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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...

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Updated: May 5, 2026

Thermochemical Studies of NiII and ZnII Ternary Complexes Using Ion Mobility-Mass Spectrometry

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Published on: June 8, 2022

射门手枪方法用于PROTAC三元复合模型和评估.

Tanfeng Zhao¹, Yi Qin Gao^1,2,3

¹New Cornerstone Science Laboratory, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.

Journal of chemical information and modeling

|November 14, 2025

概括

这项研究引入了一个新的计算框架来建模蛋白质降解复合体. 它使用分子动力学来生成精确的三元复杂组合,改进了化向仿真体 (PROTACs) 的设计.

科学领域:

生物化学生物化学
结构生物学结构生物学
药物发现药物发现药物发现

背景情况:

化向化体 (PROTACs) 是双功能分子,通过与 protein和E3泛酸酶形成三元复合物,诱导向蛋白质的降解.
基于结构的PROTAC连接器设计是有希望的,但受到这些三元复合体的灵活性和动态性质的阻碍,因此很难获得准确的结构信息.

研究的目的:

开发和验证一种新的计算框架,用于建模和评估兴趣降解剂-E3结合酶三元复合物的蛋白质.
为了解决静态晶体结构的局限性,并提高指导PROTAC降解器设计的计算模型的准确性.

主要方法:

利用来自多个并行分子动力学 (MD) 轨迹的构造分布作为三元复合模型的参考.
开发了一种新的建模协议和评分函数,用于生成和评估三元复合组合.
在五个涉及蛋白质的利息降解器-E3系统的案例中测试了框架.

主要成果:

拟议的协议成功生成了三元复杂集,这些集覆盖或接近MD轨迹中观察到的高密度区域.
证明了框架在捕捉这些动态系统固有的构造多样性的有效性.
这种方法特别适用于具有多个稳定构造和蛋白质-蛋白质相互作用 (PPI) 的系统.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

相关实验视频

Last Updated: May 5, 2026

Thermochemical Studies of NiII and ZnII Ternary Complexes Using Ion Mobility-Mass Spectrometry

Thermochemical Studies of NiII and ZnII Ternary Complexes Using Ion Mobility-Mass Spectrometry

Published on: June 8, 2022

Author Spotlight: Evaluating Biophysical Assays for Characterizing PROTACS Ternary Complexes

Author Spotlight: Evaluating Biophysical Assays for Characterizing PROTACS Ternary Complexes

Published on: January 12, 2024

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

结论:

与传统方法相比,开发的框架为模拟三元复合体提供了更准确和可靠的方法,而传统方法仅依赖于晶体结构.
这一进步为PROTAC中的基于结构的链接器设计提供了有价值的工具,有可能加速新型蛋白质降解疗法的开发.
该框架能够处理形状灵活性,这提高了其在针对蛋白质降解的药物发现工作中的适用性.