Computing methods for icosahedral and symmetry-mismatch reconstruction of viruses by cryo-electron microscopy

Three-dimensional（3 D） reconstruction of icosahedral viruses has played a crucial role in the development of cryoelectron microscopy single-particle reconstruction, with many cryo-electron microscopy techniques first established for structural studies of icosahedral viruses, owing to their high symmetry and large mass. This review summarizes the computational methods for icosahedral and symmetry-mismatch reconstruction of viruses, as well as the likely challenges and bottlenecks in virus reconstruction, such as symmetry mismatch reconstruction, contrast transformation function（CTF）correction, and particle distortion.

Structural biology revolution led by technical breakthroughs in cryo-electron microscopy

Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Frank, and Richard Henderson, who made groundbreaking contributions to the development of cryo-EM. In this review, I will give a comprehensive review of the developmental history of cryo-EM, the technical aspects of the breakthrough in cryo-EM leading to the structural biology revolution, including electron microscopy, image recording devices and image processing algorithms,and the major scientific achievements by Chinese researchers employing cryo-EM, covering protein complexes involved in or related to gene expression and regulation, protein synthesis and degradation, membrane proteins, immunity, and viruses.Finally, I will give a perspective outlook on the development of cryo-EM in the future.

Cryo-electron microscopy structure of the intact photosynthetic light-harvesting antenna-reaction center complex from a green sulfur bacterium

The photosynthetic reaction center complex(RCC)of green sulfur bacteria(GSB)consists of the membrane-imbedded RC core and the peripheric energy transmitting proteins called Fenna–Matthews–Olson(FMO).Functionally,FMO transfers the absorbed energy from a huge peripheral light-harvesting antenna named chlorosome to the RC core where charge separation occurs.In vivo,one RC was found to bind two FMOs,however,the intact structure of RCC as well as the energy transfer mechanism within RCC remain to be clarified.Here we report a structure of intact RCC which contains a RC core and two FMO trimers from a thermophilic green sulfur bacterium Chlorobaculum tepidum at 2.9A resolution by cryo-electron microscopy.The second FMO trimer is attached at the cytoplasmic side asymmetrically relative to the first FMO trimer reported previously.We also observed two new subunits(PscE and PscF)and the N-terminal transmembrane domain of a cytochrome-containing subunit(PscC)in the structure.These two novel subunits possibly function to facilitate the binding of FMOs to RC core and to stabilize the whole complex.A new bacteriochlorophyll(numbered as 816)was identified at the interspace between PscF and PscA-1,causing an asymmetrical energy transfer from the two FMO trimers to RC core.Based on the structure,we propose an energy transfer network within this photosynthetic apparatus.

岩土材料中冰分布状态的冷冻电镜表征方法

为从微观角度定量描述冰在岩土材料中的分布特征,基于冷冻电镜技术提出了一种微观尺度的实验表征方法。针对不同冰饱和度人造岩芯样品的二次电子图像和能谱分析图,通过元素含量分布、升华前后图像对比确认了冰在岩土材料中的分布状态。随着冰饱和度的增加,骨架孔隙被冰填充、骨架颗粒表面被冰包裹区域增大,样品断面更密实平整,岩土骨架的堆积结构特征变弱。在背散射电子图像中,冰的图像比岩土骨架亮度低、灰度高,基于此构建了冰饱和度的数字图像计算方法。该方法计算的升华前冰饱和度与样品预制冰饱和度偏差小于5%,验证了其可靠性。

冷冻扫描电镜制样方法及其在含水样品中的应用

常规扫描电镜要求所观察的样品必须干燥、无水,而一些含水样品在干燥过程中会发生结构变化,无法真实反映样品的结构信息。冷冻扫描电镜无需对样品进行干燥处理,可以直接分析含水样品表面、界面和内部结构,是研究高度含水样品的强有力工具。样品的制样方法在冷冻扫描电镜技术中占有重要地位,它直接关系到样品真实形貌特征的反映和对超微结构的正确解读。本文综述了冷冻扫描电镜的制样方法,并阐述冷冻扫描电镜技术在天然气水合物、微生物、乳液、水凝胶、动植物等含水样品中的应用。

Cryo-electron microscopy reconstructions of two types of wild rabbit hemorrhagic disease viruses characterized the structural features of Lagovirus

Rabbit hemorrhagic disease was described in China in 1984 and can cause hemorrhagic necrosis of the liver within two or three days after infection.The etiological agent,rabbit hemorrhagic disease virus(RHDV),belongs to the Lagovirus genus in the Caliciviridae family.Compared to other calicivirus,such as rNV and SMSV,the structure of Lagovirus members is not well characterized.In this report,structures of two types of wild RHDV particles,the intact virion and the core-like particle(CLP),were reconstructed by cryo-electron microscopy at 11Åand 17Å,respectively.This is the first time the 3D structure of wild caliciviruses CLP has been provided,and the 3D structure of intact RHDV virion is the highest resolution structure in Lagovirus.Comparison of the intact virion and CLP structures clearly indicated that CLP was produced from the intact virion with the protrusion dissociated.In contrast with the crystal structures of recombinant Norovirus and San Miguel sea lion virus,the capsomers of RHDV virion exhibited unique structural features and assembly modes.Both P1 and P2 subdomains have interactions inside the AB capsomer,while only P2 subdomains have interaction inside CC capsomer.The pseudo atomic models of RHDV capsomers were constructed by homology modeling and density map fitting,and the rotation of RHDV VP60 P domain with respect to its S domain,compared with SMSV,was observed.Collectively,our cryo-electron microscopic studies of RHDV provide close insight into the structure of Lagovirus,which is important for functional analysis and better vaccine development in the future.

Cryo-electron microscopy finds place in materials science

The fast development of electron microscopy has enabled unprecedented achievements in the field of life science and materials science[1–6].In particular,the 2017 Nobel Prize of chemistry was awarded to three scientists who contributed significantly to developing cryo-electron microscopy(Cryo-EM)[7].This technique,involving fast freezing the biological samples using liquid nitrogen,was originally designed to keep"live cells"intact from water evaporation and crystallization and immune to

Structural variation of molecular chaperone group Ⅱ by crystallography and cryo-electron microscopy

Chaperonins, a class of molecular chaperones, are oligomeric complexes acting as a protein-folding chamber in an ATP-dependent manner. Chaperonins have been classifed

一种用于冷冻电镜样品装载的工作台

本文介绍一种自行设计用于冷冻电镜样品装载的工作台。在保持操作区域相对低温及低气流扰动下,其可以将湿度降至10%以内。在该操作台里完成装载的冷冻样品,几乎没有冰晶污染,可用于冷冻电镜高分辨数据采集。

冷冻电镜观察固态锂电池界面

固态锂电池(SSLBs)有望兼顾高能量密度和高安全性,是未来电池领域的重要发展方向。固态电解质(SSE)与电极材料之间存在界面阻抗大、相容性差等问题,严重地制约着它的发展。然而,由于辐照敏感特性,难以直接采用常规透射电子显微镜(TEM)观察界面结构。冷冻电镜(Cryo⁃EM)可以有效地缓解辐照损伤,提供更准确、真实的结构信息,有助于深入理解界面微观结构与SSLBs电化学性能之间的构效关系。本文综述了Cryo⁃EM用于观测SSLBs界面的晶体结构和化学组成,揭示了界面形成和演化机制以及SSLBs的失效机制。最后展望了Cryo⁃EM在表征SSLBs界面所面临的挑战和未来的研究方向。Cryo⁃EM在SSLBs界面研究中发挥越来越重要的作用,逐渐成为推动高性能SSLBs发展的必备技术。

综述:核小体液-液相分离中早期形核过程的分子结构

研究揭示,核小体阵列在体外具有液-液相分离(liquid⁃liquid phase separation,LLPS)的内在特性,被认为在体内引导染色质区域的结构变化。然而,对于形成的异质凝聚物在分子水平的结构研究,长期以来受到技术限制,从而阻碍了研究人员对核小体液-液相分离的深入理解。为了解决这一难题,张蒙等运用先进的冷冻电子断层扫描技术(Cryo⁃electron tomography,Cryo⁃ET)、结合单分子电子断层重构(individual⁃particle electron tomography,IPET)和基于深度学习的分割技术,确定了液-液相分离在不同阶段的凝聚物的分子组织结构。该研究揭示,核小体的液-液相分离过程涉及到两个主要步骤:首先,旋节分解形成不规则的凝聚物;然后,这些凝聚物经过一个不稳定的过渡阶段,转化为更紧凑的球状核,进一步通过聚集更多旋节材料或与其它球状凝聚物的融合,逐渐形成更大的球状聚集体。此外,连接组蛋白H1催化旋节向球状凝聚物转变的速率,比旋节分解速度快出十倍以上。因此,推测这种转变可能涉及到核小体疏水表面的暴露,进而改变了核小体之间的相互作用。这些发现为染色质从间期结构向中期结构转变提供了新的物理机制线索。

The three-dimensional structure of Infectious flacherie virus capsid determined by cryo-electron microscopy

Cryo-electron microscopy and image reconstruction were used to determine the three-dimensional structure of Infectious flacherie virus (IFV). 5047 particles were selected for the final reconstruction. The FSC curve showed that the resolution of this capsid structure was 18 ·. The structure is a psuedo T=3 (P=3) icosahedral capsid with a diameter of 302.4 · and a single shell thickness of 15 ·. The density map showed that IFV has a smooth surface without any prominent protrude or depression. Comparison of the IFV structure with those of the insect picorna-like virus-Cricket paralysis virus (CrPV)and human picornavirus-Human rhinovirus 14 (HRV 14) revealed that the IFV structure resembles the CrPV structure. The "Rossmann canyon" is absent in both IFV and CrPV particles. The polypeptide topology of IFV VP2, IFV VP3 was predicted and the subunit location at the capsid surface was further analyzed.

A powerful denoising method based on non-local means filter for cryo-electron microscopic images

Cryo-electron microscopic images of biological molecules usually have high noise and low contrast. It is essential to suppress noise and enhance contrast in order to recognize

A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection

Background:Cryo-electron microscopy(Cryo-EM)and tomography(Cryo-ET)have emerged as important imaging techniques for studying structures of macromolecular complexes.In 3D reconstruction of large macromolecular complexes,many 2D projection images of macromolecular complex particles are usually acquired with low signal-tonoise ratio.Therefore,it is meaningful to select multiple images containing the same structure with identical orientation.The selected images are averaged to produce a higher-quality representation of the underlying structure with improved resolution.Existing approaches of selecting such images have limited accuracy and speed.Methods:We propose a simulated annealing-based algorithm(SA)to pick the homogeneous image set with best average.Its performance is compared with two baseline methods based on both 2D and 3D datasets.When tested on simulated and experimental 3D Cryo-ET images of Ribosome complex,SA sometimes stopped at a local optimal solution.Restarting is applied to settle this difficulty and significantly improved the performance of SA on 3D datasets.Results:Experimented on simulated and experimental 2D Cryo-EM images of Ribosome complex datasets respectively with SNR=10 and SNR=0.5,our method achieved better accuracy in terms of F-measure,resolution score,and time cost than two baseline methods.Additionally,SA shows its superiority when the proportion of homogeneous images decreases.Conclusions:SA is introduced for homogeneous image selection to realize higher accuracy with faster processing speed.Experiments on both simulated and real 2D Cryo-EM and 3D Cryo-ET images demonstrated that SA achieved expressively better performance.This approach serves as an important step for improving the resolution of structural recovery of macromolecular complexes captured by Cryo-EM and Cryo-ET.

Assembly mechanism and energy transfer pathways of plant photosystem II-LHCII supercomplexes discovered through cryo-electron microscopy

Funded by the National Natural Science Foundation of China,Chinese Ministry of Science and Technology,and Chinese Academy of Sciences,ajoint team of three laboratories from the Institute of Biophysics of Chinese Academy of Sciences,namely Liu Zhenfeng’s(柳振峰),Zhang

Cryo-electron microscopy for structural biology:current status and future perspectives

Recently, significant technical breakthroughs in both hardware equipment and software algorithms have enabled cryo-electron microscopy(cryo-EM) to become one of the most important techniques in biological structural analysis. The technical aspects of cryo-EM define its unique advantages and the direction of development. As a rapidly emerging field, cryo-EM has benefitted from highly interdisciplinary research efforts. Here we review the current status of cryo-EM in the context of structural biology and discuss the technical challenges. It may eventually merge structural and cell biology at multiple scales.

扫描电镜中半导体制冷冷台使用条件优化及在高含水量样品中的应用

目的:有效解决高含水量样品电子显微结构观察的难点。方法:通过常规扫描电子显微镜搭配半导体制冷冷台的新仪器组合模式,对一系列高含水量样品进行显微结构观察。结果:高含水量样品在以导电胶带为基质,电压5 kV,电子束斑值为50/60,冷台温度为4℃的条件下,无需对样品进行固定和脱水处理,可以在扫描电子显微镜下直接成像观察其显微结构,样品微观结构没有皱缩、拉伸、扭曲等变形现象,能够更真实地反映样品的原貌。结论:常规扫描电子显微镜搭配半导体制冷冷台的仪器自由组合模式是解决高含水量样品显微结构观察的有效手段。

Applications and prospects of cryo-EM in drug discovery

Drug discovery is a crucial part of human healthcare and has dramatically benefited human lifespan and life quality in recent centuries, however, it is usually time-and effort-consuming. Structural biology has been demonstrated as a powerful tool to accelerate drug development. Among different techniques, cryo-electron microscopy(cryo-EM) is emerging as the mainstream of structure determination of biomacromolecules in the past decade and has received increasing attention from the pharmaceutical industry. Although cryo-EM still has limitations in resolution, speed and throughput, a growing number of innovative drugs are being developed with the help of cryo-EM. Here, we aim to provide an overview of how cryo-EM techniques are applied to facilitate drug discovery. The development and typical workflow of cryo-EM technique will be briefly introduced, followed by its specific applications in structure-based drug design, fragment-based drug discovery, proteolysis targeting chimeras, antibody drug development and drug repurposing. Besides cryo-EM, drug discovery innovation usually involves other state-of-the-art techniques such as artificial intelligence(AI), which is increasingly active in diverse areas. The combination of cryo-EM and AI provides an opportunity to minimize limitations of cryo-EM such as automation, throughput and interpretation of mediumresolution maps, and tends to be the new direction of future development of cryo-EM. The rapid development of cryo-EM will make it as an indispensable part of modern drug discovery.

冷冻电镜含水切片技术观察胰岛β细胞的三维超微结构

冷冻电镜含水切片技术(CEMOVIS)作为冷冻厚生物样品制备技术,对高压冷冻的样品直接进行冷冻切片,能够获得完全含水状态的生物样品的超微结构,更好地反映出细胞接近其生理条件的真实状态。本文应用冷冻含水切片技术结合冷冻电子断层扫描和三维重构技术观察到了小鼠胰岛β细胞内细胞器的高分辨超微结构。

冷冻电镜平台3+X运行模式的探索与思考

冷冻电镜技术已成为生命科学领域研究结构和功能的重要技术手段,冷冻电镜平台的建设给高校和科研院所的学科发展带来新的突破口。现以浙江大学冷冻电镜中心的建设与运行为例,阐述了冷冻电镜平台的仪器架构和3+X创新运行模式,剖析了运行中存在的问题,提出了相应对策,旨在探索冷冻电镜平台高效、良性的运行机制和管理模式。