Defining the Paralipidome: A New Frontier in Membrane Biology

About This Grant

Many critical cellular functions depend on the collective actions of proteins and lipids in membranes. Since the inception of the fluid mosaic model, the organization and function of the lipids surrounding individual membrane proteins has been hotly debated. The past 40 years have uncovered structures of many isolated membrane proteins, revealing many cases of regulation by lipids, which can serve as cofactors, ligands, and allosteric modulators. Lipids can also regulate proteins through collective membrane properties like tension, fluidity, and domains. Despite these insights, it remains unclear why mammalian cells produce such a vast diversity of lipids, with hundreds of distinct lipids in any given membrane and dramatic differences between membranes within a cell and between cells. Recent evidence suggests that integral membrane proteins recruit a selective patch of lipids – a paralipidome – that differs from the bulk membrane in both lipid composition and biophysical properties. This local lipid environment can be tuned to meet the specific structural and functional requirements of individual proteins, evolve as proteins move between organelles, change in response to physiological triggers and metabolic status, and differ across cell types and states (e.g. diet and disease). Critically, these membrane nano- environments can regulate the conformational landscapes of membrane proteins to direct their functions. To date, there have been very few direct measurements of the functional paralipidomes of specific integral membrane proteins, especially from biological membranes. Here we propose to harness recent technical advances to directly probe the local chemical and physical environment of membrane proteins in unprecedented detail, with the overarching goal of demonstrating how local lipid nano-environments around membrane proteins regulate their structure and physiology. To tackle this challenge, we have assembled a multidisciplinary team of PIs from the UVA Center for Membrane and Cell Physiology with collective expertise in novel nanodisc development, membrane protein structural biology, lipidomics, biomimetic membrane models, high-resolution fluorescence imaging, development of probes to sense structure and environment, and membrane cell biology/physiology. Through this combined expertise, we have developed tools to measure the chemical and biophysical features of protein paralipidomes and showed that these can have functional consequences. Here, we propose to apply these approaches to several biomedically relevant contexts in a systematic investigation of membrane protein functional paralipidomes. After establishing the core pillars of the project, we will expand our reach and impact by including early-stage investigators with expertise in other areas of membrane physiology. In summary, our proposal aims to move beyond the current paradigm of membrane protein regulation by individual lipid molecules to instead reveal the critical roles of local membrane nano-environments in membrane protein function.