High-Throughput Characterization of Trends in Transmembrane Helix Partitioning into Membrane Domains

The plasma membrane is a laterally heterogeneous environment in which lipid organization plays a central role in regulating protein function. In model systems, this heterogeneity is often described in terms of coexisting liquid-ordered (Lo) and liquid-disordered (Ld) phases, commonly associated with the lipid raft concept. Despite extensive experimental and computational efforts, the molecular determinants governing protein partitioning between these domains remain poorly understood, largely due to the limited number of systems studied. Here, we address this challenge using a high-throughput computational approach, systematically analyzing the partitioning behavior of almost 5,000 helical transmembrane peptides in phase-separating lipid membranes. Across all simulations, we find that none of the peptides exhibit a clear preference for the Lo phase, while the vast majority partition into the Ld phase. This observation is consistent with experimental results in simplified membrane systems and suggests that commonly used ternary lipid mixtures may not fully capture the physicochemical environment governing protein sorting in biological membranes. In addition, we identify a subset of peptides that preferentially localize at the Lo/Ld interface. These interfacial peptides display distinct sequence characteristics, indicating that boundary localization is governed by specific combinations of residue composition and spatial arrangement rather than a single dominant feature. Overall, our results reveal that transmembrane helix partitioning in model membranes is dominated by a preference for disordered environments, with interfacial localization emerging as a distinct and potentially functional behavior.