Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1

Abstract

The voltage-dependent anion channel (VDAC) mediates metabolite and ion flow across the outer mitochondrial membrane of all eukaryotic cells. The open channel passes millions of ATP molecules per second, while the closed state exhibits no detectable ATP flux. High-resolution structures of VDAC1 revealed a 19-stranded β-barrel with an α-helix partially occupying the central pore. To understand ATP permeation through VDAC, we solved the crystal structure of mouse VDAC1 (mVDAC1) in the presence of ATP, revealing a low-affinity binding site. Guided by these coordinates, we initiated hundreds of molecular dynamics (MD) simulations to construct a Markov State Model (MSM) of ATP permeation. These simulations indicate that ATP flows through VDAC using multiple pathways, consistent with our structural data and experimentally determined physiological rates.

The N-terminus of VDAC: Structure, mutational analysis, and a potential role in regulating barrel shape

“…suggesting that not all of the VDAC molecules in the crystal contained ATP or that ATP was positioned differently in a significant number of VDAC molecules in the crystal, reinforcing a model of transient interaction [72].…”

“…18 and absence of ATP are nearly identical ( [18], [72]); ATP is positioned in the centre of the pore, interacting with K12 and K20 in the N-terminus and a structural water coordinated by K256 and E280 in the side of the barrel (Fig. 4).…”

“…The photoreactive ATP analogue, benzoyl/benzyol-ATP can be crosslinked to three sites in rVDAC1, including the tryptic peptide encompassing residues 12-28 [70]; replacement of K20 by serine greatly decreases this cross-linking [71], suggesting at least transient interactions between ATP and the N-terminus. With the availability of the detailed solution structures of hVDAC1 as well as crystal structures of mVDAC1 with and without ATP bound to the interior of the pore ( [18], [72]), a more detailed picture of nucleotide interactions emerges. NMR was used to study the interactions of ATP with VDAC and site-specific variants [56].…”

“…The molecule of ATP is in the lumen; atoms are coloured as follows: carbon (black), nitrogen (blue), oxygen (red), and phosphorous (yellow). Based on the data presented in references [56] and [72].…”

Motifs of VDAC2 required for mitochondrial Bak import and tBid-induced apoptosis

“…The α-helix is highly flexible and is likely to be associated with VDAC channeling activity for the transfer of metabolites like ATP (40,41). The literature about the orientation of the VDACs is divergent; however, a recent work by De Pinto and coworkers (42) shows that the C terminus faces the intermembrane space.…”