Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1

Abstract

The voltage-dependent anion channel 1 (VDAC-1) is an important protein of the outer mitochondrial membrane that transports energy metabolites and is involved in apoptosis. The available structures of VDAC proteins show a wide β-stranded barrel pore, with its N-terminal α-helix (N-α) bound to its interior. Electrophysiology experiments revealed that voltage, its polarity, and membrane composition modulate VDAC currents. Experiments with VDAC-1 mutants identified amino acids that regulate the gating process. However, the mechanisms for how these factors regulate VDAC-1, and which changes they trigger in the channel, are still unknown. In this study, molecular dynamics simulations and single-channel experiments of VDAC-1 show agreement for the current-voltage relationships of an "open" channel and they also show several subconducting transient states that are more cation selective in the simulations. We observed voltage-dependent asymmetric distortions of the VDAC-1 barrel and the displacement of particular charged amino acids. We constructed conformational models of the protein voltage response and the pore changes that consistently explain the protein conformations observed at opposite voltage polarities, either in phosphatidylethanolamine or phosphatidylcholine membranes. The submicrosecond VDAC-1 voltage response shows intrinsic structural changes that explain the role of key gating amino acids and support some of the current gating hypotheses. These voltage-dependent protein changes include asymmetric barrel distortion, its interaction with the membrane, and significant displacement of N-α amino acids.

Phosphorylation of purified mitochondrial Voltage-Dependent Anion Channel by c-Jun N-terminal Kinase-3 modifies channel voltage-dependence

“…For molecular interpretation of the different electrophysiological behavior of the JNK3 phosphorylated VDAC we referred to the structure of rat VDAC-1. Structure of VDAC consists of a flexible N-terminal α-helix attached to the 19 β-strands which forms its cylindrical lumen [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] . VDAC is believed to possess a single voltage sensor with net positive charge and its lumen is also overall positively charged.…”

The N-Terminal Segment of the Voltage-Dependent Anion Channel: A Possible Membrane-Bound Intermediate in Pore Unbinding

“…A second ambiguity affects VDAC dimerization, with some evidence suggesting that the NTS leaves the pore lumen and mutual interaction of these segments in the cytoplasmic region facilitates dimerization [19], while the contrary (i.e., insignificance of the NTS for VDAC association) has also been suggested [20]. Third, it is not clear whether the NTS is involved in voltage gating [5,21], and, if yes, how. Again, the NTS may be mobile [1,4] or stay within the pore lumen [3,17,22].…”

“…Previous molecular dynamics (MD) studies of VDAC have focused on the voltage dependence of the pore conformation and selectivity [21], ATP transport through the pore [26], and the effect of mutation of E73 on pore dynamics [27] or of deletion of the NTS on pore conformation [23]. Up to now, no MD studies have been performed on the dissociation of the NTS from the VDAC pore.…”

Folded Structure and Membrane Affinity of the N-Terminal Domain of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion-Selective Channel

“… 26 − 28 However, simulations were not able to show the closed state. 29 , 30 The N-terminal domain of VDAC is proposed to modulate the two states but, unless specific conditions are applied, the “closed” states are transiently and rather infrequently visited, with their structural nature still unclear. 30 …”