Data from: Bioinspired design rules for flipping across the lipid bilayer from systematic simulations of membrane protein segments

The orientation of integral membrane proteins (IMPs) with respect to the
membrane is established during protein synthesis and insertion into the
membrane. After synthesis, IMP orientation is thought to be fixed due to
the thermodynamic barrier for “flipping” protein loops or helices across
the hydrophobic core of the membrane in a process analogous to lipid
flip-flop. A notable exception is EmrE, a homodimeric IMP with an
N-terminal transmembrane helix that can flip across the membrane until
flipping is arrested upon dimerization. Understanding the features of the
EmrE sequence that permit this unusual flipping behavior would be valuable
for guiding the design of synthetic materials capable of translocating or
flipping charged groups across lipid membranes. To elucidate the molecular
mechanisms underlying flipping in EmrE and derive bioinspired design
rules, we employ atomistic molecular dynamics simulations and enhanced
sampling techniques to systematically investigate the flipping of
truncated segments of EmrE. Our results demonstrate that a
membrane-exposed charged glutamate residue at the center of the N-terminal
helix lowers the energetic barrier for flipping (from ~12.1 kcal mol-1 to
~5.4 kcal mol-1) by stabilizing water defects and minimizing membrane
perturbation. Comparative analysis reveals that the marginal
hydrophobicity of this helix, rather than the marginal hydrophilicity of
its loop, is the key determinant of flipping propensity. Our results
further indicate that interhelical hydrogen bonding upon dimerization
inhibits flipping. These findings establish several bioinspired design
principles to govern flipping in related materials: (1) marginally
hydrophobic helices with membrane-exposed charged groups promote flipping,
(2) modulating protonation states of membrane-exposed groups tunes
flipping efficiency, and (3) interhelical hydrogen bonding can be
leveraged to arrest flipping. These insights provide a foundation for
engineering synthetic peptides, engineered proteins, and biomimetic
nanomaterials with controlled flipping or translocation behavior for
applications in intracellular drug delivery and membrane protein design.