A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction

Membrane proteins are functionally regulated by the composition of the surrounding lipid bilayer. The late endosomal compartment is a central site for the generation of ceramide, a bioactive sphingolipid, which regulates responses to cell stress. The molecular interactions between ceramide and late endosomal transmembrane proteins are unknown. Here, we uncover in atomistic detail the ceramide interaction of Lysosome Associated Protein Transmembrane 4B (LAPTM4B), implicated in ceramide-dependent cell death and autophagy, and its functional relevance in lysosomal nutrient signaling. The ceramide-mediated regulation of LAPTM4B depends on a sphingolipid interaction motif and an adjacent aspartate residue in the protein’s third transmembrane (TM3) helix. The interaction motif provides the preferred contact points for ceramide while the neighboring membrane-embedded acidic residue confers flexibility that is subject to ceramide-induced conformational changes, reducing TM3 bending. This facilitates the interaction between LAPTM4B and the amino acid transporter heavy chain 4F2hc, thereby controlling mTORC signaling. These findings provide mechanistic insights into how transmembrane proteins sense and respond to ceramide.膜蛋白的功能受其周围脂质双分子层的组成调控。晚期内体区室是神经酰胺（ceramide）——一类具有生物活性的鞘脂——生成的核心位点，而神经酰胺可调控细胞应激应答。目前，神经酰胺与晚期内体跨膜蛋白之间的分子相互作用机制尚不明确。本研究以原子级细节揭示了溶酶体相关跨膜蛋白4B（Lysosome Associated Protein Transmembrane 4B, LAPTM4B）与神经酰胺的相互作用细节；该蛋白已被证实参与神经酰胺依赖性细胞死亡与自噬过程，并在溶酶体营养信号通路中发挥功能性作用。神经酰胺对LAPTM4B的调控作用，依赖于该蛋白第三个跨膜螺旋（TM3）中的鞘脂相互作用基序与邻近的天冬氨酸残基。该相互作用基序为神经酰胺提供了最优结合位点，而邻近的膜嵌入酸性残基则赋予蛋白柔性，这种柔性会因神经酰胺诱导的构象变化而发生改变，进而降低TM3的弯曲程度。这一过程可促进LAPTM4B与氨基酸转运蛋白重链4F2hc之间的相互作用，进而调控mTORC信号通路。本研究的发现为跨膜蛋白感知并响应神经酰胺的分子机制提供了全新的见解。