The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1‐PHD) binds specifically to phosphatidylinositol (3,4,5)‐triphosphate (PIP3), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1‐PHD in the presence of membranes containing PC, PS, and PIP3 lipids in varying compositions. While GRP1‐PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane‐bound configurations. We report the first observation of two distinct PIP3 binding modes on GRP1‐PHD, involving PIP3 interactions at a “canonical” and at an “alternate” site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1‐PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1‐PHD to the membrane, we demonstrate that along with the bound PIP3, surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1‐PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1‐PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.

中文翻译：

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GRP1 PH 结构域与阴离子膜相互作用的微观表征

磷酸离子醇 1 (GRP1-PHD) 通用受体的普莱克斯特林同源 (PH) 结构域与磷脂酰肌醇 (3,4,5)-三磷酸 (PIP3) 特异性结合，并充当第二信使。使用广泛的分子动力学 (MD) 模拟，采用高移动性膜模拟 (HMMM) 模型以及互补的全膜模拟，我们捕获了在含有 PC、PS 和 PIP3 的膜存在下 GRP1-PHD 的可微结合和动力学不同成分的脂质。虽然 GRP1-PHD 仅与纯 PC 膜形成短暂的相互作用，但阴离子脂质的掺入会产生稳定的膜结合构型。我们首次观察到 GRP1-PHD 上两种不同的 PIP3 结合模式，涉及 PIP3 在“规范”位点和“替代”位点的相互作用，这表明多种阴离子脂质同时结合的可能性。全膜模拟证实了从我们的 HMMM 膜结合模拟中捕获的 GRP1-PHD 膜结合姿势的稳定性。通过对与全膜结合的蛋白质进行额外的引导膜解结合模拟并计算与该过程相关的非平衡功，以及元动力学模拟，可以更定量地检查 GRP1-PHD 与膜的结合强度，我们证明与结合的 PIP3 一起，周围的阴离子 PS 脂质增加了 GRP1-PHD 从规范模式解离的能量消耗，导致它们比替代模式解离得更慢。我们的结果表明，GRP1-PHD 同时结合多种阴离子脂质有助于其膜亲和力，进而控制其信号传导活性。© 2019 Wiley 期刊公司。