The Apolipoprotein E N-Terminal Bundle Rendered Membrane-Compatible by Reverse-QTY Conversion Without Loss of Fold

Apolipoprotein E (ApoE) primarily operates at lipid interfaces, but designers often focus on its receptor interaction, structural geometry, or abundance instead of the N-terminal bundle's affinity for lipids. Researchers explored whether the reverse-QTY (rQTY) code could make this bundle compatible with membranes without altering its structure.

Within residues 11-167, every glutamine, threonine, and tyrosine within an alpha-helix were converted to leucine, valine, and phenylalanine, respectively, leaving turns and loops unchanged. This resulted in 22 substitutions, accounting for 14.0% of the segment, while preserving the receptor recognition region. The average hydrophobicity increased from -0.757 to +0.123.

When compared to five AlphaFold3 models of the native sequence, the rQTY variant bundle superimposed at a mean C-alpha root-mean-square deviation of 0.81 Å, maintaining helix content and increasing apolar solvent-accessible surface area by 59% while keeping total surface and burial constant. The hydrophobic moment also rose in five of six helical segments, preserving amphipathicity.

In molecular dynamics simulations, the native segment retained its structure in water over 100 ns, while the rQTY variant stayed folded and largely helical in a six-component neuronal bilayer for 6 seconds and a highly mobile membrane mimetic for 9 seconds, thinning the bilayer by 10.9 Å. The lipid shell remained only slightly biased, and the two membrane models disagreed.

However, determining binding affinity would require matched native trajectories and partitioning free-energy calculations. Thus, rQTY serves as a geometry-preserving, residue-resolved control for the surface chemistry of a soluble helical bundle.