A computational study of ion current modulation in hVDAC3 induced by disulfide bonds

GUARDIANI, CARLO;Leggio, L;SCORCIAPINO, MARIANO ANDREA;De Pinto, V;CECCARELLI, MATTEO

2016-01-01

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Abstract

The human VDAC channel exists in three isoforms characterized by high sequence homology and structural sim- ilarity. Yet the function and mode of action of hVDAC3 are still elusive. The presence of six surface cysteines ex- posed to the oxidizing environment of the mitochondrial inter-membrane space suggests the possible establishment of intramolecular disulfide bonds. Two natural candidates for disulfide bridge formation are Cys2 and Cys8 that, located on the flexible N-terminal domain, can easily come in contact. A third potentially im- portant residue is Cys122 that is close to Cys2 in the homology model of VDAC3. Here we analyzed the impact of SS bonds through molecular dynamics simulations of derivatives of hVDAC3 (dubbed SS-2-8, SS-2-122, SS-8- 122) including a single disulfide bond. Simulations showed that in SS-8-122, the fragment 1-7 crosses the top part of the barrel partially occluding the pore and causing a 20% drop of conductance. In order to identify other potential channel-occluding disulfide bonds, we used a set of neural networks and structural bioinformatics al- gorithms, after filtering with the steric constraints imposed by the 3D-structure. We identified other three spe- cies, namely SS-8-65, SS-2-36 and SS-8-36. While the conductance of SS-8-65 and SS-2-36 is about 30% lower than that of the species without disulfide bonds, the conductance of SS-8-36 was 40–50% lower. The results show how VDAC3 is able to modulate its pore size and current by exploiting the mobility of the N-terminal and forming, upon external stimuli, disulfide bridges with cysteine residues located on the barrel and exposed to the inter-membrane space.