Emerging methodologies to investigate lipid–protein interactions

Abstract

Cellular membranes are composed of hundreds of different lipids, ion channels, receptors and scaffolding complexes that act as signalling and trafficking platforms for processes fundamental to life. Cellular signalling and membrane trafficking are often regulated by peripheral proteins, which reversibly interact with lipid molecules in highly regulated spatial and temporal fashions. In most cases, one or more modular lipid-binding domain(s) mediate recruitment of peripheral proteins to specific cellular membranes. These domains, of which more than 10 have been identified since 1989, harbour structurally selective lipid-binding sites. Traditional in vitro and in vivo studies have elucidated how these domains coordinate their cognate lipids and thus how the parent proteins associate with membranes. Cellular activities of peripheral proteins and subsequent physiological processes depend upon lipid binding affinities and selectivity. Thus, the development of novel sensitive and quantitative tools is essential in furthering our understanding of the function and regulation of these proteins. As this field expands into new areas such as computational biology, cellular lipid mapping, single molecule imaging, and lipidomics, there is an urgent need to integrate technologies to detail the molecular architecture and mechanisms of lipid signalling. This review surveys emerging cellular and in vitro approaches for studying protein–lipid interactions and provides perspective on how integration of methodologies directs the future development of the field.

Cellular and molecular interactions of phosphoinositides and peripheral proteins

“…For instance, the requirement of two distinct lipid-binding sites within the C2, PH, and PX domains has been demonstrated for enhanced localization to the plasma membrane (Gallego et al 2010; Karathanassis et al 2002; Lemmon 2008; Lucas and Cho 2011; Moravcevic et al 2012; Scott et al 2012). This mode of dual lipid recognition termed “coincidence detection” (Balla 2005; Lemmon 2008; Moravcevic et al 2012) is seen for plasma membrane PI(4,5)P 2 and PS, which coordinate different sites in the C2 domain of PKCα (Guerrero-Valero et al 2009; Corbalan-Garcia and Gomez-Fernandez 2014) and full-length PTEN (Shenoy et al 2012; Gericke et al 2013).…”

The molecular basis of ceramide-1-phosphate recognition by C2 domains

“…A large number of peripheral proteins and lipid binding domains act as coincidence detectors ( 62,63 ). These proteins contain either multiple lipid binding sites or the ability to recognize a membrane physical property such as charge or curvature in addition to a key target lipid.…”

The Ebola Virus Matrix Protein Penetrates into the Plasma Membrane

“…Our studies support this finding and demonstrate that membrane insertion is a prerequisite for oligomerization and that, in addition to hexamers, VP40 also forms larger oligomeric structures. In closing, VP40 behaves similarly to a large number of peripheral proteins (37,39) where hydrophobic interactions with the membrane bilayer regulate not only membrane penetration but also cellular localization and biological function (37,39). Moreover, in the case of VP40, membrane penetration may induce conformational changes that can induce oligomerization through loss of N-and C-terminal latch properties.…”