The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO, CO, Cl, Na, K, NH, and H, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl/HCO exchanger) and NBCe1 (Na-COcotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na-CO/Cl exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.

中文翻译：

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SLC4 蛋白中脂质-蛋白相互作用的分子动力学模拟


SLC4 次级碳酸氢根转运蛋白家族负责 HCO、CO、Cl、Na、K、NH 和 H 的转运，这些对于调节 pH 和离子稳态是必需的。它们广泛表达于全身的众多组织中，并在具有不同膜特性的不同细胞类型中发挥作用。实验研究已报道了 SLC4 功能中潜在的脂质作用，主要关注该家族的两个成员：AE1（Cl/HCO 交换器）和 NBCe1（Na-CO 协同转运蛋白）。先前对 AE1 的外向状态与模型脂质膜的计算研究表明，胆固醇 (CHOL) 和磷脂酰肌醇二磷酸 (PIP2) 之间的蛋白质-脂质相互作用增强。然而，该家族其他成员中的蛋白质-脂质相互作用和其他构象状态仍然知之甚少，这妨碍了对 SLC4 家族中脂质的潜在调节作用的详细研究。在这项工作中，我们对具有不同传输模式的 SLC4 家族的三个成员进行了粗粒度和原子分子动力学模拟：AE1、NBCe1 和 NDCBE（Na-CO/Cl 交换器），模型 HEK293 膜由 CHOL、 PIP2、磷脂酰胆碱、磷脂酰乙醇胺、磷脂酰丝氨酸和鞘磷脂。最近解决的 AE1 的内向状态也包含在模拟中。使用 ProLint 服务器对模拟轨迹进行脂质-蛋白质接触分析，该服务器提供多种可视化工具，用于说明增强的脂质-蛋白质接触区域并识别蛋白质基质内假定的脂质结合位点。 我们观察到 CHOL 和 PIP2 在所有蛋白质周围富集，根据蛋白质类型和构象状态，它们的分布存在细微差异。在三种研究的蛋白质中确定了 CHOL、PIP2、磷脂酰胆碱和鞘磷脂的假定结合位点，并讨论了它们在 SLC4 转运功能、构象转变和蛋白质二聚化中的潜在作用。