Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins

Abstract

Conserved lipid transfer proteins of the Ups/PRELI family regulate lipid accumulation in mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space. Here, we combine structural analysis, unbiased genetic approaches in yeast and molecular dynamics simulations to unravel determinants of lipid specificity within the conserved Ups/PRELI family. We present structures of human PRELID1-TRIAP1 and PRELID3b-TRIAP1 complexes, which exert lipid transfer activity for phosphatidic acid and phosphatidylserine, respectively. Reverse yeast genetic screens identify critical amino acid exchanges that broaden and swap their lipid specificities. We find that amino acids involved in head group recognition and the hydrophobicity of flexible loops regulate lipid entry into the binding cavity. Molecular dynamics simulations reveal different membrane orientations of PRELID1 and PRELID3b during the stepwise release of lipids. Our experiments thus define the structural determinants of lipid specificity and the dynamics of lipid interactions by Ups/ PRELI proteins.

Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

“…For instance, the fibroblast growth factor receptor 4 (FGFR4) gene is a transmembrane tyrosine kinase receptor that may play essential roles in the regulation of hepatic bile acid and lipid metabolism [ 53 ]. PRELID1 (PRELI Domain Containing 1), another gene located in the same region, is a protein-coding gene that regulates lipid accumulation in the mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space [ 54 ]. Other important genes within this window include HK3 (Hexokinase 3), which is crucial for glucose metabolism pathways and phosphorylates glucose to produce glucose-6-phosphate; the RGS14 (Regulator of G Protein Signaling 14) gene, which encodes a member of the regulator of G-protein signaling family and as a GTPase activating protein (GAP), it increases the rate of conversion of GTP to GDP; PDLIM7 (PDZ and LIM domain 7), which is known to regulate muscle development and function, and associates with—and localizes to—actin filaments in fibroblasts via its PDZ domain [ 55 ].…”

Structural and functional contributions of lipids to the stability and activity of the photosynthetic cytochrome b6f lipoprotein complex

“…The thylakoid lipids provide a bilayer matrix to support the proteolipid heterooligomeric complexes and, as a result of their hydrophobicity and low dielectric constant, facilitate generation of a transmembrane proton electrochemical gradient coupled to electron transport (3). In addition, the lipids function as essential structural components in the photosynthetic complexes, inferred from high-resolution crystal structures (4 -10) and MS analyses (11)(12)(13)(14)(15)(16). All four classes of lipids have been implicated in the biogenesis of the thylakoid membrane (3).…”

Molecular mechanism of mitochondrial phosphatidate transfer by Ups1

“…We discovered that residues W65 and F69 of the α2-loop would be inserted into the membrane alternately during PA transfer. Although Miliara et al suggested that the α3-helix and the Ω-loop (here, α2-loop) undergo subtle conformational changes, potentially contributing to phospholipid binding and release 26 and speculated that conformational differences in the Ω-loop (here, α2-loop) and α3helix between PRELID1 and PRELID3b are potentially important for lipid specificity 23 , no experimental data have supported this finding. Our disulfide-bridge experiments not only verified these conformational changes but also suggest a synergistic conformational change between the α2-loop and N-α3-helix.…”

“…Although numerous crystal structures of Ups1/Mdm35 (or its homologs) in different states have been reported 17 , 18 , 21 , 23 , the mechanism underlying PA transfer between mitochondrial membranes remains elusive. Here, we reported two new crystal structures of Ups1/Mdm35, performed all-atom simulations of Ups1-membane and Ups1/Mdm35-membrane, and various biochemical and biophysical experiments, revealing how Ups1/Mdm35 interacts with the membrane and potential conformational changes of Ups1 during PA transfer.…”

“…Furthermore, Mdm35 dissociation enhanced Ups1 binding to the membrane 17 . Crystal structures of human PRELID1-TRIAP1 and PRELID3b-TRIAP1 were resolved recently, and the structural determinants of lipid specificity were studied through yeast genetic screens and coarse-grain simulations 23 .…”