Prediction and characterization of lipid-interacting proteins

Lipids are essential to all life forms. These molecules serve diverse purposes that range from cell membrane formation to energy storage and inter-cellular signaling. Lipids can be natively synthesized or sourced from the environment, often through the action of proteins engaging with specific lipid molecules. Characterizing lipid-interacting proteins is a key frontier in therapeutic science, as dysfunction in lipid metabolism is implicated in a range of human diseases. A substantial bottleneck that precludes the identification and characterization of lipid-interacting proteins pertains to the nature of the lipid substrates: they are not genetically encoded, their hydrophobic nature results in non-specific interactions, they exist in complex cellular environments, and they are structurally diverse. Regardless, the identification, characterization, and specific targeting of proteins that maintain proper lipid homeostasis is important for efforts to restore dysregulated metabolism. In this chapter, we outline bioinformatic and experimental approaches employed by our research group and others to study lipids and the proteins that directly bind them. The chapter covers methods for proteome-wide computational screening to reveal lipid binding proteins, characterization of total lipid composition in mammalian and bacterial cells, and the use of analytical and biophysical methods to study target protein-lipid interactions.