Origami in the outer membrane: the transmembrane arrangement of mitochondrial porins

2002 ◽  
Vol 80 (5) ◽  
pp. 551-562 ◽  
Author(s):  
Denice C Bay ◽  
Deborah A Court
Keyword(s):  
Outer Membrane ◽  
Structural Information ◽  
Mitochondrial Outer Membrane ◽  
Wild Type ◽  
Mitochondrial Porin ◽  
Electrophysiological Properties ◽  
Common Structure ◽  
Outer Membrane Porins ◽  
Voltage Dependent ◽  
Bacterial Porins

Voltage-dependent anion-selective channels (VDAC), also known as mitochondrial porins, are key regulators of metabolite flow across the mitochondrial outer membrane. Porins from a wide variety of organisms share remarkably similar electrophysiological properties, in spite of considerable sequence dissimilarity, indicating that they share a common structure. Based on primary sequence considerations, analogy with bacterial porins, and circular dichroism analysis, it is agreed that VDAC spans the outer membrane as a β-barrel. However, the residues that form the antiparallel β-strands comprising this barrel remain unknown. Various predictive methods, largely based on the known structures of bacterial β-barrels, have been applied to the primary sequences of VDAC. Refinement and confirmation of these predictions have developed through numerous investigations of wild-type and variant porins, both in mitochondria and in artificial membranes. These experiments have involved VDAC from several sources, precluding the generation of a unified model. Herein, using the Neurospora VDAC sequence as a template, the published structural information and predictions have been reassessed to delineate a model that satisfies most of the available data.Key words: VDAC, mitochondrial porin, β-barrel.

Cryo-Electron Microscopy and Correlation Averaging of Frozen-Hydrated, Polymorphic 2D Crystals of the Mitochondrial Outer Membrane Channel

1990 ◽  
Vol 48 (1) ◽  
pp. 100-101
Author(s):  
Xiao-Wei Guo
Keyword(s):  
Outer Membrane ◽  
Hexagonal Lattice ◽  
Mitochondrial Outer Membrane ◽  
Rectangular Lattice ◽  
Electron Microscopic ◽  
Cryo Electron Microscopy ◽  
Voltage Dependent ◽  
Outer Membrane Channel ◽  
2D Crystals ◽  
Vdac Channel

Voltage-dependent, anion-selective channels (VDAC) are formed in the mitochondrial outer membrane (mitOM) by a 30-kDa polypeptide. These channels form ordered 2D arrays when mitOMs from Neurospora crassa are treated with soluble phospholipase A2. We obtain low-dose electron microscopic images of unstained specimens of VDAC crystals preserved in vitreous ice, using a Philips EM420 equipped with a Gatan cryo-transfer stage. We then use correlation analysis to compute average projections of the channel crystals. The procedure involves Fourier-filtration of a region within a crystal field to obtain a preliminary average that is subsequently cross-correlated with the entire crystal. Subregions are windowed from the crystal image at coordinates of peaks in the cross-correlation function (CCF, see Figures 1 and 2) and summed to form averages (Figure 3).The VDAC channel forms several different types of crystalline arrays in mitOMs. The polymorph first observed during phospholipase treatment is a parallelogram array (a=13 run, b=11.5 run, θ==109°) containing 6 water-filled pores per unit cell. Figure 1 shows the CCF of a sub-field of such an “oblique” array used to compute the correlation average of Figure 3A. With increased phospholipase treatment, other polymorphs are observed, often co-existing within the same crystal. For example, two distinct (but closely related) types of lattices occur in the field corresponding to the CCF of Figure 2: a “contracted” version of the parallelogram lattice (a=13 run, b=10 run, θ=99°), and a near-rectangular lattice (a=8.5 run, b=5 nm). The pattern of maxima in this CCF suggests that a third, near-hexagonal lattice (a=4.5 nm) may also be present. The correlation averages of Figures 3B-D were computed from polycrystalline fields, using peak coordinates in regions of CCFs corresponding to each of the three lattice types.

Effects of cytochrome c on the mitochondrial apoptosis-induced channel MAC

2004 ◽  
Vol 286 (5) ◽  
pp. C1109-C1117 ◽  
Author(s):  
Liang Guo ◽  
Dawn Pietkiewicz ◽  
Evgeny V. Pavlov ◽  
Sergey M. Grigoriev ◽  
John J. Kasianowicz ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Outer Membrane ◽  
Cell Types ◽  
Rnase A ◽  
Mitochondrial Outer Membrane ◽  
Dependent Manner ◽  
Mitochondrial Apoptosis ◽  
Noise Type ◽  
Voltage Dependent

Recent studies indicate that cytochrome c is released early in apoptosis without loss of integrity of the mitochondrial outer membrane in some cell types. The high-conductance mitochondrial apoptosis-induced channel (MAC) forms in the outer membrane early in apoptosis of FL5.12 cells. Physiological (micromolar) levels of cytochrome c alter MAC activity, and these effects are referred to as types 1 and 2. Type 1 effects are consistent with a partitioning of cytochrome c into the pore of MAC and include a modest decrease in conductance that is dose and voltage dependent, reversible, and has an increase in noise. Type 2 effects may correspond to “plugging” of the pore or destabilization of the open state. Type 2 effects are a dose-dependent, voltage-independent, and irreversible decrease in conductance. MAC is a heterogeneous channel with variable conductance. Cytochrome c affects MAC in a pore size-dependent manner, with maximal effects of cytochrome c on MAC with conductance of 1.9–5.4 nS. The effects of cytochrome c, RNase A, and high salt on MAC indicate that size, rather than charge, is crucial. The effects of dextran molecules of various sizes indicate that the pore diameter of MAC is slightly larger than that of 17-kDa dextran, which should be sufficient to allow the passage of 12-kDa cytochrome c. These findings are consistent with the notion that MAC is the pore through which cytochrome c is released from mitochondria during apoptosis.

scholarly journals Identification of two voltage-dependent anion channel-like protein sequences conserved in Kinetoplastida

2012 ◽  
Vol 8 (3) ◽  
pp. 446-449 ◽  
Author(s):  
Nadine Flinner ◽  
Enrico Schleiff ◽  
Oliver Mirus
Keyword(s):  
Outer Membrane ◽  
Trypanosoma Brucei ◽  
Protein Sequences ◽  
Anion Channel ◽  
Mitochondrial Outer Membrane ◽  
Voltage Dependent Anion Channel ◽  
Voltage Dependent

The eukaryotic porin superfamily consists of two families, voltage-dependent anion channel (VDAC) and Tom40, which are both located in the mitochondrial outer membrane. In Trypanosoma brucei , only a single member of the VDAC family has been described. We report the detection of two additional eukaryotic porin-like sequences in T. brucei . By bioinformatic means, we classify both as putative VDAC isoforms.

scholarly journals Arabidopsis Voltage-Dependent Anion Channels (VDACs): Overlapping and Specific Functions in Mitochondria

Cells ◽  
2020 ◽  
Vol 9 (4) ◽  
pp. 1023 ◽  
Author(s):  
Mickaële Hemono ◽  
Élodie Ubrig ◽  
Kevin Azeredo ◽  
Thalia Salinas-Giegé ◽  
Laurence Drouard ◽  
...  
Keyword(s):  
Stress Response ◽  
Outer Membrane ◽  
Mitochondrial Outer Membrane ◽  
Anion Channels ◽  
Essential Components ◽  
New Knowledge ◽  
Trna Import ◽  
Voltage Dependent ◽  
Mutant Lines ◽  
Mrna Isoform

Voltage-dependent anion channels (VDACs) are essential components of the mitochondrial outer membrane. VDACs are involved in the exchange of numerous ions and molecules, from ATP to larger molecules such as tRNAs, and are supposed to adjust exchanges in response to cell signals and stresses. Four major VDACs have been identified in Arabidopsis thaliana. The goal of this study was to explore the specific functions of these proteins, in particular, in tRNA import into mitochondria and stress response. The main results were: (i) VDACs appeared to differentially interact with tRNAs, and VDAC4 could be the major tRNA channel on the outer membrane, (ii) a VDAC3 mRNA isoform was found induced by different stresses, suggesting that VDAC3 might be specifically involved in early steps of stress response and (iii) an analysis of vdac3 and vdac1 mutant lines showed that VDAC3 and VDAC1 shared some, but not all functions. In conclusion, this work brings new knowledge on VDACs, which do not appear as interchangeable pores of the outer membrane and each VDAC has its own specificity.

Nature of In-Plane Phase Transitions in 2D Crystals of the Mitochondrial Porin, VDAC

1997 ◽  
Vol 3 (S2) ◽  
pp. 1065-1066
Author(s):  
C.A. Mannella
Keyword(s):  
Electron Microscopy ◽  
Phase Transitions ◽  
Pore Structure ◽  
Mitochondrial Outer Membrane ◽  
Mitochondrial Porin ◽  
Outer Membranes ◽  
Voltage Gated ◽  
Bacterial Porins ◽  
Source Of Information ◽  
2D Crystals

VDAC is a voltage-gated ion and metabolite channel that occurs at high density in the mitochondrial outer membrane. Although VDAC is probably related structurally to bacterial porins, small transmembrane voltages cause it to undergo reversible, partial closures that are not seen with the prokaryotic pores. The “closed” states, which are impermeable to ATP, can be induced by effectors, including a synthetic polyanion. There is evidence that closure involves major rearrangements of the pore structure that are difficult to explain in terms of porin-like β-barrels.The main source of information about the structure of VDAC is electron microscopy of 2D crystals obtained by phospholipase treatment of outer membranes of fungal mitochondria. The unit cell observed after partial lipid hydrolysis (a = 13.3 nm, b = 11.5 nm, γ = 109°) contains six pores which appear to be structurally equivalent at the resolution of correlation averages of crystals embedded in aurothioglucose or vitreous ice (∼1/1.5 nm−1).

scholarly journals Prohibitin Family Members Interact Genetically with Mitochondrial Inheritance Components in Saccharomyces cerevisiae

1998 ◽  
Vol 18 (7) ◽  
pp. 4043-4052 ◽  
Author(s):  
Karen H. Berger ◽  
Michael P. Yaffe
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Outer Membrane ◽  
Integral Membrane Proteins ◽  
Mitochondrial Outer Membrane ◽  
Mitochondrial Morphology ◽  
Mitochondrial Inheritance ◽  
Loss Of Function ◽  
Wild Type ◽  
Mitochondrial Inner Membrane ◽  
Synthetically Lethal

ABSTRACT Phb2p, a homolog of the tumor suppressor protein prohibitin, was identified in a genetic screen for suppressors of the loss of Mdm12p, a mitochondrial outer membrane protein required for normal mitochondrial morphology and inheritance in Saccharomyces cerevisiae. Phb2p and its homolog, prohibitin (Phb1p), were localized to the mitochondrial inner membrane and characterized as integral membrane proteins which depend on each other for their stability. In otherwise wild-type genetic backgrounds, null mutations in PHB1 andPHB2 did not confer any obvious phenotypes. However, loss of function of either PHB1 or PHB2 in cells with mitochondrial DNA deleted led to altered mitochondrial morphology, and phb1 or phb2 mutations were synthetically lethal when combined with a mutation in any of three mitochondrial inheritance components of the mitochondrial outer membrane, Mdm12p, Mdm10p, and Mmm1p. These results provide the first evidence of a role for prohibitin in mitochondrial inheritance and in the regulation of mitochondrial morphology.

Phosphorothioate oligonucleotides reduce mitochondrial outer membrane permeability to ADP

2007 ◽  
Vol 292 (4) ◽  
pp. C1388-C1397 ◽  
Author(s):  
Wenzhi Tan ◽  
Johnathan C. Lai ◽  
Paul Miller ◽  
C. A. Stein ◽  
Marco Colombini
Keyword(s):  
Cytochrome C ◽  
Membrane Permeability ◽  
Outer Membrane ◽  
Mitochondrial Outer Membrane ◽  
Cytochrome C Release ◽  
Voltage Dependent ◽  
Selective Channel ◽  
Vdac Channels ◽  
Outer Membrane Permeability ◽  
Apoptotic Cascade

G3139, an antisense Bcl-2 phosphorothioate oligodeoxyribonucleotide, induces apoptosis in melanoma and other cancer cells. This apoptosis happens before and in the absence of the downregulation of Bcl-2 and thus seems to be Bcl-2-independent. Binding of G3139 to mitochondria and its ability to close voltage-dependent anion-selective channel (VDAC) have led to the hypothesis that G3139 acts, in part, by interacting with VDAC channels in the mitochondrial outer membrane ( 21 ). In this study, we demonstrate that G3139 is able to reduce the mitochondrial outer membrane permeability to ADP by a factor of 6 or 7 with a Ki between 0.2 and 0.5 μM. Because VDAC is responsible for this permeability, this result strengthens the aforesaid hypothesis. Other mitochondrial respiration components are not affected by [G3139] up to 1 μM. Higher levels begin to inhibit respiration rates, decrease light scattering and increase uncoupled respiration. These results agree with accumulating evidence that VDAC closure favors cytochrome c release. The speed of this effect (within 10 min) places it early in the apoptotic cascade with cytochrome c release occurring at later times. Other phosphorothioate oligonucleotides are also able to induce VDAC closure, and there is some length dependence. The phosphorothioate linkages are required to induce the reduction of outer membrane permeability. At levels below 1 μM, phosphorothioate oligonucleotides are the first specific tools to restrict mitochondrial outer membrane permeability.

scholarly journals Functional characterization of an N-terminally-truncated mitochondrial porin expressed in Neurospora crassa

2017 ◽  
Vol 63 (8) ◽  
pp. 730-738 ◽  
Author(s):  
Sabbir R. Shuvo ◽  
Uliana Kovaltchouk ◽  
Abdullah Zubaer ◽  
Ayush Kumar ◽  
William A.T. Summers ◽  
...  
Keyword(s):  
Neurospora Crassa ◽  
Outer Membrane ◽  
Functional Characterization ◽  
Helical Structure ◽  
Terminal Segment ◽  
Wild Type ◽  
Mitochondrial Porin ◽  
N Terminus

Mitochondrial porin, which forms voltage-dependent anion-selective channels (VDAC) in the outer membrane, can be folded into a 19-β-stranded barrel. The N terminus of the protein is external to the barrel and contains α-helical structure. Targeted modifications of the N-terminal region have been assessed in artificial membranes, leading to different models for gating in vitro. However, the in vivo requirements for gating and the N-terminal segment of porin are less well-understood. Using Neurospora crassa porin as a model, the effects of a partial deletion of the N-terminal segment were investigated. The protein, ΔN2-12porin, is assembled into the outer membrane, albeit at lower levels than the wild-type protein. The resulting strain displays electron transport chain deficiencies, concomitant expression of alternative oxidase, and decreased growth rates. Nonetheless, its mitochondrial genome does not contain any significant mutations. Most of the genes that are expressed in high levels in porin-less N. crassa are expressed at levels similar to that of wild type or are slightly increased in ΔN2-12porin strains. Thus, although the N-terminal segment of VDAC is required for complete function in vivo, low levels of a protein lacking part of the N terminus are able to rescue some of the defects associated with the absence of porin.

scholarly journals VDAC oligomers form mitochondrial pores to release mtDNA fragments and promote lupus-like disease

Science ◽  
2019 ◽  
Vol 366 (6472) ◽  
pp. 1531-1536 ◽  
Author(s):  
Jeonghan Kim ◽  
Rajeev Gupta ◽  
Luz P. Blanco ◽  
Shutong Yang ◽  
Anna Shteinfer-Kuzmine ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Lupus Erythematosus ◽  
Anion Channel ◽  
Live Cells ◽  
Mitochondrial Outer Membrane ◽  
Voltage Dependent Anion Channel ◽  
Mitochondrial Outer Membrane Permeabilization ◽  
Extracellular Traps ◽  
Voltage Dependent ◽  
Positively Charged

Mitochondrial stress releases mitochondrial DNA (mtDNA) into the cytosol, thereby triggering the type Ι interferon (IFN) response. Mitochondrial outer membrane permeabilization, which is required for mtDNA release, has been extensively studied in apoptotic cells, but little is known about its role in live cells. We found that oxidatively stressed mitochondria release short mtDNA fragments via pores formed by the voltage-dependent anion channel (VDAC) oligomers in the mitochondrial outer membrane. Furthermore, the positively charged residues in the N-terminal domain of VDAC1 interact with mtDNA, promoting VDAC1 oligomerization. The VDAC oligomerization inhibitor VBIT-4 decreases mtDNA release, IFN signaling, neutrophil extracellular traps, and disease severity in a mouse model of systemic lupus erythematosus. Thus, inhibiting VDAC oligomerization is a potential therapeutic approach for diseases associated with mtDNA release.

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