Control of human VDAC-2 scaffold dynamics by interfacial tryptophans is position specific

•Aromatic belt of membrane proteins has key stabilization role.•Human voltage-dependent anion channel isoform-2 (hVDAC-2) has four interfacial indoles.•Tryptophans act in concert to drive folding and stabilization of the barrel.•The 86th position shows preference for phenylalanine due to its buried environment.•Strands β10-14 promote barrel folding and stabilize hVDAC-2.

Membrane proteins employ specific distribution patterns of amino acids in their tertiary structure for adaptation to their unique bilayer environment. The solvent-bilayer interface, in particular, displays the characteristic 'aromatic belt' that defines the transmembrane region of the protein, and satisfies the amphipathic interfacial environment. Tryptophan-the key residue of this aromatic belt-is known to influence the folding efficiency and stability of a large number of well-studied α-helical and β-barrel membrane proteins. Here, we have used functional and biophysical techniques coupled with simulations, to decipher the contribution of strategically placed four intrinsic tryptophans of the human outer mitochondrial membrane protein, voltage-dependent anion channel isoform-2 (VDAC-2). We show that tryptophans help in maintaining the structural and functional integrity of folded hVDAC-2 barrel in micellar environments. The voltage gating characteristics of hVDAC-2 are affected upon mutation of tryptophans at positions 75, 86 and 221. We observe that Trp-160 and Trp-221 play a crucial role in the folding pathway of the barrel, and once folded, Trp-221 helps stabilize the folded protein in concert with Trp-75 and Trp-160. We further demonstrate that substituting Trp-86 with phenylalanine leads to the formation of stable barrel. We find that the region comprising strand β4 (Trp-86) and β10-14 (Trp-160 and Trp-221) display slower and faster folding kinetics, respectively, providing insight into a possible directional folding of hVDAC-2 from the C-terminus to N-terminus. Our results show that residue selection in a protein during evolution is a balancing compromise between optimum stability, function, and regulating protein turnover inside the cell.

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