摘要
冷冻电镜单颗粒三维重构技术是用来解析生物大分子三维结构的常用方法.然而目前在单颗粒三维重构过程中,溶剂平滑操作还存在一定缺陷:没有一款主流的单颗粒三维重构程序能够自动寻找掩模(mask)三维密度图,使得三维重构过程难免受到噪音统计学模型计算偏差的干扰.为解决这一问题,本研究借鉴X射线晶体学中解析优化相位所广泛采用的溶剂平滑方法,采用高斯滤波、坎尼边缘检测、最小误差阈值处理等方法处理重构所得三维密度图,优化溶剂平滑操作,发展在单颗粒三维重构过程中自动寻找mask三维密度图的方法.运用三维密度图傅里叶壳层相关系数(fourier shell correlation,FSC)曲线图、模拟颗粒数据重构角度误差散点图等指标评估此方法的效果.结果表明,自动寻找mask密度图的方法能够较好地找到涵盖分子结构信号区域的mask密度图,较为明显提高三维重构所得密度图分辨率.
CryoEM single particle reconstruction technique is a widely used method for solving macromolecular structures in structural biology. However, there are still some shortcomings in the current processes of single particle three-dimensional reconstruction. None of the current single particle reconstruction software has implemented the function of automatically finding soft mask for binary mapping out the reconstructed map, which can import bias in the computation of statistical model of noise, influencing effectiveness of three-dimensional reconstruction. To solve this problem and to improve the solvent flattening operation in single particle reconstruction, here, we report a new method for automatically finding soft mask for mapping out the reconstructed map in single particle reconstruction, by using Gaussian filtering, Canny edge detection, minimum error thresholding etc., for processing reconstructed map. This new method is derived from the solvent flattening method, which is widely used in X-ray crystallography for solving and improving macromolecular phases. In the experiment, we implemented FSC between reconstructed maps, Euler angular error scatter plot etc. methods to assess effect of auto-mask method. It was shown that mask map generated by auto-mask method can soundly cover molecular signal region of reconstructed map, and our new auto-mask method in three-dimensional reconstruction can help to improve resolution of three-dimensional reconstruction.
作者
宿锐
张叔阳
王佳伟
SU Rui;ZHANG Shu-Yang;WANG Jia-Wei(School for Life Sciences,Tsinghua University,Beijing 100084,China)
出处
《生物化学与生物物理进展》
SCIE
CAS
CSCD
北大核心
2019年第10期1020-1030,共11页
Progress In Biochemistry and Biophysics
基金
国家重点研发计划蛋白质机器与生命过程调控重点专项资助项目(2016YFA0501103)~~
关键词
单颗粒
冷冻电子显微学
三维重构
溶剂平滑
ingle particle
cryo electron microscopy
three-dimensional reconstruction
solvent flattening
