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Science Bulletin 2024年第6期69卷 792-802页

作者：宋凯王叶菁董文杰李珍珍夏庆友朱平何华伟 Integrative Science Center of Germplasm Creation in Western China(CHONGQING)Science City Biological Science Research CenterSouthwest UniversityChongqing 400715China National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Chongqing Key Laboratory of Sericultural Science Chongqing Engineering and Technology Research Center for Novel Silk MaterialsSouthwest UniversityChongqing 400715China University of Chinese Academy of Sciences Beijing 100049China Chongqing Key Laboratory of Soft-Matter Material Chemistry and Function Manufacturing Chongqing 400715China

Silk is one of the toughest fibrous materials known despite spun at ambient temperature and pressure with water as a solvent.It is a great challenge to reproduce high-performance artificial fibers comparable to natural silk by bionic for the incomplete understanding of silkworm spinning in vivo.Here,we found that amphipol and digitonin stabilized the structure of natural silk fibroin(NSF)by a large-scale screening in vitro,and then studied the close-to-native ultrastructure and hierarchical assembly of NSF in the silk gland lumen.Our study showed that NSF formed reversible flexible nanofibrils mainly composed of random coils with a sedimentation coefficient of 5.8 S and a diameter of about 4 nm,rather than a micellar or rod-like structure assembled by the aggregation of globular NSF molecules.Metal ions were required for NSF nanofibril formation.The successive p H decrease from posterior silk gland(PSG)to anterior silk gland(ASG)resulted in a gradual increase in NSF hydrophobicity,thus inducing the sol-gelation transition of NSF nanofibrils.NSF nanofibrils were randomly dispersed from PSG to ASG-1,and self-assembled into anisotropic herringbone patterns at ASG-2 near the spinneret ready for silkworm spinning.Our findings reveal the controlled self-assembly mechanism of the multi-scale hierarchical architecture of NSF from nanofibrils to herringbone patterns programmed by metal ions and p H gradient,which provides novel insights into the spinning mechanism of silk-secreting animals and bioinspired design of high-performance fibers.

关键词： Natural silk fibroin Nanofibril Self-assembly Silkworm cryo-em

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8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-em and AI

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Protein & Cell 2022年第10期13卷 760-777页

作者： Linhua Tai Yun Zhu He Ren Xiaojun Huang Chuanmao Zhang Fei Sun National Key Laboratory of Biomacromolecules Institute of BiophysicsCAS Center for Excellence in BiomacromoleculesChinese Academy of SciencesBeijing 100101China The Ministry of Education Key Laboratory of Cell Proliferation and Differentiation and the State Key Laboratory of Membrane Biology College of Life SciencesPeking UniversityBeijing 100871China Center for Biological Imaging Institute of BiophysicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Guangzhou 510005China

The nuclear pore complex(NPC),one of the largest protein complexes in eukaryotes,serves as a physical gate to regulate nucleocytoplasmic transport.Here,we determined the 8Åresolution cryo-electron microscopic(cryo-em)structure of the outer rings containing nuclear ring(NR)and cytoplasmic ring(CR)from the Xenopus laevis NPC,with local resolutions reaching 4.9Å.With the aid of AlphaFold2,we managed to build a pseudoatomic model of the outer rings,including the Y complexes and flanking components.In this most comprehensive and accurate model of outer rings to date,the almost complete Y complex structure exhibits much tighter interaction in the hub region.In addition to two copies of Y complexes,each asymmetric subunit in CR contains five copies of Nup358,two copies of the Nup214 complex,two copies of Nup205 and one copy of newly identified Nup93,while that in NR contains one copy of Nup205,one copy of ELYS and one copy of Nup93.These in-depth structural features represent a great advance in understanding the assembly of NPCs.

关键词： nuclear pore complex cryo-em Xenopus laevis AlphaFold2 nuclear ring cytoplasmic ring

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cryo-em structures reveal the dynamic transformation of human alpha-2-macroglobulin working as a protease inhibitor

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Science China(Life Sciences) 2022年第12期65卷 2491-2504页

作者： Xiaoxing Huang Youwang Wang Cong Yu Hui Zhang Qiang Ru Xinxin Li Kai Song Min Zhou Ping Zhu National Laboratory of Biomacromolecules CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China The Institute of Medicinal Plant Development Chinese Academy of Medical Sciences(CAMS)and Peking Union Medical College(PUMC)Beijing 100193China University of Chinese Academy of Sciences Beijing 100049China

Human alpha-2-macroglobulin is a well-known inhibitor of a broad spectrum of proteases and plays important roles in immunity,inflammation,and infections.Here,we report the cryo-em structures of human alpha-2-macroglobulin in its native state,induced state transformed by its authentic substrate,human trypsin,and serial intermediate states between the native and fully induced states.These structures exhibit distinct conformations,which reveal the dynamic transformation of alpha-2-macroglobulin that acts as a protease inhibitor.The results shed light on the molecular mechanism of alpha-2-macroglobulin in entrapping substrates.

关键词： alpha-2-macroglobulin cryo-em dynamic transformation protease inhibitor structure

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cryo-em snapshots of mycobacterial arabinosyltransferase complex embB2-AcpM2

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Protein & Cell 2020年第7期11卷 505-517页

作者： Lu Zhang Yao Zha Ruogu Gao Jun Li Xiuna Yang Yan Gao Wei Zhao Sudagar S.Gurcha Natacha Veerapen Sarah M.Batt Kajelle Kaur Besra Wenqing Xu Lijun Bi Xian'en Zhang Luke W.Guddat Haitao Yang Quan Wang Gurdyal S.Besra Zihe Rao State Key Laboratory of Medicinal Chemical Biology College of Life Sciences and College of PharmacyNankai UniversityTianjin 300353China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell BiologyChinese Academy of Sciences(CAS)Shanghai 200031China University of Chinese Academy of Sciences Beijing 100101China National Laboratory of Biomacromolecules and Key Laboratory of RNA Biology CAS Center for Excellence in BiomacromoleculesInstitute of BiophysicsCASBeijing 100101China Laboratory of Structural Biology Tsinghua UniversityBeijing 100084China School of Biosciences Institute of Microbiology and InfectionUniversity of BirminghamBirmingham B152TTUK School of Chemistry and Molecular Biosciences The University of QueenslandBrisbaneQLD 4072Australia

Inhibition of Mycobacterium tuberculosis(Mtb)cell wall assembly is an established strategy for anti-TB chemotherapy.Arabinosyltransferase embB,which catalyzes the transfer of arabinose from the donor decaprenyl-phosphate-arabinose(DPA)to its arabinosyl acceptor is an essential enzyme for Mtb cell wall synthesis.Analysis of drug resistance mutations suggests that embB is the main target of the front-line anti-TB drug,ethambutol.Herein,we report the cryo-em structures of Mycobacterium smegmatis embB in its"resting state"and DPA-bound"active state".embB is a fifteen-transmembrane-spanning protein,assembled as a dimer.Each protomer has an associated acyl-carrier-protein(AcpM)on their cytoplasmic surface.Confor-mational changes upon DPA binding indicate an asym-metric movement within the embB dimer during catalysis.Functional studies have identified critical residues in substrate recognition and catalysis,and demonstrated that ethambutol inhibits transferase activity of embB by competing with DPA.The structures represent the first step directed towards a rational approach for anti-TB drug discovery.

关键词： Mycobacterium tuberculosis embB cryo-em ethambutol cell wall synthesis arabinoglacatan arabinosyltransferase acyl-carrier-protein drug discovery

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cryo-em structure of the plant 26S proteasome

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Plant Communications 2022年第3期3卷 116-126页

作者： Susanne Kandolf Irina Grishkovskaya Katarina Belacic Derek L.Bolhuis Sascha Amann Brent Foster Richard Imre Karl Mechtler Alexander Schleiffer Hemant D.Tagare Ellen D.Zhong Anton Meinhart Nicholas G.Brown David Haselbach Research Institute of Molecular Pathology(IMP) Vienna BioCenter(VBC)Campus-Vienna-BioCenter 11030 ViennaAustria Department of Radiology and Biomedical Imaging Yale UniversityNew HavenCT 06510USA Department of Pharmacology and Lineberger Comprehensive Cancer Center University of North Carolina School of MedicineChapel HillNC 27599USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of TechnologyCambridgeMA 02139USA Vienna BioCenter PhD Program Doctoral School of the University at Vienna and Medical University of ViennaVienna BioCenter(VBC)ViennaAustria Institute of Physical Chemistry University of FreiburgAlbertstraße 21Freiburg 79104Germany CIBSS Centre for Integrative Biological Signalling Studies University of FreiburgFreiburgGermany

Targeted proteolysis is a hallmark of life.It is especially important in long-lived cells that can be found in higher eukaryotes,like plants.This task is mainly fulfilled by the ubiquitin–proteasome system.Thus,proteolysis by the 26S proteasome is vital to development,immunity,and cell division.Although the yeast and animal proteasomes are well characterized,there is only limited information on the plant proteasome.We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 A°.We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast.Nevertheless,we noticed a structural difference in the proteolytic active b1 subunit.Furthermore,we uncovered an unseen compression state by characterizing the proteasome’s conformational landscape.We suspect that this new conformation of the 20S core protease,in correlation with a partial opening of the unoccupied gate,may contribute to peptide release after proteolysis.Our data provide a structural basis for the plant proteasome,which is crucial for further studies.

关键词： 26S proteasome spinach UPS cryo-em conformational landscape

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cryo-em structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate

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Protein & Cell 2019年第2期10卷 120-130页

作者： Dejian Zhou Xing Zhu Sanduo Zheng Dan Tan Meng-Qiu Dong Keqiong Ye Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences Beijing 100730China Key Laboratory of RNA Biology Institute of BiophysicsCAS Center for Excellenee in BiomacromoleculesChinese Academy of SciencesBeijing 100101China National Institute of Biological Sciences Beijing 102206China University of Chinese Academy of Sciences Beijing 100049China

Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates.It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established.Here,we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 A resolution,revealing a half-assembled subunit.DomainsⅠ,ⅡandⅣof 25S/5.8S rRNA pack tightly into a native-like substructure,but domains Ⅲ,ⅣandⅤare not assembled.The structure contains 12 assembly factors and 19 ribosomal proteins,many of which are required for early processing of large subunit rRNA.The Brx1-Ebp2 complex would interfere with the assembly of domains Ⅳ and Ⅴ.Rpf1,Mak16,Nsa1 and Rrp1 form a cluster that consolidates the joining of domainsⅠandⅡ.Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.

关键词： ribosome assembly cryo-em pre-60S ribosome nucleolar

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cryo-em structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

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Plant Communications 2022年第1期3卷 53-70页

作者： Dmitry A.Semchonok Jyotirmoy Mondal Connor J.Cooper Katrina Schlum Meng Li Muhamed Amin Carlos O.S.Sorzano Erney Ramirez-Aportela Panagiotis L.Kastritis Egbert J.Boekema Albert Guskov Barry D.Bruce Groningen Biomolecular Sciences&Biotechnology Institute University of GroningenGroningenthe Netherlands Biochemistry&Cellular and Molecular Biology Department University of TennesseeKnoxvilleTNUSA Program in Genome Science and Technology University of TennesseeKnoxvilleTNUSA Bredesen Center for Interdisciplinary Research&Education University of TennesseeKnoxvilleTNUSA Department of Sciences University College GroningenGroningenthe Netherlands Biocomputing Unit National Center for Biotechnology(CSIC)Darwin 3Campus Universidad Auto´noma de MadridCantoblanco28049 MadridSpain Universidad CEU San Pablo Campus Urb.Monteprı´ncipeBoadilla del Monte28668 MadridSpain Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany Microbiology Department University of TennesseeKnoxvilleTNUSA Present address:Institute of Biochemistry and Biotechnology Martin Luther University Halle-WittenbergHalle/SaaleGermany School of Oceanography University of WashingtonSeattleWAUSA

Photosystem I(PSI)is one of two photosystems involved in oxygenic photosynthesis.PSI of cyanobacteria exists in monomeric,trimeric,and tetrameric forms,in contrast to the strictly monomeric form of PSI in plants and algae.The tetrameric organization raises questions about its structural,physiological,and evolutionary significance.Here we report the3.72 A˚resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic,unicellular cyanobacterium Chroococcidiopsis sp.TS-821.The structure resolves 44 subunits and 448 cofactor molecules.We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization.The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers.Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state.Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

关键词： cryo-em photosystem I non-heterocyst-forming cyanobacteria Chroococcidiopsis evolution of chloroplast high light adaptation

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cryo-em structure of L-fucokinase/GDP-fucose pyrophosphorylase(FKP)in Bacteroides fragilis

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Protein & Cell 2019年第5期10卷 365-369页

作者： Ying Liu Huifang Hu Jia Wang Qiang Zhou Peng Wu Nieng Yan Hong-Wei Wang Jia-Wei Wu Linfeng Sun Tsinghua-Peking Joint Center for Life Sciences School of Life SciencesTsinghua UniversityBeijing 100084China School of Life Sciences Tsinghua UniversityBeijing 100084China Department of Molecular Medicine The Scripps Research InstituteLa JollaCA 92037USA Ministry of Education Key Laboratory of Protein Sciences Beijing Advaneed Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China State Key Laboratory of Membrane Biology Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China CAS Center for Excellence in Molecular Cell Science Hefei National Laboratory for Physical Sciences at MicroscaleSchool of Life Scien cesUniversity of Science and Tech no logy of ChinaHefei 230027China

Dear Editor,L-Fucose(6-deoxy-L-galactose,fucose)is the basic compone nt of a variety of glyca n structures.The fucosylated oligosaccharides participate in a variety of cellular activities,like the cell-cell recognition,selectin-mediated leukocyteendothelial adhesion and the formation of Lewis blood group antigens(Ma et al.,2006).GDP-fucose is an important fucose donor in the process of fucosylated oligosaccharides formation.Two pathways of GDP-fucose synthesis are present in the cytosol of mammalian cells,including the de novo pathway and the salvage pathway(Becker et al.,2003).In the salvage pathway,cells use fucose from the extracellular or lysosomal sources to synthesize GDP-fucose.

关键词： cryo-em structure pyrophosphorylase Bacteroides fragilis

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A Noise Extraction Method for cryo-em Single-Particle Denoising

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Journal on Big Data 2022年第1期4卷 61-76页

作者： Huanrong Tang Sihan Wang Jianquan Ouyang Tianming Liu Key Laboratory of Intelligent Computing Information Processing Ministry of EducationSchool of Computer Science and School of Cyberspace ScienceXiangtan UniversityXiangtan411100China Department of Computer Science The University of GeorgiaGeorgia30301USA

cryo-Electron Microscopy(cryo-em)has become a powerful method to study the structure and function of biological macromolecules.However,in clustering tasks based on the projection angle of particles in cryoem,the noise considerably affects the clustering results.Existing denoising algorithms are ineffective due to the extremely low signal-to-noise ratio(SNR)of cryo-em images and the complexity of noise types.The noise of a single particle greatly influences the orientation estimation of the subsequent clustering task,and the result of the clustering task directly affects the accuracy of the 3D reconstruction.In this paper,we propose a construction method of cryo-em denoising dataset that uses U-Net to extract noise blocks from cryoem images,superimpose the noise block with the projected pure particles to construct our simulated dataset.Then we adopt a supervised generative adversarial network(GAN)with perceptual loss to train on our simulated dataset and denoise the real cryo-em single particle.The method can solve the problem of poor denoising performance caused by assuming that the noise of the Gaussian distribution does not conform to the noise distribution of cryo-em,and it can retain the useful information of particles to a great extent.We compared traditional image filtering methods and the classic deep learning denoising algorithm DnCNN on the simulated and real datasets.Experiment results show that the method based on deep learning has more advantages than traditional image denoising methods.It is worth mentioning that our method achieves a competitive peak signal to noise ratio(PSNR)and structural similarity(SSIM).Moreover,visualization results,indicate that our method can retain the structure information and orientation information of particles to a greater extent compared with other state-of-the-art image denoising methods.It means that our denoising task can provide considerable help for subsequent cryo-em clustering tasks.

关键词： cryo-em noise extraction denoising GAN

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Reduced graphene oxide membrane as supporting film for high-resolution cryo-em

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Biophysics Reports 2021年第3期7卷 227-238页

作者： Nan Liu Liming Zheng Jie Xu Jia Wang Cuixia Hu Jun Lan Xing Zhang Jincan Zhang Kui Xu Hang Cheng Zi Yang Xin Gao Xinquan Wang Hailin Peng Yanan Chen Hong-Wei Wang Ministry of Education Key Laboratory of Protein Sciences Beijing Advanced Innovation Center for Structural BiologySchool of Life SciencesTsinghua University Tsinghua-Peking Joint Center for Life Sciences Tsinghua University Center for Nanochemistry Beijing Science and Engineering Center for NanocarbonsBeijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking University Joint Graduate Program of Peking-Tsinghua-NIBS School of Life SciencesTsinghua University Beijing Frontier Research Center for Biological Structures Tsinghua University Academy for Advanced Interdisciplinary Studies Peking University School of Materials Science and Engineering Tianjin University

Although single-particle cryogenic electron microscopy(cryo-em) has been applied extensively for elucidating many crucial biological mechanisms at the molecular level, this technique still faces critical challenges, the major one of which is to prepare the high-quality cryo-em specimen. Aiming to achieve a more reproducible and efficient cryo-em specimen preparation, novel supporting films including graphene-based two-dimensional materials have been explored in recent years. Here we report a robust and simple method to fabricate em grids coated with single-or few-layer reduced graphene oxide(RGO) membrane in large batch for high-resolution cryo-em structural determination. The RGO membrane has decreased interlayer space and enhanced electrical conductivity in comparison to regular graphene oxide(GO) membrane. Moreover, we found that the RGO supporting film exhibited nice particle-absorption ability, thus avoiding the air–water interface problem. More importantly, we found that the RGO supporting film is particularly useful in cryo-em reconstruction of sub-100-k Da biomolecules at near-atomic resolution, as exemplified by the study of RBD-ACE2 complex and other small protein molecules. We envision that the RGO membranes can be used as a robust graphene-based supporting film in cryo-em specimen preparation.

关键词： Reduced graphene oxide cryo-em 3D reconstruction Air-water interface

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