Structure of the human voltage-dependent anion channel

Abstract

The voltage-dependent anion channel (VDAC), also known as mitochondrial porin, is the most abundant protein in the mitochondrial outer membrane (MOM). VDAC is the channel known to guide the metabolic flux across the MOM and plays a key role in mitochondrially induced apoptosis. Here, we present the 3D structure of human VDAC1, which was solved conjointly by NMR spectroscopy and x-ray crystallography. Human VDAC1 (hVDAC1) adopts a ␤-barrel architecture composed of 19 ␤-strands with an ␣-helix located horizontally midway within the pore. Bioinformatic analysis indicates that this channel architecture is common to all VDAC proteins and is adopted by the general import pore TOM40 of mammals, which is also located in the MOM.T he outer membrane of mitochondria (MOM) contains three integral membrane protein families, two of which form channels as part of larger protein complexes (for review, see ref. 1). These two MOM complexes, the general import pore TOM and the SAM insertase, allow for the entire translocation and insertion of nearly all newly synthesized proteins destined to the mitochondrial organelle (2, 3). The third protein family of typically high abundance (Ϸ10,000 copies per mitochondrion) is termed voltage-dependent anion channels (VDACs), because of the voltage sensitivity of its open probability (4, 5). Together, this small number of protein families is sufficient for full communication between mitochondria with their cellular environment (1).The VDAC channel was initially described as being reminiscent of bacterial porins and primarily responsible for the exchange of chemical energy equivalents between the cytosol and the mitochondrion (4, 6). Indeed, a variety of structural features (like barrel geometry and dimension) known from the bacterial precursors are maintained (7,8). By contrast, a variety of functions have been ascribed to the VDAC isoforms among which the direct coupling of the mitochondrial matrix to the energy maintenance of the cytosol seems to be the most general function (9). The structure of VDAC is of interest because of a substantial body of evidence connecting VDAC to apoptosis. It is suggested that VDAC is a critical player in the release of apoptogenic factors from mitochondria of mammalian cells, and consequently several hypotheses describing the mechanism of mitochondria-mediated apoptosis involving VDAC have been proposed (for review, see ref. 10). Results and DiscussionStructure Determination of hVDAC1: Combining NMR Spectroscopy and X-Ray Crystallography. In a parallel structural biology approach, we set out to characterize the structure of hVDAC1, the major isoform of this channel in mammalian tissues, by a combination of NMR spectroscopy and x-ray crystallography. The idea behind this project was to gain complementary structural information to have a solid basis for future studies, e.g., analysis of protein heterocomplex formation by NMR and crystal structures as a basis for drug target design. Only information derived from both methods and the application of an iterative s...

High‐Resolution NMR Determination of the Dynamic Structure of Membrane Proteins

“…of 2.5 Å (Figure 1 b and Table S2). Similar to other NOE‐based structures of hVDAC1,10a, 12 the definition of the barrel shape and the conformation and position of the N‐terminal helix could only be determined with modest accuracy (Figure 1 b, Table S3, and Figure S3). …”

Probing the orientation of yeast VDAC1 in vivo

“…VDAC1 structure and FLAG-epitope positions. (A) Three-dimensional model of hsVDAC1 drawn with Pymol [DeLano Scientific] using PDB coordinates 2K4T from [11] (see also 2JK4 [12] and 3EMN [13]) indicating FLAG-epitope locations used in the current study (1)(2)(3)(4)(5). FLAG3, which contradicts the structure, is highlighted (Ã).…”

“…It has also been suggested to play a role in apoptosis [5] although this remains controversial [6]. Despite its importance, the structure of VDAC1 was unclear [7][8][9][10] until recently published high resolution structures of human and mouse VDAC1 revealed a 19 stranded b-barrel capable of dimerization and dynamic fluctuation [11][12][13] (Fig. 1).…”

“…Therefore, this work is based upon the hypothesis that VDAC1 adopts a similar structure in yeast and human mitochondria. Antibody binding to FLAG-epitopes (DYKDDDDK) indicates their surface exposure [15,16] and FLAG was placed in selected regions of VDAC and probed by immunoprecipitation (IP) [11][12][13]17]. …”

Voltage-dependent structural changes of the membrane-bound anion channel hVDAC1 probed by SEIRA and electrochemical impedance spectroscopy

“…6 Although this effect was studied extensively, the nature of the underlying conformational changes associated with channel closing is still elusive. 7,8 In 2008, three structures were published in three independent approaches, two for human VDAC1 (hVDAC1) 9,10 and one for murine VDAC (mVDAC), 11 and unveiled a unique structural architecture. VDAC is a b-barrel composed of an odd number of 19 b-strands leading to a parallel sheet pairing of strands b1-b19.…”