The characterization of lipid binding to lipid transfer proteins (LTPs) is fundamental to understand their molecular mechanism. However, several structures of LTPs, and notably those proposed to act as bridges between membranes, do not provide the precise location of their endogenous lipid ligands. To address this limitation, computational approaches are a powerful alternative methodology, but they are often limited by the high flexibility of lipid substrates. Here, we develop a protocol based on unbiased coarse-grain molecular dynamics simulations in which lipids placed away from the protein can spontaneously bind to LTPs. This approach accurately determines binding pockets in LTPs and provides a working hypothesis for the lipid entry pathway. We apply this approach to characterize lipid binding to bridge LTPs of the Vps13-Atg2 family, for which the lipid localization inside the protein is currently unknown. Overall, our work paves the way to determine binding pockets and entry pathways for several LTPs in an inexpensive, fast, and accurate manner.

中文翻译：

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无偏 MD 模拟可识别脂质转移蛋白中的脂质结合位点。


脂质与脂质转移蛋白 (LTP) 结合的表征对于理解其分子机制至关重要。然而，LTP 的几种结构，特别是那些被提议充当膜之间桥梁的结构，并不能提供其内源性脂质配体的精确位置。为了解决这一限制，计算方法是一种强大的替代方法，但它们通常受到脂质底物的高灵活性的限制。在这里，我们开发了一种基于无偏粗粒分子动力学模拟的协议，其中远离蛋白质的脂质可以自发地与 LTP 结合。这种方法准确地确定了 LTP 中的结合袋，并为脂质进入途径提供了工作假设。我们应用这种方法来表征脂质与 Vps13-Atg2 家族桥 LTP 的结合，目前该蛋白内部的脂质定位尚不清楚。总的来说，我们的工作为以廉价、快速和准确的方式确定几种 LTP 的结合口袋和进入途径铺平了道路。