Inconspicuous Little Allies: How Membrane Lipids Help Modulate Protein Function.

A common denominator of life is the existence of cellular membranes consisting of a dynamic and complex network of proteins and lipids. For many years membrane lipids were primarily regarded as structural components of bilayers that separate the interior of a cell from the environment and are key to the formation of different types of organelles with specialized functions in eukaryotes. In addition, a growing body of evidence suggests that a fraction of these membrane lipid species actively participate in modulating protein activities. As yet another example, Zhou et al. now provide compelling evidence for the role of a cell membrane lipid, ceramide, in controlling the function of a membrane protein involved in a signaling pathway that is responsible for cell metabolism, proliferation, and survival.[1]

Cellular metabolism is tightly coordinated in response to the availability of nutrients. If nutrients are scarce, anabolic processes are minimized while catabolic reactions are turned on. The situation is reversed when nutrients are not limited. The membrane protein complex is a key player in adapting cellular metabolism of nucleotides, proteins, and lipids to intrinsic and extrinsic signals.[2] Increased availability of amino acids, for example, triggers assembly of the membrane protein complex in membrane-bound organelles, lysosomes. One pathway leading to the activation of this complex is amino acid transport across the lysosomal membrane mediated by amino acid transporters.[3,4] Recruitment to lysosomes of such transporters facilitates membrane passage of leucine and was shown to depend on the transmembrane protein, lysosome associated protein transmembrane 4B (LAPTM4B).[4] However, the mode and site of interaction between the two proteins as well as factors that either trigger or block this interaction remained unclear.

Two independent studies provided a hint for a potential role of protein–lipid interactions in modulating the association of LAPTM4B with amino acid transporters. First, increasing intracellular ceramide levels led to a decrease in plasma membrane-localized amino acid transporter and, subsequently, to starvation and cell death.[5] Second, Blom et al. in a previous publication described a specific interaction of LAPTM4B with ceramide.[6] The authors suggested a role of LAPTM4B in clearing ceramide from the lysosomal membrane, which accumulated in lysosomes in the absence of the protein. The authors also showed that elevated levels of ceramide in LAPTM4B-silenced cells conferred resistance to drug-induced, ceramide-dependent cell death.[6] Together these data suggest a functional link between the LAPTM4B–ceramide interaction and lysosomal amino acid transporter function.

In order to decipher the interplay between the two proteins and ceramide within the membrane, Zhou et al. combined atomistic molecular dynamics simulations with in vitro and cellular studies.[1] On the basis of a previously described lipid binding motif in single- and multispanning membrane proteins,[7,8] the authors identified a similar motif in LAPTM4B. Experiments on transmembrane (TM) domain swapping in LAPTM4B together with atomistic simulations pinpointed the site of interaction to TM3 domain. Interestingly, the simulation studies suggest an important structural role of a single aspartate residue within TM3 (Figure ). This amino acid located in the center of TM3 induces a kink in the transmembrane helix. Is this kink functionally important for the interaction with ceramide? In the first protein described to contain this feature, its function was attributed to facilitating dimerization of the protein.[8] Indeed, in analogy to the lipid-facilitated dimerization of the transmembrane trafficking protein,[8] the absence of the lipid-binding feature in LAPTM4B attenuated dimerization with the amino acid transporter.[1] Contradictory at first glance, exchange of the central aspartate residue in the TM3 domain, which contributes to ceramide binding, led to a stronger rather than a weaker interaction of LAPTM4B and the amino acid transporter. However, the absence of this aspartate residue compromised downstream signaling. Supported by atomistic simulations, the authors suggest that reduced bending of TM3 domain compensates for the loss of ceramide binding and facilitates protein dimerization but is not sufficient to trigger downstream signaling. This finding of lipid-dependent regulation of a protein involved in cell metabolism activation suggests yet another level of metabolism-dependent coregulation of protein and lipid metabolism in membrane-bound organelles.[9]

Figure 1

Transmembrane domain 3 of LAPTM4B contains a putative lipid-binding feature (upper panel, underlined in red), predominantly interacting with ceramide in simulations.

In essence, Blom and Ikonen describe at a molecular level the dynamic regulation of membrane protein dimerization by a single lipid species, providing another compelling example of functions of membrane lipids that go beyond their well-described structural role.

Indeed, in their original model on membrane bilayer structures, Singer and Nicolson already suggested a small fraction of membrane lipids to undergo specific interactions with membrane proteins.[10] Almost 50 years later, exciting tools and advanced methods, including functionalized lipids, molecular dynamics simulations, and native mass spectrometry, now enable identifying this fraction of membrane lipids with unique functions in modulating protein activities within the hydrophobic phase of membranes.