Lipid-Assisted Membrane Protein Folding and Topogenesis

Abstract

Due to the heterogenous lipid environment in which integral membrane proteins are embedded, they should follow a set of assembly rules, which govern transmembrane protein folding and topogenesis accordingly to a given lipid profile. Recombinant strains of bacteria have been engineered to have different membrane phospholipid compositions by molecular genetic manipulation of endogenous and foreign genes encoding lipid biosynthetic enzymes. Such strains provide a means to investigate the in vivo role of lipids in many different aspects of membrane function, folding and biogenesis. In vitro and in vivo studies established a function of lipids as molecular chaperones and topological determinants specifically assisting folding and topogenesis of membrane proteins. These results led to the extension of the Positive Inside Rule to Charge Balance Rule, which incorporates a role for lipid-protein interactions in determining membrane protein topological organization at the time of initial membrane insertion and dynamically after initial assembly. Membrane protein topogenesis appears to be a thermodynamically driven process in which lipid-protein interactions affect the potency of charged amino acid residues as topological signals. Dual topology for a membrane protein can be established during initial assembly where folding intermediates in multiple topological conformations are in rapid equilibrium (thus separated by a low activation energy), which is determined by the lipid environment. Postassembly changes in lipid composition or post-translational modifications can trigger a reorganization of protein topology by inducing destabilization and refolding of a membrane protein. The lipid-dependent dynamic nature of membrane protein organization provides a novel means of regulating protein function.

Fungal Ice2p is in the same superfamily as SERINCs, restriction factors for HIV and other viruses

“…Therefore, the loop can only access lipid droplets in vivo if two or more TMHs change topology reversibly. Such changes have been reported for bacterial permeases and transporters, and they have been predicted in eukaryotes (Dowhan et al, 2019), with a few examples reported, though not yet studied in detail (Herate et al, 2016;Zhang et al, 2014).…”

Importance of phosphorylation/dephosphorylation cycles on lipid-dependent modulation of membrane protein topology by posttranslational phosphorylation

“…Studies of the structure and function of several bacterial secondary transporters have established that orientation of a membrane protein TMD in a lipid bilayer depends on the net positive charge of EMDs facing the cytoplasm and the net negative charge density of the membrane surface, determined by anionic phospholipid content (42,49,50). We established that lipid-dependent membrane protein organization is dynamic during and after membrane protein assembly in vivo and independent of other cellular factors in vitro (28,(51)(52)(53).…”

The lipid-dependent structure and function of LacY can be recapitulated and analyzed in phospholipid-containing detergent micelles

“…Structural studies on LacY and many membrane proteins support the Positive Inside Rule 59 , which is based on the statistical and experimentally determined observation that the majority of membrane protein EMDs facing the cytoplasm have a net positive charge while those facing the trans side are negative or neutral thus defining the orientation of TMDs residing in the lipid bilayer. Extensive studies on the effect of lipid environment on the structure and function of LacY, as well as several other secondary transporters, in cell membranes and proteoliposomes has established lipid-protein interactions as a defining parameter in determining membrane protein structure and function 60–62 . These studies have extended the Positive Inside Rule to the Charge Balance Rule, which incorporates the effect of charge interactions between membrane lipid head groups and EMDs of proteins in establishing TMD orientation in the lipid bilayer 36,61 .…”

“…The ratio of two membrane protein topological conformers can be adjusted as a continuum between two extremes by altering the net charge of EMDs or changing the ratio of net neutral to anionic phospholipids 34,40 . Thus, the Charge Balance Rule provides the basis for proteins that display multiple topologies or change their topological organization in response to changes in their lipid environment or post-translational modification 60 . In order to further our understanding of how lipid-protein interactions govern protein structure, high-resolution structures of membrane proteins as a function of lipid environment must be obtained.…”