Ten Years of High Resolution Structural Research on the Voltage Dependent Anion Channel (VDAC)-Recent Developments and Future Directions

Abstract

Mitochondria are evolutionarily related to Gram-negative bacteria and both comprise two membrane systems with strongly differing protein composition. The major protein in the outer membrane of mitochondria is the voltage-dependent anion channel (VDAC), which mediates signal transmission across the outer membrane but also the exchange of metabolites, most importantly ADP and ATP. More than 30 years after its discovery three identical high-resolution structures were determined in 2008. These structures show a 19-stranded anti-parallel beta-barrel with an N-terminal helix located inside. An odd number of beta-strands is also shared by Tom40, another member of the VDAC superfamily. This indicates that this superfamily is evolutionarily relatively young and that it has emerged in the context of mitochondrial evolution. New structural information obtained during the last decade on Tom40 can be used to cross-validate the structure of VDAC and vice versa. Interpretation of biochemical and biophysical studies on both protein channels now rests on a solid basis of structural data. Over the past 10 years, complementary structural and functional information on proteins of the VDAC superfamily has been collected from in-organello, in-vitro, and in silico studies. Most of these findings have confirmed the validity of the original structures. This short article briefly reviews the most important advances on the structure and function of VDAC superfamily members collected during the last decade and summarizes how they enhanced our understanding of the channel.

Keywords: NMR; Tom40; VDAC; structural biology; x-ray.

Figure 1

First electron micrographs of VDAC from the early 1980s. (A) Electron-microscopic investigations of ncVDAC arranged in isolated native membrane vesicles show three two-dimensional molecular arrays: two slightly different hexameric arrangements of VDAC pores around a two-fold symmetry axis (right and left) and another arrangement where dimeric VDAC pores form chain-like superstructures (colored circles mark two independent monomers) (Mannella et al., 1983). (B) A single particle analysis of small membrane arrays yielded the first 3D representation of VDAC at a resolution of ~2 nm (Guo et al., 1995). Figures reproduced with permission.

Figure 2

Superposition of the three VDAC structures published simultaneously in 2008. The three structures were determined by X-ray, NMR spectroscopy, and a combination of both methods (Bayrhuber et al., ; Hiller et al., ; Ujwal et al., 2008). (A) Here, we superimposed the three structures and displayed them in ribbon representation to highlight their analogies and differences. The X-ray structure (3EMN) is shown in green, the NMR structure (2K4T) is shown in red, while the hybrid structure (2JK4) is displayed in blue. The structures are viewed from two different perspectives related by a 90° rotation around the x-axis. The major difference between the structures is the location and secondary structure assigned to the N-terminal helix in the NMR structure. (B) Structure of mVDAC displaying the fold of the VDAC superfamily proteins. The structure is color coded from the N- (blue) to the C-terminus (red) and secondary structure elements are annotated (alpha, beta1-beta19). (C) A primary function of VDAC in the MOM is to translocate nucleotides and the surface representation of VDAC color coded in surface charge potentials is provided. This representation shows the channel pore together with the electrostatic surface potential which is primarily positive around the channel eyelet. (D) The crystal structure of 2JK4 showed a potential VDAC dimer in the crystal lattice and although the dimer contacts are rather weak, the interface formed by strands beta1 and beta19 appears to be biologically important. All figures were prepared using PYMOL (www.pymol.org).

Figure 3

New structural details collected on members of the VDAC-superfamily of 19-stranded β-barrels. (A) Structure determination of the E73V mutant of human VDAC. This mutant was previously described to have altered biophysical properties in comparison to the wildtype protein. The NMR determination of the structure yielded a structurally significantly changed beta-barrel with an oval rather than a circular form and a smaller channel diameter. Three structures of the mVDAC1 (in green), hVDAC1 (in red), and the mutant structure (in light blue) were superimposed to show the deviation in the barrel section. A surface representation of the latest NMR structure (5JDP) shows the particular small diameter of the pore eyelet in E73V (Jaremko et al., 2016). (B) (a) High resolution AFM topographs of densely packed scVDAC natively embedded in membranes of S. cerevisiae (large picture) and (b) high resolution view of VDAC molecules in an arrangement similar to the early electron microsocopy images (inset picture). (c) Peak analysis of the separation between two VDAC molecules yields a distance of 53 Å (pore to pore; see graph) (Gonçalves et al., 2007). (C) Structural analysis of the Tom40 complex shows a dimeric arrangement of the pore structures with the alpha-helix inside the barrel or exposed to the surface. The structure at 1 nm resolution was modeled by a Tom40-homology model based on the mVDAC structure (PDB-entry 3EMN) and can accommodate the 19 beta-strands unambiguously. The dimeric arrangement is mediated by the same beta1/beta19 strands as previously reported for the hVDAC1 dimer (2JK4—dimer shown in orange and dark blue) (Bayrhuber et al., ; Bausewein et al., 2017). Figures reproduced with permission.