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冷电磁结构和B因子精细化与集体表示

Joseph G Beton¹, Thomas Mulvaney¹, Tristan Cragnolini^1,2

¹Leibniz Institute of Virology (LIV) and Universitätsklinikum Hamburg Eppendorf (UKE), Centre for Structural Systems Biology (CSSB), 22607, Hamburg, Germany.

Nature communications

|January 10, 2024

概括

我们开发了TEMPy-ReFF,这是一种在冷电子显微镜 (cryo-EM) 密度图中提炼原子结构的新方法. 这种方法增强了宏分子组合的表现,改善了灵活的生物结构的解释.

科学领域:

结构生物学结构生物学
生物物理学的生物物理.
计算生物学计算生物学

背景情况:

低温电子显微镜 (cryo-EM) 可以生成宏分子组件的3D密度图.
原子模型通常使用密度导向方法被安装和改进到这些地图中.

研究的目的:

引入TEMPy-ReFF,这是一个用于冷电磁密度图中的原子结构精细化的新方法.
为了提供高质量的冷电磁图表,特别是对于灵活的结构.

主要方法:

原子位置表示为高斯混合模型组件.
用差异作为B因子用于整体描述.
在229个冷电磁图 (2.1-4.9 Å分辨率) 上测试,使用PDB和CERES模型.

主要成果:

与标准方法相比,TEMPy-ReFF合集提供了较好的冷电磁图表表现.
单一模型的性能相当于CERES再精炼,在某些情况下更好地适合.
允许创建没有边界工件的复合地图.

结论:

TEMPy-ReFF提供了一种先进的方法,用于在冷EM中精制原子结构.
整体方法改善了对灵活的生物大分子 (如RNA,DNA和连接体) 的解释.

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相关概念视频

Cryo-electron Microscopy

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

Electron Microscope Tomography and Single-particle Reconstruction

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...