• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

用于柔性单颗粒重建的粒子分割算法

Particle segmentation algorithm for flexible single particle reconstruction.

作者信息

Zhou Qiang, Zhou Niyun, Wang Hong-Wei

机构信息

State Key Laboratory of Biomembrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China.

Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084 China.

出版信息

Biophys Rep. 2017;3(1):43-55. doi: 10.1007/s41048-017-0038-7. Epub 2017 May 19.

DOI:10.1007/s41048-017-0038-7
PMID:28782000
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5515998/
Abstract

As single particle cryo-electron microscopy has evolved to a new era of atomic resolution, sample heterogeneity still imposes a major limit to the resolution of many macromolecular complexes, especially those with continuous conformational flexibility. Here, we describe a particle segmentation algorithm towards solving structures of molecules composed of several parts that are relatively flexible with each other. In this algorithm, the different parts of a target molecule are segmented from raw images according to their alignment information obtained from a preliminary 3D reconstruction and are subjected to single particle processing in an iterative manner. This algorithm was tested on both simulated and experimental data and showed improvement of 3D reconstruction resolution of each segmented part of the molecule than that of the entire molecule.

摘要

随着单颗粒冷冻电子显微镜技术发展到原子分辨率的新时代，样品的异质性仍然是许多大分子复合物分辨率的主要限制因素，尤其是那些具有连续构象灵活性的复合物。在此，我们描述了一种颗粒分割算法，用于解析由几个相对彼此灵活的部分组成的分子结构。在该算法中，目标分子的不同部分根据从初步三维重建获得的对齐信息从原始图像中分割出来，并以迭代方式进行单颗粒处理。该算法在模拟数据和实验数据上均进行了测试，结果表明，与整个分子相比，分子各分割部分的三维重建分辨率有所提高。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/a26b691286fd/41048_2017_38_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/19de7da83922/41048_2017_38_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/5f0eab19e0cc/41048_2017_38_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/6a5933ef3ef3/41048_2017_38_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/1d68d371b8dd/41048_2017_38_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/23dae1981acf/41048_2017_38_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/0e1c7d2b973f/41048_2017_38_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/a26b691286fd/41048_2017_38_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/19de7da83922/41048_2017_38_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/5f0eab19e0cc/41048_2017_38_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/6a5933ef3ef3/41048_2017_38_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/1d68d371b8dd/41048_2017_38_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/23dae1981acf/41048_2017_38_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/0e1c7d2b973f/41048_2017_38_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6caf/5515998/a26b691286fd/41048_2017_38_Fig7_HTML.jpg

相似文献

1
Particle segmentation algorithm for flexible single particle reconstruction.用于柔性单颗粒重建的粒子分割算法
Biophys Rep. 2017;3(1):43-55. doi: 10.1007/s41048-017-0038-7. Epub 2017 May 19.
2
Rapid near-atomic resolution single-particle 3D reconstruction with SIMPLE.使用 SIMPLE 进行快速近原子分辨率单颗粒 3D 重建。
J Struct Biol. 2018 Nov;204(2):172-181. doi: 10.1016/j.jsb.2018.08.005. Epub 2018 Aug 6.
3
DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images.深度HEMNMA：基于ResNet对冷冻电镜单颗粒图像中连续构象异质性的混合分析
Front Mol Biosci. 2022 Sep 8;9:965645. doi: 10.3389/fmolb.2022.965645. eCollection 2022.
4
Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes.结构异质大分子复合物的冷冻电子显微镜分析
Comput Struct Biotechnol J. 2016 Oct 14;14:385-390. doi: 10.1016/j.csbj.2016.10.002. eCollection 2016.
5
Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit.利用单颗粒冷冻电子显微镜进行结构测定：只有天空（和固有无序）是极限。
Int J Mol Sci. 2019 Aug 27;20(17):4186. doi: 10.3390/ijms20174186.
6
Determining the Crystal Structure of TRPV6确定瞬时受体电位香草酸亚型6（TRPV6）的晶体结构
7
Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules.利用合成数据进行深度学习可以实现生物大分子冷冻电镜粒子图像的自动挑选。
Bioinformatics. 2020 Feb 15;36(4):1252-1259. doi: 10.1093/bioinformatics/btz728.
8
Hands on Methods for High Resolution Cryo-Electron Microscopy Structures of Heterogeneous Macromolecular Complexes.异质大分子复合物高分辨率冷冻电子显微镜结构的实践方法
Front Mol Biosci. 2019 May 15;6:33. doi: 10.3389/fmolb.2019.00033. eCollection 2019.
9
A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.一种用于冷冻电子显微镜中单颗粒识别的深度卷积神经网络方法。
BMC Bioinformatics. 2017 Jul 21;18(1):348. doi: 10.1186/s12859-017-1757-y.
10
Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction.通过透射电子显微镜、单颗粒分析和三维重建确定生物大分子的结构。
Prog Biophys Mol Biol. 2001;75(3):121-64. doi: 10.1016/s0079-6107(01)00004-9.

引用本文的文献

1
Exceptionally potent human monoclonal antibodies are effective for prophylaxis and treatment of tetanus in mice.异常有效的人源化单克隆抗体可有效预防和治疗破伤风。
J Clin Invest. 2021 Nov 15;131(22). doi: 10.1172/JCI151676.
2
Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution.3.2 埃分辨率下单颗粒冷冻电镜重构 52kDa 链霉亲和素。
Nat Commun. 2019 Jun 3;10(1):2386. doi: 10.1038/s41467-019-10368-w.
3
Mechanistic insights into the SNARE complex disassembly.SNAR 复合体解体的机制见解。

本文引用的文献

1
Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM.通过冷冻电镜中单颗粒数据的流形嵌入映射结构的连续变化。
Methods. 2016 May 1;100:61-7. doi: 10.1016/j.ymeth.2016.02.007. Epub 2016 Feb 13.
2
COVARIANCE ESTIMATION USING CONJUGATE GRADIENT FOR 3D CLASSIFICATION IN CRYO-EM.在冷冻电镜三维分类中使用共轭梯度进行协方差估计
Proc IEEE Int Symp Biomed Imaging. 2015 Apr;2015:200-204. doi: 10.1109/ISBI.2015.7163849.
3
A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.
Sci Adv. 2019 Apr 10;5(4):eaau8164. doi: 10.1126/sciadv.aau8164. eCollection 2019 Apr.
4
In vivo assembly and large-scale purification of a GPCR - Gα fusion with Gβγ, and characterization of the active complex.体内组装和大规模纯化具有 Gβγ 的 GPCR-Gα 融合蛋白，并对活性复合物进行表征。
PLoS One. 2019 Jan 8;14(1):e0210131. doi: 10.1371/journal.pone.0210131. eCollection 2019.
5
Image processing for cryogenic transmission electron microscopy of symmetry-mismatched complexes.对称不匹配复合物的低温透射电子显微镜图像处理
Biosci Rep. 2018 Apr 27;38(2):BSR20170203. doi: 10.1042/BSR20170203.
一种用于具有多个刚性模块的大分子复合物的单颗粒分析中的局部优化细化算法。
Protein Cell. 2016 Jan;7(1):46-62. doi: 10.1007/s13238-015-0229-2. Epub 2015 Dec 17.
4
Sampling the conformational space of the catalytic subunit of human γ-secretase.对人γ-分泌酶催化亚基的构象空间进行采样。
Elife. 2015 Dec 1;4:e11182. doi: 10.7554/eLife.11182.
5
Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.从大分子复合物的电子冷冻显微镜图像中进行亚基的局部重建。
Nat Commun. 2015 Nov 4;6:8843. doi: 10.1038/ncomms9843.
6
In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus.双链RNA病毒内部基因组片段和RNA聚合酶复合物的原位结构。
Nature. 2015 Nov 26;527(7579):531-534. doi: 10.1038/nature15767. Epub 2015 Oct 26.
7
Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus.低温电子显微镜显示聚合酶结构和双链 RNA 病毒内的非螺旋基因组。
Science. 2015 Sep 18;349(6254):1347-50. doi: 10.1126/science.aaa4938.
8
Structure of a yeast spliceosome at 3.6-angstrom resolution.酵母剪接体的 3.6 埃分辨率结构。
Science. 2015 Sep 11;349(6253):1182-91. doi: 10.1126/science.aac7629. Epub 2015 Aug 20.
9
Directly reconstructing principal components of heterogeneous particles from cryo-EM images.从冷冻电镜图像直接重建异质颗粒的主成分
J Struct Biol. 2015 Aug;191(2):245-62. doi: 10.1016/j.jsb.2015.05.007. Epub 2015 Jun 4.
10
Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.基于透射电子显微镜数据的单颗粒分析中的三维重建方法。
Arch Biochem Biophys. 2015 Sep 1;581:39-48. doi: 10.1016/j.abb.2015.05.003. Epub 2015 May 22.