小柯机器人

美国杜克大学Alberto Bartesaghi团队近期取得重要工作进展，他们研究开发了nextYP工具，一个使用单粒子冷冻电子断层扫描原位表征蛋白质变异性的全面可扩展平台。相关研究成果2023年10月26日在线发表于《自然—方法学》杂志上。

据介绍，单粒子冷冻电子断层扫描是一种新兴的技术，能够以分子分辨率确定在细胞的天然环境中成像的蛋白质的结构。尽管用于样品制备和倾斜序列采集的高通量技术开始提供足够的数据，以允许在生理浓度下对蛋白质进行结构研究，但复杂的数据分析管道以及苛刻的存储和计算要求对该技术的开发和更广泛的采用构成了主要障碍。

研究人员为单粒子冷冻电子断层扫描数据分析提供了一个可扩展的端到端框架，从倾斜序列的实时预处理到高分辨率细化和分类，这允许对具有数百个倾斜序列和成千上万个粒子的数据集进行高效分析和可视化。研究人员使用体外和细胞数据集验证了这一方法，证明了它在实现高分辨率和原位揭示构象异质性方面的有效性。该框架通过直观易用的计算机应用程序nextYP提供(http://nextpyp.app)。

附：英文原文

Title: nextPYP: a comprehensive and scalable platform for characterizing protein variability in situ using single-particle cryo-electron tomography

Author: Liu, Hsuan-Fu, Zhou, Ye, Huang, Qinwen, Piland, Jonathan, Jin, Weisheng, Mandel, Justin, Du, Xiaochen, Martin, Jeffrey, Bartesaghi, Alberto

Issue&Volume: 2023-10-26

Abstract: Single-particle cryo-electron tomography is an emerging technique capable of determining the structure of proteins imaged within the native context of cells at molecular resolution. While high-throughput techniques for sample preparation and tilt-series acquisition are beginning to provide sufficient data to allow structural studies of proteins at physiological concentrations, the complex data analysis pipeline and the demanding storage and computational requirements pose major barriers for the development and broader adoption of this technology. Here, we present a scalable, end-to-end framework for single-particle cryo-electron tomography data analysis from on-the-fly pre-processing of tilt series to high-resolution refinement and classification, which allows efficient analysis and visualization of datasets with hundreds of tilt series and hundreds of thousands of particles. We validate our approach using in vitro and cellular datasets, demonstrating its effectiveness at achieving high-resolution and revealing conformational heterogeneity in situ. The framework is made available through an intuitive and easy-to-use computer application, nextPYP (http://nextpyp.app).

DOI: 10.1038/s41592-023-02045-0

Source: https://www.nature.com/articles/s41592-023-02045-0

Nature Methods：《自然—方法学》，创刊于2004年。隶属于施普林格·自然出版集团，最新IF：47.99
官方网址：https://www.nature.com/nmeth/
投稿链接：https://mts-nmeth.nature.com/cgi-bin/main.plex