Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy-based method for ensemble analysis of membrane protein nanodomains. The method, termed nanoscale deciphering of membrane protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterized the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function.

质膜上的大多数蛋白质并不是均匀分布的，而是定位于纳米级尺寸的动态域。为了研究它们的功能相关性，需要能够全面分析细胞群中膜蛋白纳米域的组成和空间组织的方法。在这里，我们描述了一种用于膜蛋白纳米域整体分析的非显微镜方法的开发。该方法被称为膜蛋白纳米域的纳米级破译 (NanoDeep)，它基于使用 DNA 纳米组件将膜蛋白组织信息转化为 DNA 测序读数。我们使用 NanoDeep 表征了 Her2 的纳米环境，Her2 是一种与癌症具有关键相关性的膜受体。重要的，我们能够通过设计来调节 NanoDeep 分析的蛋白质库存。NanoDeep 有可能为蛋白质纳米环境的组成和空间组织在膜蛋白功能调节中的作用提供新的见解。