While it is known that lipids play an essential role in regulating membrane protein structure and function, it remains challenging to identify specific protein-lipid interactions. Here, we present an innovative...

No abstract

Lipids play critical roles in modulating membrane protein structure, interactions, and activity. Nanodiscs provide a tunable membrane mimetic that can model these endogenous protein-lipid interactions in a nanoscale lipid bilayer. However, most studies of membrane proteins with nanodiscs use simple synthetic lipids that lack the head group and fatty acyl diversity of natural extracts. Prior research has successfully used natural lipid extracts in nanodiscs that more accurately mimic natural environments, but it is not clear how nanodisc assembly may bias the incorporated lipid profiles. Here, we applied lipidomics to investigate how nanodisc assembly conditions affect the profile of natural lipids in nanodiscs. Specifically, we tested the effects of assembly temperature, nanodisc size, and lipidome extract complexity. Globally, our analysis demonstrates that the lipids profiles are largely unaffected by nanodisc assembly conditions. However, a few notable changes emerged within individual lipids and lipid classes, such as a differential incorporation of cardiolipin and phosphatidylglycerol lipids from the E. coli polar lipid extract at different temperatures. Conversely, some classes of brain lipids were affected by nanodisc size at higher temperatures. Collectively, these data enable the application of nano-discs to study protein-lipid interactions in complex lipid environments.

Lipidomic analyses using mass spectrometry have traditionally been complicated by an abundance of isomeric species. The recent emergence of experimental platforms allowing for isomer separation has significantly benefitted lipidomic studies by allowing further speciation and the acquisition of species-specific information. Data interpretation for this detailed information, however, still faces challenges as existing lipid pathways are often defined such that single nodes represent entire lipid classes and not individual species (e.g., pathways may indicate that phosphatidylcholines as a class are increasing). Therefore, most bioinformatic tools cannot assess comprehensively annotated lipid studies. To overcome this limitation, we developed a structural-based connectivity and omic phenotypic evaluation (SCOPE) cheminformatic data analysis toolbox to relate individual lipid species with their associated biological significance and clinical data. The caveat of this work thus far has however been its accessibility to users with limited coding experience. Thus, we have now developed an online graphical user interface (GUI) program removing all previous coding requirements called SCOPE Online. SCOPE Online offers lipidomic researchers the capability to explore trends of lipid perturbations through two steps. Initially, head group and fatty acyl composition are used to relate lipids by shared structural moieties through hierarchical clustering and parsing of groups. Once relationships between lipid structures have been established, summary statistics of fold change, p-value and other metrics can then be overlaid to probe biological trends. To facilitate user annotation, a series of customizable features including color gradient, line thickness, and figure annotations are also possible within the SCOPE Online platform. Altogether, our SCOPE Online cheminformatics toolbox allows for the visualization of structural and phenotypic effects on the biology of individual species that has been made more accessible by the development of a GUI platform for lipidomic data visualization. Example data and SCOPE Online utilities will be showcased in this presentation.