Hydrophobic Mismatch Modulates Stability and Plasticity of Human Mitochondrial VDAC2

Abstract

The human mitochondrial outer membrane protein voltage-dependent anion channel isoform 2 (hVDAC2) is a β-barrel metabolite flux channel that is indispensable for cell survival. It is well established that physical forces imposed on a transmembrane protein by its surrounding lipid environment decide protein structure and stability. Yet, how the mitochondrial membrane and protein-lipid interplay together regulate hVDAC2 stability is unknown. Here, we combine experimental biophysical investigations of protein stability with all-atom molecular dynamics simulations to study the effect of the most abundant mitochondrial phosphocholine (PC) lipids on hVDAC2. We demonstrate experimentally that increasing the PC lipid acyl chain length from diC14:0 to diC18:0-PC has a nonlinear effect on the β-barrel. We show that protein stability is highest in diC16:0-PC, which exhibits a negative mismatch with the hVDAC2 barrel. Our simulations also reveal that structural rigidity of hVDAC2 is highest under optimal negative mismatch provided by diC16:0-PC bilayers. Further, we validate our observations by altering the physical properties of PC membranes indirectly using cholesterol. We propose that VDAC plasticity and stability in the mitochondrial outer membrane are modulated by physical properties of the bilayer.

Evolutionary selection of a 19-stranded mitochondrial β-barrel scaffold bears structural and functional significance

“…hV2 WT is highly aggregation-prone, and misfolding results in the formation of visible aggregates within minutes of initiating the folding process. We have observed previously that hV2 WT is stabilized under conditions of bilayer mismatch ( 32 ). Therefore, we examined the influence of the lipidic environment on the stability of hV2 WT and the engineered barrels using temperature-mediated barrel unfolding in PC and doped PC–PG and PC–PE membranes.…”

“…2 A and Figs. S2 and S3 ) ( 32 , 34 ). They provide two important parameters, namely (i) T m , which is the midpoint temperature wherein half the population is unfolded ( Fig.…”

“…1 were expressed tag-less as inclusion bodies in Escherichia coli BL21(DE3) cells and purified by anion exchange chromatography ( Fig. S1 ), as explained in previous reports ( 32 , 37 ).…”

A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology

“…S2 B), which could lead to a different lipid bilayer organization in proximity of the β-barrels of the two isoforms. Indeed, it has been shown previously that VDAC and other transmembrane proteins can distort the lipid bilayer through mechanisms such as lipid–protein interactions, hydrophobic mismatch, or lipid perturbation and sorting (O’Keeffe et al, 2000; Ellena et al, 2011; Eddy et al, 2012; Yin and Kindt, 2012; Duneau et al, 2017; Srivastava et al, 2018). In addition, a specific interaction between channel loops and PE headgroups has been proposed for plant VDAC (Mlayeh et al, 2017).…”

Membrane lipid requirements of the lysine transporter Lyp1 fromSaccharomyces cerevisiae

“…The length of the lipids should approximately match the hydrophobic region of the protein, and the polar headgroups of the lipids can interact with the hydrophilic regions of the membrane protein(2). These parameters are referred to as hydrophobic-hydrophilic matching of proteins and lipids(3), which has been shown to affect the activity and or stability of membrane proteins(4–6). The degree of saturation of acyl chains influence the packing of lipids and thus the fluidity of the bilayer.…”