Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
Department of Physiology, Anatomy & Genetics, University of Oxford, South Parks Road, Oxford, OX1 3PT, U.K.
J Chem Theory Comput. 2021 Oct 12;17(10):6548-6558. doi: 10.1021/acs.jctc.1c00547. Epub 2021 Sep 15.
Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-electron microscopy (cryo-EM) densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities using experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in, e.g., cryo-EM derived membrane protein structures surrounded by an array of ancillary lipid densities.
脂质与膜蛋白的特定相互作用有助于蛋白质的稳定性和功能。在分子动力学（MD）模拟中经常会识别出围绕膜蛋白的多种脂质相互作用，并且越来越多地在冷冻电子显微镜（cryo-EM）密度中得到解决。使用实验或模拟方法确定脂质结合亲和力有助于确定特定相互作用位点的相对重要性。在这里，我们开发了一种从平衡粗粒度 MD 模拟中确定蛋白质-脂质结合亲和力的方法，使用结合饱和度曲线，旨在模拟实验方案。我们将该方法应用于直接获得胆固醇与一系列膜蛋白上多个位点的结合亲和力，并将我们的结果与基于密度的平衡方法获得的自由能以及平均势力计算进行比较，在不同位点亲和力的排序方面得到了很好的一致性。因此，我们的结合饱和度方法为确定例如冷冻电子显微镜衍生的膜蛋白结构周围存在的大量辅助脂质密度的单个位点的相对影响提供了一种稳健、高通量的替代方法。
