Regulation of membrane protein structure and function by their lipid nano-environment

Abstract

Transmembrane proteins comprise ~30% of the mammalian proteome, mediating metabolism, signalling, transport and many other functions required for cellular life. The microenvironment of integral membrane proteins (IMPs) is intrinsically different from that of cytoplasmic proteins, with IMPs solvated by a compositionally and biophysically complex lipid matrix. These solvating lipids affect protein structure and function in a variety of ways, from stereospecific, high-affinity protein-lipid interactions to modulation by bulk membrane properties. Specific examples of functional modulation of IMPs by their solvating membranes have been reported for various transporters, channels and signal receptors; however, generalizable mechanistic principles governing IMP regulation by lipid environments are neither widely appreciated nor completely understood. Here, we review recent insights into the inter-relationships between complex lipidomes of mammalian membranes, the membrane physicochemical properties resulting from such lipid collectives, and the regulation of IMPs by either or both. The recent proliferation of high-resolution methods to study such lipid-protein interactions has led to generalizable insights, which we synthesize into a general framework termed the 'functional paralipidome' to understand the mutual regulation between membrane proteins and their surrounding lipid microenvironments.

Figure 1.. Inter-relationships between membrane lipidomes, protein structure/function, and collective membrane physical properties.

Individual lipid molecules can serve as specific cofactors for MPs, but lipids also collectively comprise the complex, dynamic solvent that determines the functional behavior of MPs. In turn, IMPs produce and transduce signals that can regulate membrane lipidomes, which themselves determine the biophysical properties of a given membrane.

Figure 2.. How collective membrane properties can affect protein organization and function.

(a) Membranes comprised of lipids with long acyl chains and/or cholesterol have thicker hydrophobic cores and thus prefer IMPs with longer hydrophobic transmembrane domains (vice versa for thinner membranes). (b) In membranes containing domains of different thicknesses, proteins can be sorted by their TMD length. (c) Hydrophobic mismatches create disturbances in optimal lipid configurations. These can be minimized by clustering of misfit TMDs. (d) Mechanical tension applied to a membrane decreases lipid packing, thins the membrane, and disorders lipid acyl chains. These effects can be transduced by transmembrane channels to sense touch and pressure. (e) IMPs sorting via preferences for lipid domains can facilitate interactions with other domain residents or restrict collisions with domain-excluded components. (f) Domains can affect IMP dynamics, with more ordered and tightly packed domains slowing protein diffusion. (g) The distinct compositions and physical properties of various membrane environments can directly regulate protein structure and activity. (h) TMD shape can promote sorting to membrane subdomains of different curvature.

Figure 3.. Physical and compositional variations in subcellular membranes.

Membranes of various subcellular organelles can differ dramatically in their compositions and resulting physical properties. The secretory pathway is experienced by most MPs, because they are synthesized in the ER, modified and sorted in the Golgi, and function at the PM. In their journey through these membranes, IMPs experience increasing cholesterol, sphingolipids, and saturated lipid concentrations. The membranes likely become more asymmetric with respect to the lipid compositions of the two bilayer leaflets, with the outer leaflet become more tightly packed and ordered, while the inner leaflet adopts greater negative charge due to increasing concentrations of anionic lipids. As they progress through the secretory pathway, membrane also become less fluid, more rigid, and thicker. In polarized cells, specialized regions of the PM like the apical PM of epithelial cells ^,, may be especially rich in tightly packing lipids and therefore thicker, less permeable, and more viscous. These features can be used to sort proteins between organelles and regulate their function within them. For example, TMDs of IMPs in the PM are longer and more asymmetric (i.e. bulkier near the exoplasmic leaflet, thinner near the cytoplasmic) compared to those of the ER and Golgi ^,.

Figure 4.. Methods to study MP-lipid interactions.

(a) Nanodiscs supported via amphiphilic protein or polymer scaffolds provide a native-like membrane environment for MPs. (b) Photoactivatable crosslinks can be introduced into lipid acyl chains, facilitating identification of protein-lipid interactions in situ. (c) FRET between fluorescently labeled lipids and proteins can report on interaction potentials. (d) Mass spectrometry of undigested proteins extracted from cells can reveal exact molecular identities and stoichiometries of bound lipids.

Figure 5.. Possible modes of lipid interactions with transmembrane proteins.

(a) A shell of annular lipids stably associates with transmembrane protein regions. The exchange rate of these annular lipids with the bulk is slow, such that these lipids can be conceptualized as an extended part of the protein. (b) Charged and large lipids like PIP2 (orange), can be tightly and specifically bound by protein domains to introduce large scale conformational changes. In these cases, lipids act as allosteric ligands for protein function. (c) Interactions between IMPs and individual lipid molecules (colored) are in constant competition with those from bulk lipids (gray). The affinity for a particular lipid species determines how likely it is to occupy a particular site, relative to its bulk concentration. The lifetime of those interactions is directly related to affinity. Simulations suggest that protein-lipid interactions span a range of lifetimes from relatively high affinity interactions (which are rare) to very common short-lived interactions (nanosecond range), which indicate rapid lipid exchange not influenced by protein binding. These observations imply that there is no single characteristic scale for protein-lipid interactions, but rather that specific, semi-selective, and bulk solvent-like effects could potentially be simultaneously relevant.

Figure 6.. The functional paralipidome.

(a) IMPs can prefer distinct lipid environments in different conformations. (b) Conversely, the conformational equilibrium of a protein is determined in part by the lipid environment. If the closed state of an ion channel (A) recruits unsaturated lipids (blue) into its paralipidome (top left), the open state will be favored in membranes rich unsaturated lipids (i.e. those in which the chemical activity of unsaturated lipids is higher; top panels). (bottom panels) Membranes rich in saturated lipids, which preferentially solvate or bind the open conformation (B), will tend to favor the open state. Importantly, these effects depend not on absolute compositions, but rather on chemical activities. For example, inclusion of other lipids (e.g. cholesterol) into the bulk may influence the chemical activity of saturated lipids and thereby change the conformational equilibria. (c) various IMPs have unique preferences of their local membrane nano-environment (i.e. membrane fingerprints), selecting both paralipidomes and consequent biophysical parameters based on subtleties of their conformation and dynamics.