The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating

• Published in: Journal of the American Chemical Society 2022-08, Vol.144 (32), p.14564-14577
• Main Authors: Ngo, Van A., Queralt-Martín, María, Khan, Farha, Bergdoll, Lucie, Abramson, Jeff, Bezrukov, Sergey M., Rostovtseva, Tatiana K., Hoogerheide, David P., Noskov, Sergei Yu
• Format: Article
• Language: English
• Subjects: ATOMIC AND MOLECULAR PHYSICS; BASIC BIOLOGICAL SCIENCES; Biochemistry, Molecular Biology; Biophysics; Brownian Dynamics; Life Sciences; MD simulations; single-channel electrophysiology; voltage gating; x-ray crystallography
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.2c03316

The voltage-dependent anion channel (VDAC) is a β-barrel channel of the mitochondrial outer membrane (MOM) that passively transports ions, metabolites, polypeptides, and single-stranded DNA. VDAC responds to a transmembrane potential by “gating,” i.e. transitioning to one of a variety of low-conducting states of unknown structure. The gated state results in nearly complete suppression of multivalent mitochondrial metabolite (such as ATP and ADP) transport, while enhancing calcium transport. Voltage gating is a universal property of β-barrel channels, but VDAC gating is anomalously sensitive to transmembrane potential. Here, we show that a single residue in the pore interior, K12, is responsible for most of VDAC’s voltage sensitivity. Using the analysis of over 40 μs of atomistic molecular dynamics (MD) simulations, we explore correlations between motions of charged residues inside the VDAC pore and geometric deformations of the β-barrel. Residue K12 is bistable; its motions between two widely separated positions along the pore axis enhance the fluctuations of the β-barrel and augment the likelihood of gating. Single channel electrophysiology of various K12 mutants reveals a dramatic reduction of the voltage-induced gating transitions. The crystal structure of the K12E mutant at a resolution of 2.6 Å indicates a similar architecture of the K12E mutant to the wild type; however, 60 μs of atomistic MD simulations using the K12E mutant show restricted motion of residue 12, due to enhanced connectivity with neighboring residues, and diminished amplitude of barrel motions. We conclude that β-barrel fluctuations, governed particularly by residue K12, drive VDAC gating transitions.