High-resolution cryo-EM structures of a protein pore reveal diverse roles of membrane lipids

Abstract

The structure and function of membrane proteins depend on their interactions with the lipid molecules that constitute lipid membranes. Actinoporins are a family of -pore-forming proteins that bind specifically to sphingomyelin-containing lipid membranes, where they oligomerize and form transmembrane pores. The numerous contacts they form with the lipid membrane make them an exemplary object for studying the different roles that lipids play in the structure and function of membrane proteins. Through a comprehensive cryo-electron microscopic analysis of a pore formed by an actinoporin Fav from the coral Orbicella faveolata, we show that the octameric pore interacts with 112 lipids in the upper leaflet of the membrane. The structures of Fav pores formed on different lipid membranes reveal the different roles of lipids and demonstrate that the actinoporin surface is perfectly suited for binding multiple receptor sphingomyelin molecules. When cholesterol is present in the membrane, it forms nanodomains associated with the pore, leading to a tighter arrangement of lipids, which in turn increases the stability of the pores. Atomistic simulations support the structural data, show that the protein-bound lipids are not mobile, and reveal additional effects of the pore on the lipid membrane. Overall, these data reveal a complex network of protein-lipid and lipid-lipid interactions, and an underrated role of lipids in the structure and function of transmembrane protein complexes.