Viral diseases constitute one of the major challenges in modern medicine. Membrane-targeting have broad-spectrum potential and could distinguish viral membranes from the host cell plasma membrane... Show moreViral diseases constitute one of the major challenges in modern medicine. Membrane-targeting have broad-spectrum potential and could distinguish viral membranes from the host cell plasma membrane by the difference in membrane curvature. In this thesis, we used a combination of molecular dynamics simulations and an evolutionary algorithm to inverse design such curvature-sensing antiviral peptides, purely from physical principles. Show less
Crone, N.S. A.; Hilten, N. van; Ham, A. van der; Risselada. H.J.; Kros, A.; Boyle, A.L. 2023
Heterogeneities (e.g., membrane proteins and lipid domains) and deformations (e.g., highly curved membrane regions) in biological lipid membranes cause lipid packing defects that may trigger... Show moreHeterogeneities (e.g., membrane proteins and lipid domains) and deformations (e.g., highly curved membrane regions) in biological lipid membranes cause lipid packing defects that may trigger functional sorting of lipids and membrane-associated proteins. To study these phenomena in a controlled and efficient way within molecular simulations, we developed an external field protocol that artificially enhances packing defects in lipid membranes by enforcing local thinning of a flat membrane region. For varying lipid compositions, we observed strong thinning-induced depletion or enrichment, depending on the lipid's intrinsic shape and its effect on a membrane's elastic modulus. In particular, polyunsaturated and lysolipids are strongly attracted to regions high in packing defects, whereas phosphatidylethanolamine (PE) lipids and cholesterol are strongly repelled from it. Our results indicate that externally imposed changes in membrane thickness, area, and curvature are underpinned by shared membrane elastic principles. The observed sorting toward the thinner membrane region is in line with the sorting expected for a positively curved membrane region. Furthermore, we have demonstrated that the amphipathic lipid packing sensor (ALPS) protein motif, a known curvature and packing defect sensor, is effectively attracted to thinner membrane regions. By extracting the force that drives amphipathic molecules toward the thinner region, our thinning protocol can directly quantify and score the lipid packing sensing of different amphipathic molecules. In this way, our protocol paves the way toward high-throughput exploration of potential defect- and curvature-sensing motifs, making it a valuable addition to the molecular simulation toolbox. Show less
