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

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Quantitative Biology 2020年第1期8卷 51-63页

作者： Jie Shi Xiangrui Zeng Rui Jiang Tao Jiang Min Xu Department of Computer Science The University of Hong KongHong Kong 999077China Computational Biology Department Carnegie Mellon UniversityPittsburghPA 15213USA Department of Automation Tsinghua UniversityBeijing 100084China Department of Computer Science and Engineering University of California-RiversideRiversideCA 92521USA

Background:cryo-electron microscopy(cryo-EM)and tomography(cryo-ET)have emerged as important imaging techniques for studying structures of macromolecular *** 3D reconstruction of large macromolecular complexes,many 2D projection images of macromolecular complex particles are usually acquired with low signal-tonoise ***,it is meaningful to select multiple images containing the same structure with identical *** selected images are averaged to produce a higher-quality representation of the underlying structure with improved *** approaches of selecting such images have limited accuracy and ***:We propose a simulated annealing-based algorithm(SA)to pick the homogeneous image set with best *** performance is compared with two baseline methods based on both 2D and 3D *** tested on simulated and experimental 3D cryo-ET images of Ribosome complex,SA sometimes stopped at a local optimal *** is applied to settle this difficulty and significantly improved the performance of SA on 3D ***: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 ***,SA shows its superiority when the proportion of homogeneous images ***:SA is introduced for homogeneous image selection to realize higher accuracy with faster processing *** on both simulated and real 2D cryo-EM and 3D cryo-ET images demonstrated that SA achieved expressively better *** approach serves as an important step for improving the resolution of structural recovery of macromolecular complexes captured by cryo-EM and cryo-ET.

关键词： simulated annealing image averaging cryo-electron microscopy cryo-electron tomography

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

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生物物理学报 2009年第S1期25卷 7-8页

作者： Gabe Lander 孙飞 The Scripps Research Institute 10550 North Torrey Pines RdLa JollaCA 92037U.S.A 中国科学院生物物理研究所

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

关键词： chaperonin thermosome cryo-electron microscopy symmetry conformation change

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

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生物物理学报 2009年第S1期25卷 508-508页

作者： Dai-Yu Wei, Chang-Cheng Yin Department of Biophysics, Health Science Center, Peking University,38 Xueyuan Road, Beijing,100191

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

关键词： cryo-electron microscopy noise reduction image processing non-local means filter

cryo-EM Studies of Virus-Antibody Immune Complexes

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Virologica Sinica 2020年第1期35卷 1-13页

作者： Na Li Zhiqiang Li Yan Fu Sheng Cao CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of VirologyWuhan 430071China Center for Biosafety Mega-Science Chinese Academy of SciencesWuhan 430071China University of Chinese Academy of Sciences Beijing 100049China

Antibodies play critical roles in neutralizing viral infections and are increasingly used as therapeutic drugs and diagnostic tools. Structural studies on virus-antibody immune complexes are important for better understanding the molecular mechanisms of antibody-mediated neutralization and also provide valuable information for structure-based vaccine ***-electron microscopy(cryo-EM) has recently matured as a powerful structural technique for studying bio-macromolecular complexes. When combined with X-ray crystallography, cryo-EM provides a routine approach for structurally characterizing the immune complexes formed between icosahedral viruses and their antibodies. In this review, recent advances in the structural understanding of virus-antibody interactions are outlined for whole virions with icosahedral T = pseudo 3(picornaviruses) and T = 3(flaviviruses) architectures, focusing on the dynamic nature of viral shells in different functional states. Glycoprotein complexes from pleomorphic enveloped viruses are also discussed as immune complex antigens. Improving our understanding of viral epitope structures using virus-based platforms would provide a fundamental road map for future vaccine development.

关键词： cryo-electron microscopy(cryo-EM) Icosahedral Antigen Virion Immune complex

Development of Neutralizing Antibodies against Zika Virus Based on Its Envelope Protein Structure

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Virologica Sinica 2019年第2期34卷 168-174页

作者： Chunpeng Yang Rui Gong Natalia de Val CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China University of Chinese Academy of Sciences Beijing 100049 China Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda MD 20892 USA Cancer Research Tech no logy Program Frederick National Laboratory for Cancer Research Leidos Biomedical Research Inc Frederick MD 21701 USA

As we know more about Zika virus(ZIKV), as well as its linkage to birth defects(microcephaly) and autoimmune neurological syndromes, we realize the importance of developing an efficient vaccine against it. Zika virus disease has affected many countries and is becoming a major public health concern. To deal with the infection of ZIKV, plenty of experiments have been done on selection of neutralizing antibodies that can target the envelope(E) protein on the surface of the virion. However, the existence of antibody-dependent enhancement(ADE) effect might limit the use of them as therapeutic candidates. In this review, we classify the neutralizing antibodies against ZIKV based on the epitopes and summarize the resolved structural information on antibody/antigen complex from X-ray crystallography and cryo-electron microscopy(cryo-EM), which might be useful for further development of potent neutralizing antibodies and vaccines toward clinical use.

关键词： Zika virus (ZIKV Envelope protein Neutralizing antibody X-ray crystallography cryo-electron microscopy (cryo-EM)