Abstract Background A major challenge for lipidomic analyses is the handling of large amounts data and translation results to interpret involvement lipids in biological systems. Results We built a new lipid ontology (LION) that associates >50,000 species biophysical, chemical, cell features. By making use enrichment algorithms, we used LION develop web-based interface (LION/web, www.lipidontology.com) allows identification lipid-associated terms lipidomes. LION/web was validated by...

Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is lateral diffusion proteins slow. These findings suggest degree lipid order, which raises question how function in such an environment. yeast PM segregated into Micro-Compartment-of-Can1 (MCC) Pma1 (MCP), have different compositions. We extracted from these microdomains via stoichiometric capture lipids styrene-maleic-acid-lipid-particles (SMALPs). purified...

Membrane lipids play critical roles in the structure and function of membrane-embedded transporters. Salmonella typhimurium MelB (MelBSt) is a symporter coupling melibiose translocation with cation (Na+, Li+, or H+). We present an extensive study on effects specific phospholipids MelBSt transport catalyzed by this protein.Lipidomic analysis thin-layer chromatography (TLC) experiments reveal that at least one phosphatidylethanolamine (PE) phosphatidylglycerol (PG) molecule associate high...

Abstract Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist an integral membrane unit, S-component, a tripartite ECF module. It has been proposed that S-component mediates substrate transport by toppling over when docking onto Here, we present multi-scale molecular dynamics simulations vitro experiments to study mechanism folate-specific transporter. Simulations reveal strong bending around module provides driving...

Abstract Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that S-component topples within membrane to alternately expose binding site either side membrane. In ECF transporters, substrate-free can be expelled from module. Here we study this enigmatic expulsion step by cryogenic electron microscopy reveal ATP induces...

E. coli has three Cls-isoenzymes for cardiolipin (CL) synthesis but the differences between these enzymes remain unresolved. All Cls contain phospholipase D (PLD) characteristic HKD motive and synthesize CL using PLD activity. Here, LC-MS we show effect of overexpressing or deletion individual on lipidome, which included changes in lipid class distribution species profiles. We demonstrate, first time, that overexpression only ClsB resulted appreciable a variety phosphatidylalcohols, thereby...

High-throughput screening of biologically active substances in cell cultures remains challenging despite great progress contemporary lipidomic techniques. These experiments generate large amounts data that are translated into lipid fingerprints. The subsequent visualization changes is key to meaningful interpretation experimental results. As a demonstration rapid and versatile pipeline for analysis, we cultured HeLa cells 96-well format four days the presence or absence various inhibitors...

Membrane lipids act as solvents and functional cofactors for integral membrane proteins. The yeast plasma is unusual in that it may have a high lipid order, which coincides with low passive permeability small molecules slow lateral diffusion of Yet, proteins whose functions require altered conformation must flexibility within membranes. We determined the molecular composition located defined diameter model proteins, including APC-superfamily lysine transporter Lyp1. now use naturally...

Chemical probes that covalently modify proteins of interest are powerful tools for the research biological processes. Important in design a probe is choice reactive group forms covalent bond, as it decides success probe. However, choosing right not simple feat and methodologies expedient screening different groups needed. We herein report modular approach allows easy coupling to ligand. α-Nucleophile ligands combined with 2-formylphenylboronic acid derived form iminoboronate selectively...

SUMMARY A major challenge for lipidomic analyses is the handling of large amounts data and translation results to interpret involvement lipids in biological systems. We built a new lipid ontology (LION) that associates over 50,000 species biophysical, chemical cell features. By making use enrichment algorithms, we used LION develop web-based interface (LION/web, www.lipidontology.com ) allows identification lipid-associated terms lipidomes. LION/web was validated by analyzing dataset derived...

The versatile compound n-butanol is one of the most promising biofuels for use in existing internal combustion engines, contributing to a smooth transition towards clean energy society. Furthermore, valuable resource produce more complex molecules such as bioplastics. Microbial production from waste materials hampered by biotoxicity it interferes with proper functioning lipid membranes. In this study we perform large-scale investigation complete lipid-related enzyme machinery and its...

Reversible bioorthogonal conjugation reactions have been exploited in the chemoproteomic field to prepare protein labeling reagents and visualize labeled proteins. We recently demonstrated that reversible iminoboronates can be used probes from fragment libraries linkage subsequently detect In this study, we determined effect of stability iminoboronate on efficiency protocol. Our study reveals should stable enough allow for efficient targeting, but labile protein. Acyl hydrazides were...

Abstract The yeast plasma membrane is segregated into domains: the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP) have a different protein composition, but their lipid composition largely unknown. We extracted proteins residing in these microdomains via stoichiometric capture of lipids styrene-maleic-acid-lipid-particles (SMALPs). purified SMALPs by affinity chromatography quantitatively analyzed mass spectrometry role transporter function. found that phospholipid sterol concentrations are...

Abstract Membrane lipids act as solvents and functional cofactors for integral membrane proteins. The yeast plasma is unusual in that it may have a high lipid order, which coincides with low passive permeability small molecules slow lateral diffusion of Yet, proteins whose functions require altered conformation must flexibility within membranes. We determined the molecular composition located defined diameter model proteins, including APC-superfamily lysine transporter Lyp1. now use...

Abstract Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is lateral diffusion proteins slow. These findings suggest degree lipid order, which raises question how function in such an environment. yeast PM segregated into Micro-Compartment-of-Can1 (MCC) Pma1 (MCP), have different compositions. We extracted from these microdomains via stoichiometric capture lipids styrene-maleic-acid-lipid-particles (SMALPs). purified...