Lipids are distributed unevenly across the two leaflets of the plasma membrane. Phosphatidylserine is enriched on the inner leaflet by ATP driven flippases, and scramblases allow it to equilibrate to the outer leaflet, where it is recognised by clearance receptors. Methods for perturbing this asymmetry experimentally are limited to apoptosis induction, calcium ionophores and flippase knockout, each of which alters many cellular properties at once.
We observed this limitation in our own work. Deleting the flippase subunit TMEM30A in Jurkat and K562 cells produced constitutive phosphatidylserine exposure, faster lipid diffusion and reduced outer leaflet order, while inner leaflet order was unchanged (Gurdap et al., J Cell Sci 2026). The result is consistent with independent regulation of the two leaflets, though chronic knockout does not exclude compensatory adaptation, and we could not separate direct consequences of asymmetry loss from secondary ones.
This project uses computation to design a possible alternative perturbation: a peptide added extracellularly that inserts into the membrane and permits lipid exchange between leaflets on a short timescale. The approach builds on reported minimal peptide scramblases, in which a single polar residue at the centre of a transmembrane helix lowers the barrier for headgroup translocation without apparent pore formation, and on variants reported to insert from solution without genetic delivery. Reported activity varies with helix hydrophobic length, which has been interpreted as local bilayer thinning. These are published observations in model membranes; whether they transfer to cell membranes of physiological composition is untested, and establishing that is part of the proposal.
Three aims: First, molecular dynamics of active and inactive peptide variants in bilayers of defined composition. Second, design of minibinders against lymphocyte surface markers with RFdiffusion, ProteinMPNN and AlphaFold2, so the peptide acts only on marker positive cells. Third, redesign of the scrambling helix to separate lipid scrambling from membrane permeabilisation.
Computational predictions will be tested against measurements our group already performs, including single cell membrane order by spectral flow cytometry (Gurdap et al., Nat Nanotechnol 2026), lactadherin C2 for outer leaflet phosphatidylserine, NileRed HaloTag lifetime for inner leaflet order, scanning FCS for diffusion, and the matched wild type and TMEM30A knockout lines. The immediate test is whether an acute peptide perturbation reproduces the leaflet specific signature we measured under chronic flippase loss, or does not.
Main supervisor: Erdinc Sezgin, Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet.