Open Access
Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC)
(Elsevier, 2016) Noskov, Sergei Y.; Rostovtseva, Tatiana K.; Chamberlin, Adam; Teijido Hermida, Óscar; Jiang, Wei; Bezrukov, Sergey M.; Ciencias de la Salud; Osasun Zientziak
Voltage-dependent anion channel (VDAC), the major channel of the mitochondrial outer membrane provides a controlled pathway for respiratory metabolites in and out of the mitochondria. In spite of the wealth of experimental data from structural, biochemical, and biophysical investigations, the exact mechanisms governing selective ion and metabolite transport, especially the role of titratable charged residues and interactions with soluble cytosolic proteins, remain hotly debated in the field. The computational advances hold a promise to provide a much sought-after solution to many of the scientific disputes around solute and ion transport through VDAC and hence, across the mitochondrial outer membrane. In this review, we examine how Molecular Dynamics, Free Energy, and Brownian Dynamics simulations of the large β-barrel channel, VDAC, advanced our understanding. We will provide a short overview of non-conventional techniques and also discuss examples of how the modeling excursions into VDAC biophysics prospectively aid experimental efforts.
Open Access
Lipid dynamics and protein-lipid interactions in 2D crystals formed with the beta-barrel integral membrane protein VDAC1
(American Chemical Society, 2012) Eddy, Matthew T.; Ong, Ta-Chung; Clark, Lindsay; Teijido Hermida, Óscar; Van der Wel, Patrick C. A.; Garces, Robert; Wagner, Gerhard; Rostovtseva, Tatiana K.; Griffin, Robert G.; Ciencias de la Salud; Osasun Zientziak
We employ a combination of 13C/15N magic angle spinning (MAS) NMR and 2H NMR to study the structural and functional consequences of different membrane environments on VDAC1 and, conversely, the effect of VDAC1 on the structure of the lipid bilayer. MAS spectra reveal a well-structured VDAC1 in 2D crystals of dimyristoylphosphatidylcholine (DMPC) and diphytanoylphosphatidylcholine (DPhPC), and their temperature dependence suggests that the VDAC structure does not change conformation above and below the lipid phase transition temperature. The same data show that the N-terminus remains structured at both low and high temperatures. Importantly, functional studies based on electrophysiological measurements on these same samples show fully functional channels, even without the presence of Triton X-100 that has been found necessary for in vitro-refolded channels. 2H solid-state NMR and differential scanning calorimetry were used to investigate the dynamics and phase behavior of the lipids within the VDAC1 2D crystals. 2H NMR spectra indicate that the presence of protein in DMPC results in a broad lipid phase transition that is shifted from 19 to -27 °C and show the existence of different lipid populations, consistent with the presence of both annular and bulk lipids in the functionally and structurally homogeneous samples.
Open Access
Magic angle spinning nuclear magnetic resonance characterization of voltage-dependent anion channel gating in two-dimensional lipid crystalline bilayers
(American Chemical Society, 2014-12-29) Eddy, Matthew T.; Andreas, Loren; Teijido Hermida, Óscar; Su, Yongchao; Clark, Lindsay; Noskov, Sergei Y.; Wagner, Gerhard; Rostovtseva, Tatiana K.; Griffin, Robert G.; Ciencias de la Salud; Osasun Zientziak
The N-terminus of the voltage-dependent anion channel (VDAC) has been proposed to contain the mechanistically important gating helices that modulate channel opening and closing. In this study, we utilize magic angle spinning nuclear magnetic resonance (MAS NMR) to determine the location and structure of the N-terminus for functional channels in lipid bilayers by measuring long-range 13C–13C distances between residues in the N-terminus and other domains of VDAC reconstituted into DMPC lipid bilayers. Our structural studies show that the distance between A14 Cβ in the N-terminal helix and S193 Cβ is ∼4–6 Å. Furthermore, VDAC phosphorylation by a mitochondrial kinase at residue S193 has been claimed to delay mitochondrial cell death by causing a conformational change that closes the channel, and a VDAC-Ser193Glu mutant has been reported to show properties very similar to those of phosphorylated VDAC in a cellular context. We expressed VDAC-S193E and reconstituted it into DMPC lipid bilayers. Two-dimensional 13C–13C correlation experiments showed chemical shift perturbations for residues located in the N-terminus, indicating possible structural perturbations to that region. However, electrophysiological data recorded on VDAC-S193E showed that channel characteristics were identical to those of wild type samples, indicating that phosphorylation of S193 does not directly affect channel gating. The combination of NMR and electrophysiological results allows us to discuss the validity of proposed gating models.
Open Access
Conductance hysteresis in the voltage-dependent anion channel
(Springer, 2015) Rappaport, Shay M.; Teijido Hermida, Óscar; Hoogerheide, David P.; Rostovtseva, Tatiana K.; Berezhkovskii, Alexander M.; Bezrukov, Sergey M.; Ciencias de la Salud; Osasun Zientziak
Open Access
Affixing N-terminal a-helix to the wall of the voltage-dependent anion channel does not prevent its voltage gating
(Elsevier, 2012-03-30) Teijido Hermida, Óscar; Ujwal, Rachna; Hillerdal, Carl-Olof; Kullman, Lisen; Rostovtseva, Tatiana K.; Abramson, Jeff; Ciencias de la Salud; Osasun Zientziak
The voltage-dependent anion channel (VDAC) governs the free exchange of ions and metabolites between the mitochondria and the rest of the cell. The three-dimensional structure of VDAC1 reveals a channel formed by 19 β-strands and an N-terminal α-helix located near the midpoint of the pore. The position of this α-helix causes a narrowing of the cavity, but ample space for metabolite passage remains. The participation of the N-terminus of VDAC1 in the voltage-gating process has been well established, but the molecular mechanism continues to be debated; however, the majority of models entail large conformational changes of this N-terminal segment. Here we report that the pore-lining N-terminal α-helix does not undergo independent structural rearrangements during channel gating. We engineered a double Cys mutant in murine VDAC1 that cross-links the α-helix to the wall of the β-barrel pore and reconstituted the modified protein into planar lipid bilayers. The modified murine VDAC1 exhibited typical voltage gating. These results suggest that the N-terminal α-helix is located inside the pore of VDAC in the open state and remains associated with β-strand 11 of the pore wall during voltage gating
Open Access
Acidification asymmetrically affects voltage-dependent anion channel implicating the involvement of salt bridges
(Elsevier, 2014-06-24) Teijido Hermida, Óscar; Rappaport, Shay M.; Chamberlin, Adam; Noskov, Sergei Y.; Aguilella, Vicente M.; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.; Ciencias de la Salud; Osasun Zientziak
The voltage-dependent anion channel (VDAC) is the major pathway for ATP, ADP, and other respiratory substrates through the mitochondrial outer membrane, constituting a crucial point of mitochondrial metabolism regulation. VDAC is characterized by its ability to 'gate' between an open and several 'closed' states under applied voltage. In the early stages of tumorigenesis or during ischemia, partial or total absence of oxygen supply to cells results in cytosolic acidification. Motivated by these facts, we investigated the effects of pH variations on VDAC gating properties. We reconstituted VDAC into planar lipid membranes and found that acidification reversibly increases its voltage-dependent gating. Furthermore, both VDAC anion selectivity and single channel conductance increased with acidification, in agreement with the titration of the negatively charged VDAC residues at low pH values. Analysis of the pH dependences of the gating and open channel parameters yielded similar pKa values close to 4.0. We also found that the response of VDAC gating to acidification was highly asymmetric. The presumably cytosolic (cis) side of the channel was the most sensitive to acidification, whereas the mitochondrial intermembrane space (trans) side barely responded to pH changes. Molecular dynamic simulations suggested that stable salt bridges at the cis side, which are susceptible to disruption upon acidification, contribute to this asymmetry. The pronounced sensitivity of the cis side to pH variations found here in vitro might provide helpful insights into the regulatory role of VDAC in the protective effect of cytosolic acidification during ischemia in vivo.
Open Access
A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology
(Rockefeller University Press, 2020-01-14) Queralt-Martín, María; Bergdoll, Lucie; Teijido Hermida, Óscar; Munshi, Nabill; Jacobs, Daniel; Kuszak, Adam J.; Protchenko, Olga; Reina, Simona; Magrì, Andrea; De Pinto, Vito; Bezrukov, Sergey M.; Abramson, Jeff; Rostovtseva, Tatiana K.; Ciencias de la Salud; Osasun Zientziak
Voltage-dependent anion channel (VDAC) is the major pathway for the transport of ions and metabolites across the mitochondrial outer membrane. Among the three known mammalian VDAC isoforms, VDAC3 is the least characterized, but unique functional roles have been proposed in cellular and animal models. Yet, a high-sequence similarity between VDAC1 and VDAC3 is indicative of a similar pore-forming structure. Here, we conclusively show that VDAC3 forms stable, highly conductive voltage-gated channels that, much like VDAC1, are weakly anion selective and facilitate metabolite exchange, but exhibit unique properties when interacting with the cytosolic proteins α-synuclein and tubulin. These two proteins are knowntobepotent regulators of VDAC1 andinduce similar characteristic blockages (on the millisecond time scale) of VDAC3, but with 10- to 100-fold reduced on-rates and altered α-synuclein blocking times, indicative of an isoform-specific function. Through cysteine scanning mutagenesis, we found that VDAC3’s cysteine residues regulate its interaction with α-synuclein, demonstrating VDAC3-unique functional properties and further highlighting a general molecular mechanism for VDAC isoform-specific regulation of mitochondrial bioenergetics.
Open Access
Reply to Thinnes: to include plasmalemmal VDAC/porin pays
(American Society for Biochemistry and Molecular Biology, 2012-02-06) Teijido Hermida, Óscar; Ujwal, Rachna; Hillerdal, Carl-Olof; Kullman, Lisen; Rostovtseva, Tatiana K.; Abramson, Jeff; Ciencias de la Salud; Osasun Zientziak
Our study was focused entirely on the properties of VDAC from the mitochondrial outer membrane; therefore, discussion of possible VDAC N-terminal exposure on the plasma membrane surface is totally irrelevant to this work. Our experiments did not aim to test the position of the VDAC1Nterminus in the channel¿s closed conformation. We cannot rule out the possibility that, when closed, the first amino acids of the VDAC N terminus could be exposed at the channel entrance, but these speculations are beyond our present study.