Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy
Trace_y: Software algorithms for structural analysis of individual helical filaments by three-dimensional contact point reconstruction atomic force microscopy
复制标题
Trace_y：通过三维接触点重建原子力显微镜对单个螺旋丝进行结构分析的软件算法
DOI：
10.1101/2023.07.05.547812
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Wei
中科院分区：
文献类型：
--
作者：
Wei
原子力显微镜（AFM）是一种功能强大且日益普及的技术，具有广泛的成像应用。AFM能够产生具有高信噪比的详细三维形貌高度图像。这是原子力显微镜的一个关键能力，它使单个分子的结构特征能够在不需要系综平均的情况下进行研究，并且可以提供结构分析应用，其中分子群体的异质性，单个分子之间的结构变化或总体上的群体分布特性，具有重要的信息。在这里，介绍了一种名为Trace_y的软件工具，旨在根据地形AFM高度图像重建单个螺旋丝结构的三维（3D）表面包络。使用Trace_y的工作流程在单个螺旋淀粉样蛋白原纤维的结构分析上得到了证明，其中由于结构多态性，来自单个氨基酸序列的异质、复杂和多样的原纤维群体的组装机制尚未完全理解。这里介绍的软件和工作流程允许在地形AFM高度图像中编码的结构信息被提取和理解为3D接触点云。这种方法将促进原子力显微镜在结构生物学中的应用，与其他结构分析工具一起使用，以了解单个分子水平的结构和行为。
Atomic force microscopy (AFM) is a powerful and increasingly accessible technology that has a wide range of imaging applications. AFM is capable of producing detailed three-dimensional topographical height images with a high signal-to-noise ratio. This is a key capability of AFM, which enables the structural features of individual molecules to be studied without the need for ensemble averaging, and could offer structural analysis applications where heterogeneity of molecular populations, structural variations between individual molecules, or population distribution properties in general, hold important information. Here, a software tool called Trace_y designed to reconstruct the three-dimensional (3D) surface envelopes of individual helical filament structures from topographical AFM height images is presented. Workflow using Trace_y is demonstrated on the structural analysis of individual helical amyloid protein fibrils where the assembly mechanism of heterogeneous, complex and diverse fibril populations from a single amino-acid sequence due to structural polymorphism is not fully understood. The software and the workflow presented here allows the structural information encoded in topographical AFM height images to be extracted and understood as 3D contact point clouds. This approach will facilitate the use of AFM in structural biology, in integrated methodologies together with other structural analysis tools to understand the structures and behaviours at individual molecule level.
影响因子：
64.8
作者：
Heath GR;Kots E;Robertson JL;Lansky S;Khelashvili G;Weinstein H;Scheuring S
通讯作者：
Scheuring S
淀粉样蛋白颗粒通过充当混杂的纳米颗粒来促进表面催化的交叉播种
DOI：
10.1101/2020.09.01.278481
发表时间：
2020
期刊：
--
影响因子：
--
作者：
Koloteva-Levine N
通讯作者：
Koloteva-Levine N