of Piosson-Boltzmann electrostatics calculations (2004) Nucleic Acids Res., 32, pp. 665-W667
Amodeo, G.F., Scorciapino, M.A., 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 (2014) PLoS One, 9, p. 103879
Hiller, S., Abramson, J., Mannella, C., Wagner, G., Zeth, K., The 3D structures of VDAC represent a native conformation (2010) Trends Biochem. Sci., 35, pp. 514-521
Guo, X.W., Smith, P.R., Cognon, B., D'Arcangelis, D., Dolginova, E., Mannella, C.A., Molecular Design of the Voltage-Dependent, Anion-Selective Channel in the Mitochondrial Outer Membrane (1995) J. Struct. Biol., 114, pp. 41-59
Schneider, R., Etzkorn, M., Giller, K., Daebel, V., Eisfeld, J., Zweckstetter, M., Griesinger, C., Lange, A., The native conformation of the human VDAC1 N terminus (2010) Angew. Chem., Int. Ed., 49, pp. 1882-1885
D'Abramo, M., Rinaldi, A.C., Bozzi, A., Amadei, A., Mignogna, G., Di Nola, A., Aschi, M., Conformational behavior of temporin A and temporin L in aqueous solution: A computational/experimental study (2006) Biopolymers, 81, pp. 215-224
Roccatano, D., Colombo, G., Fioroni, M., Mark, A.E., Mechanism by which 2,2,2-trifluoroethanol/water mixtures stabilize secondary-structure formation in peptides: A molecular dynamics study (2002) Proc. Natl. Acad. Sci. U. S. A., 99, pp. 12179-12184
Geula, S., Ben-Hail, D., Shoshan-Barmatz, V., Structure-based analysis of VDAC1: N-terminus location, translocation, channel gating and association with anti-apoptotic proteins (2012) Biochem. J., 444, pp. 475-485
Villinger, S., Briones, R., Giller, K., Zachariae, U., Lange, A., De Groot, B.L., Griesinger, C., Zweckstetter, M., Functional dynamics in the voltage-dependent anion channel (2010) Proc. Natl. Acad. Sci. U. S. A., 107, pp. 22546-22551
Reina, S., Magrì, A., Lolicato, M., Guarino, F., Impellizzeri, A., Maier, E., Benz, R., Messina, A., Deletion of b-strands 9 and 10 converts VDAC1 voltage-dependence in an asymmetrical process (2013) Biochim. Biophys. Acta, Bioenerg., 1827, pp. 793-805
Boehr, D.D., Nussinov, R., Wright, P.E., The role of dynamic conformational ensembles in biomolecular recognition (2009) Nat. Chem. Biol., 5, pp. 789-796
Reina, S., Palermo, V., Guarnera, A., Guarino, F., Messina, A., Mazzoni, C., De Pinto, V., Swapping of the N-terminus of VDAC1 with VDAC3 restores full activity of the channel and confers anti-aging features to the cell (2010) FEBS Lett., 584, pp. 2837-2844
The N-Terminal Peptides of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion Channel Have Different Helical Propensities
Petraglia F, Singh AA, Carafa V, Nebbioso A, Conte M, Scisciola L, Valente S, Baldi A, Mandoli A, Petrizzi VB, Ingenito C, De Falco S, Cicatiello V, Apicella I, Janssen-megens EM, Kim B, Yi G, Logie C, Heath S, Ruvo M, Wierenga ATJ, Flicek P, Yaspo ML, Della Valle V, Bernard O, Tomassi S, Novellino E, Feoli A, Sbardella G, Gut I, Vellenga E, Stunnenberg HG, Mai A, Martens JHA, Altucci L * Combined HAT/EZH2 modulation leads to cancer-selective cell death(284 views) Oncotarget (ISSN: 1949-2553electronic, 1949-2553linking), 2018 May 22; 9(39): 25630-25646. Impact Factor:5.008 ViewExport to BibTeXExport to EndNote
Ntziachristos V, Cuénod CA, Fournier L, Balvay D, Pradel C, Siauve N, Clement O, Jouannot E, Lucidarme O, Vecchio SD, Salvatore M, Law B, Tung C-H, Jain RK, Fukumura D, Munn LL, Brown EB, Schellenberger E, Montet X, Weissleder R, Clerck ND, Postnov A * Tumor Imaging(350 views) Textbook Of In Vivo Imaging In Vertebrates (ISSN: 9780-4700), 2007 Jul 16; 1: 277-309. Impact Factor:1.148 ViewExport to BibTeXExport to EndNote