1
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Banjan B, Vishwakarma R, Ramakrishnan K, Dev RR, Kalath H, Kumar P, Soman S, Raju R, Revikumar A, Rehman N, Abhinand CS. Targeting AFP-RARβ complex formation: a potential strategy for treating AFP-positive hepatocellular carcinoma. Mol Divers 2024:10.1007/s11030-024-10915-8. [PMID: 38955977 DOI: 10.1007/s11030-024-10915-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/09/2024] [Indexed: 07/04/2024]
Abstract
Alpha-fetoprotein (AFP) is a glycoprotein primarily expressed during embryogenesis, with declining levels postnatally. Elevated AFP levels correlate with pathological conditions such as liver fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Recent investigations underscore AFP's intracellular role in HCC progression, wherein it forms complexes with proteins like Phosphatase and tensin homolog (PTEN), Caspase 3 (CASP3), and Retinoic acid receptors and Retinoid X receptors (RAR/RXR). RAR and RXR regulate gene expression linked to cell death and tumorigenesis in normal physiology. AFP impedes RAR/RXR dimerization, nuclear translocation, and function, promoting gene expression favoring cancer progression in HCC that provoked us to target AFP as a drug candidate. Despite extensive studies, inhibitors targeting AFP to disrupt complex formation and activities remain scarce. In this study, employing protein-protein docking, amino acid residues involved in AFP-RARβ interaction were identified, guiding the definition of AFP's active site for potential inhibitor screening. Currently, kinase inhibitors play a significant role in cancer treatment and, the present study explores the potential of repurposing FDA-approved protein kinase inhibitors to target AFP. Molecular docking with kinase inhibitors revealed Lapatinib as a candidate drug of the AFP-RARβ complex. Molecular dynamics simulations and binding energy calculations, employing Mechanic/Poisson-Boltzmann Surface Area (MM-PBSA), confirmed Lapatinib's stability with AFP. The study suggests Lapatinib's potential in disrupting the AFP-RARβ complex, providing a promising avenue for treating molecularly stratified AFP-positive HCC or its early stages.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Riya Vishwakarma
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Krishnapriya Ramakrishnan
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Radul R Dev
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Haritha Kalath
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Pankaj Kumar
- Nitte (Deemed to Be University), Department of Pharmaceutical Chemistry, NGSMPS, NGSM Institute of Pharmaceutical Sciences, Mangalore, 575018, Karnataka, India
| | - Sowmya Soman
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Vazhuthacaud, Thiruvananthapuram, Kerala, 695014, India
| | - Niyas Rehman
- Centre for Integrative Omics Data Science, Yenepoya (Deemed to Be University), Mangalore, 575018, India.
| | - Chandran S Abhinand
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to Be University), Deralakatte, Mangalore, 575018, Karnataka, India.
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2
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Yadav S, Vinothkumar KR. Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol 2024; 80:535-550. [PMID: 38935342 PMCID: PMC11220838 DOI: 10.1107/s2059798324005229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
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Affiliation(s)
- Swati Yadav
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
| | - Kutti R. Vinothkumar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
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3
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Wang J, Zhou H, Liang R, Qin W. Chronopotentiometric Nanopore Sensor Based on a Stimulus-Responsive Molecularly Imprinted Polymer for Label-Free Dual-Biomarker Detection. Anal Chem 2024; 96:9370-9378. [PMID: 38683892 DOI: 10.1021/acs.analchem.3c05817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The development of sensors for detection of biomarkers exhibits an exciting potential in diagnosis of diseases. Herein, we propose a novel electrochemical sensing strategy for label-free dual-biomarker detection, which is based on the combination of stimulus-responsive molecularly imprinted polymer (MIP)-modified nanopores and a polymeric membrane chronopotentiometric sensor. The ion fluxes galvanostatically imposed on the sensing membrane surface can be blocked by the recognition reaction between the target biomarker in the sample solution and the stimulus-responsive MIP receptor in the nanopores, thus causing a potential change. By using two external stimuli (i.e., pH and temperature), the recognition abilities of the stimulus-responsive MIP receptor can be effectively modulated so that dual-biomarker label-free chronopotentiometric detection can be achieved. Using alpha fetoprotein (AFP) and prostate-specific antigen (PSA) as model biomarkers, the proposed sensor offers detection limits of 0.17 and 0.42 ng/mL for AFP and PSA, respectively.
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Affiliation(s)
- Junhao Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huihui Zhou
- The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai, Shandong 264099, China
| | - Rongning Liang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS); Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong 264003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
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4
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Liu N, Wang HW. Graphene in cryo-EM specimen optimization. Curr Opin Struct Biol 2024; 86:102823. [PMID: 38688075 DOI: 10.1016/j.sbi.2024.102823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/16/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
Abstract
Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule embedding in ice, reduces beam-induced motion, while imposing negligible background noise. Various types of graphene-coated cryo-EM grids were implemented to improve the robustness and efficiency of specimen preparation. Graphene functionalization by different means has been proved specifically useful in addressing challenges related to the air-water interface (AWI), such as preferential orientation and sample denaturation. Graphene sandwich specimen preparation sets a new direction to explore in cryo-EM analysis of biological specimens. In this review, we discuss the current challenges and future prospects of graphene application in cryo-EM analysis of macromolecules.
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Affiliation(s)
- Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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5
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Amontree J, Yan X, DiMarco CS, Levesque PL, Adel T, Pack J, Holbrook M, Cupo C, Wang Z, Sun D, Biacchi AJ, Wilson-Stokes CE, Watanabe K, Taniguchi T, Dean CR, Hight Walker AR, Barmak K, Martel R, Hone J. Reproducible graphene synthesis by oxygen-free chemical vapour deposition. Nature 2024; 630:636-642. [PMID: 38811732 DOI: 10.1038/s41586-024-07454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 04/22/2024] [Indexed: 05/31/2024]
Abstract
Chemical vapour deposition (CVD) synthesis of graphene on copper has been broadly adopted since the first demonstration of this process1. However, widespread use of CVD-grown graphene for basic science and applications has been hindered by challenges with reproducibility2 and quality3. Here we identify trace oxygen as a key factor determining the growth trajectory and quality for graphene grown by low-pressure CVD. Oxygen-free chemical vapour deposition (OF-CVD) synthesis is fast and highly reproducible, with kinetics that can be described by a compact model, whereas adding trace oxygen leads to suppressed nucleation and slower/incomplete growth. Oxygen affects graphene quality as assessed by surface contamination, emergence of the Raman D peak and decrease in electrical conductivity. Epitaxial graphene grown in oxygen-free conditions is contamination-free and shows no detectable D peak. After dry transfer and boron nitride encapsulation, it shows room-temperature electrical-transport behaviour close to that of exfoliated graphene. A graphite-gated device shows well-developed integer and fractional quantum Hall effects. By highlighting the importance of eliminating trace oxygen, this work provides guidance for future CVD system design and operation. The increased reproducibility and quality afforded by OF-CVD synthesis will broadly influence basic research and applications of graphene.
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Affiliation(s)
- Jacob Amontree
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Xingzhou Yan
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | | | - Pierre L Levesque
- Infinite Potential Laboratories, Waterloo, Ontario, Canada
- Département de Chimie, Université de Montréal, Montréal, Quebec, Canada
- Institut Courtois, Université de Montréal, Montréal, Quebec, Canada
| | - Tehseen Adel
- Quantum Metrology Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Jordan Pack
- Department of Physics, Columbia University, New York, NY, USA
| | | | - Christian Cupo
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Zhiying Wang
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Dihao Sun
- Department of Physics, Columbia University, New York, NY, USA
| | - Adam J Biacchi
- Nanoscale Device Characterization Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Charlezetta E Wilson-Stokes
- Quantum Metrology Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
- Department of Mechanical Engineering, Howard University, Washington, DC, USA
| | - Kenji Watanabe
- Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Takashi Taniguchi
- Research Center for Functional Materials, National Institute for Materials Science, Tsukuba, Japan
| | - Cory R Dean
- Department of Physics, Columbia University, New York, NY, USA
| | - Angela R Hight Walker
- Quantum Metrology Division, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Katayun Barmak
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA.
| | - Richard Martel
- Département de Chimie, Université de Montréal, Montréal, Quebec, Canada.
- Institut Courtois, Université de Montréal, Montréal, Quebec, Canada.
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY, USA.
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6
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Liu K, Wu C, Zhu M, Xu J, Lin B, Lin H, Liu Z, Li M. Structural characteristics of alpha-fetoprotein, including N-glycosylation, metal ion and fatty acid binding sites. Commun Biol 2024; 7:505. [PMID: 38678117 PMCID: PMC11055904 DOI: 10.1038/s42003-024-06219-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
Alpha-fetoprotein (AFP), a serum glycoprotein, is expressed during embryonic development and the pathogenesis of liver cancer. It serves as a clinical tumor marker, function as a carcinogen, immune suppressor, and transport vehicle; but the detailed AFP structural information has not yet been reported. In this study, we used single-particle cryo-electron microscopy(cryo-EM) to analyze the structure of the recombinant AFP obtained a 3.31 Å cryo-EM structure and built an atomic model of AFP. We observed and identified certain structural features of AFP, including N-glycosylation at Asn251, four natural fatty acids bound to distinct domains, and the coordination of metal ions by residues His22, His264, His268, and Asp280. Furthermore, we compared the structural similarities and differences between AFP and human serum albumin. The elucidation of AFP's structural characteristics not only contributes to a deeper understanding of its functional mechanisms, but also provides a structural basis for developing AFP-based drug vehicles.
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Affiliation(s)
- Kun Liu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Cang Wu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China
| | - Mingyue Zhu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Junnv Xu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
- Department of Medical Oncology, Second Affiliated Hospital, Hainan Medical College, Haikou, 570023, Hainan, PR China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China
| | - Haifeng Lin
- Department of Medical Oncology, Second Affiliated Hospital, Hainan Medical College, Haikou, 570023, Hainan, PR China
| | - Zhongmin Liu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China.
| | - Mengsen Li
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical College, Haikou, 571199, Hainan, PR China.
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, PR China.
- Institution of Tumor, Hainan Medical College, Haikou, 570102, Hainan, PR China.
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7
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Zhu Y, Shi Z, Zhao Y, Bu S, Hu Z, Liao J, Lu Q, Zhou C, Guo B, Shang M, Li F, Xu Z, Zhang J, Xie Q, Li C, Sun P, Mao B, Zhang X, Liu Z, Lin L. Recent trends in the transfer of graphene films. NANOSCALE 2024; 16:7862-7873. [PMID: 38568087 DOI: 10.1039/d3nr05626k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Recent years have witnessed advances in chemical vapor deposition growth of graphene films on metal foils with fine scalability and thickness controllability. However, challenges for obtaining wrinkle-free, defect-free and large-area uniformity remain to be tackled. In addition, the real commercial applications of graphene films still require industrially compatible transfer techniques with reliable performance of transferred graphene, excellent production capacity, and suitable cost. Transferred graphene films, particularly with a large area, still suffer from the presence of transfer-related cracks, wrinkles and contaminants, which would strongly deteriorate the quality and uniformity of transferred graphene films. Potential applications of graphene films include moisture barrier films, transparent conductive films, electromagnetic shielding films, and optical communications; such applications call different requirements for the performance of transferred graphene, which, in turn, determine the suitable transfer techniques. Besides the reliable transfer process, automatic machines should be well developed for the future batch transfer of graphene films, ensuring the repeatability and scalability. This mini-review provides a summary of recent advances in the transfer of graphene films and offers a perspective for future directions of transfer techniques that are compatible for industrial batch transfer.
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Affiliation(s)
- Yaqi Zhu
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266000, China.
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Beijing Graphene Institute, Beijing 100095, P. R. China.
| | - Zhuofeng Shi
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266000, China.
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Beijing Graphene Institute, Beijing 100095, P. R. China.
| | - Yixuan Zhao
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Center for Nanochemistry, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
| | - Saiyu Bu
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
| | - Zhaoning Hu
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Beijing Graphene Institute, Beijing 100095, P. R. China.
| | - Junhao Liao
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
- National Center for Nanoscience and Technology, Beijing 100190, China
| | - Qi Lu
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- State Key Laboratory of Heavy Oil Processing, College of Science, China University of Petroleum, Beijing 102249, P. R. China
| | - Chaofan Zhou
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Beijing Graphene Institute, Beijing 100095, P. R. China.
| | - Bingbing Guo
- Beijing Graphene Institute, Beijing 100095, P. R. China.
| | - Mingpeng Shang
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Center for Nanochemistry, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Fangfang Li
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Zhiying Xu
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, P. R. China
| | - Jialin Zhang
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, P. R. China
| | - Qin Xie
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Chunhu Li
- Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, P. R. China
| | - Pengzhan Sun
- Institute of Applied Physics and Materials, Engineering, University of Macau, Avenida da Universidade, Taipa, Macau SAR 999078, P.R. China
| | - Boyang Mao
- Department of Engineering, University of Cambridge, Cambridge, CB3 0FA, U.K
| | - Xiaodong Zhang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao, 266000, China.
| | - Zhongfan Liu
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Center for Nanochemistry, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Li Lin
- School of Materials Science and Engineering, Peking University, Beijing 100871, P. R. China.
- Beijing Graphene Institute, Beijing 100095, P. R. China.
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
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8
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Zhu Y, Zhang J, Cheng T, Tang J, Duan H, Hu Z, Shao J, Wang S, Wei M, Wu H, Li A, Li S, Balci O, Shinde SM, Ramezani H, Wang L, Lin L, Ferrari AC, Yakobson BI, Peng H, Jia K, Liu Z. Controlled Growth of Single-Crystal Graphene Wafers on Twin-Boundary-Free Cu(111) Substrates. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308802. [PMID: 37878366 DOI: 10.1002/adma.202308802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Single-crystal graphene (SCG) wafers are needed to enable mass-electronics and optoelectronics owing to their excellent properties and compatibility with silicon-based technology. Controlled synthesis of high-quality SCG wafers can be done exploiting single-crystal Cu(111) substrates as epitaxial growth substrates recently. However, current Cu(111) films prepared by magnetron sputtering on single-crystal sapphire wafers still suffer from in-plane twin boundaries, which degrade the SCG chemical vapor deposition. Here, it is shown how to eliminate twin boundaries on Cu and achieve 4 in. Cu(111) wafers with ≈95% crystallinity. The introduction of a temperature gradient on Cu films with designed texture during annealing drives abnormal grain growth across the whole Cu wafer. In-plane twin boundaries are eliminated via migration of out-of-plane grain boundaries. SCG wafers grown on the resulting single-crystal Cu(111) substrates exhibit improved crystallinity with >97% aligned graphene domains. As-synthesized SCG wafers exhibit an average carrier mobility up to 7284 cm2 V-1 s-1 at room temperature from 103 devices and a uniform sheet resistance with only 5% deviation in 4 in. region.
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Affiliation(s)
- Yeshu Zhu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Jincan Zhang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Ting Cheng
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
| | - Jilin Tang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Hongwei Duan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Zhaoning Hu
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jiaxin Shao
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Shiwei Wang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Mingyue Wei
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Haotian Wu
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Ang Li
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- College of Science, China University of Petroleum, Beijing, 102249, P. R. China
| | - Sheng Li
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Osman Balci
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Sachin M Shinde
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Hamideh Ramezani
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Luda Wang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, School of Integrated Circuits, Peking University, Beijing, 100871, P. R. China
| | - Li Lin
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
- School of Materials Science and Engineering, Peking University, Beijing, 100871, P. R. China
| | - Andrea C Ferrari
- Cambridge Graphene Centre, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Boris I Yakobson
- Department of Materials Science & NanoEngineering, Rice University, Houston, TX, 77005, USA
- Department of Chemistry, Rice University, Houston, TX, 77005, USA
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Kaicheng Jia
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
| | - Zhongfan Liu
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Science, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
- Technology Innovation Center of Graphene Metrology and Standardization for State Market Regulation, Beijing Graphene Institute, Beijing, 100095, P. R. China
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9
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Cui X, Liu Y, Chen Y. Ultrafast micro/nano-manufacturing of metastable materials for energy. Natl Sci Rev 2024; 11:nwae033. [PMID: 38469545 PMCID: PMC10926976 DOI: 10.1093/nsr/nwae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 03/13/2024] Open
Abstract
The structural engineering of metastable nanomaterials with abundant defects has attracted much attention in energy-related fields. The high-temperature shock (HTS) technique, as a rapidly developing and advanced synthesis strategy, offers significant potential for the rational design and fabrication of high-quality nanocatalysts in an ultrafast, scalable, controllable and eco-friendly way. In this review, we provide an overview of various metastable micro- and nanomaterials synthesized via HTS, including single metallic and bimetallic nanostructures, high entropy alloys, metal compounds (e.g. metal oxides) and carbon nanomaterials. Note that HTS provides a new research dimension for nanostructures, i.e. kinetic modulation. Furthermore, we summarize the application of HTS-as supporting films for transmission electron microscopy grids-in the structural engineering of 2D materials, which is vital for the direct imaging of metastable materials. Finally, we discuss the potential future applications of high-throughput and liquid-phase HTS strategies for non-equilibrium micro/nano-manufacturing beyond energy-related fields. It is believed that this emerging research field will bring new opportunities to the development of nanoscience and nanotechnology in both fundamental and practical aspects.
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Affiliation(s)
- Xiaoya Cui
- School of Materials Science and Engineering, Key Laboratory of Advanced Ceramics and Machining Technology (Ministry of Education), and Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300072, China
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanchang Liu
- School of Materials Science and Engineering, Key Laboratory of Advanced Ceramics and Machining Technology (Ministry of Education), and Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300072, China
| | - Yanan Chen
- School of Materials Science and Engineering, Key Laboratory of Advanced Ceramics and Machining Technology (Ministry of Education), and Tianjin Key Laboratory of Composite and Functional Materials, Tianjin University, Tianjin 300072, China
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10
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Chen X, Zou Z, Li W, Dong X, Chen Y, Lu Y, Zhu M, Li M, Lin B. α-Conotoxin recombinant protein ImI-AFP3 efficiently inhibits the growth and migration of lung cancer cells. Protein Expr Purif 2024; 215:106405. [PMID: 37979629 DOI: 10.1016/j.pep.2023.106405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/11/2023] [Accepted: 11/13/2023] [Indexed: 11/20/2023]
Abstract
α-Conotoxin ImI is a selective antagonist of alpha7 nicotinic acetylcholine receptor (α7 nAChR) that is involved in cancer development. Human alpha fetoprotein domain 3 (AFP3) is a prototype of anticancer agents. In an effort to design drugs for anticancer treatments, we fused the ImI peptide to AFP3 as a fusion protein for testing. The fusion protein (ImI-AFP3) was highly expressed in the insect Bac-to-Bac system. The purified fusion protein was found to have improved anticancer activity and synergized with the drug gefitinib to inhibit the growth and migration of A549 and NCI-H1299 lung cancer cells. Our data have demonstrated that the recombinant protein ImI-AFP3 is a promising candidate for drug development to suppress lung cancer cell growth, especially to suppress hepatoid adenocarcinoma of the lung (HAL) cell growth.
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Affiliation(s)
- Xiaobing Chen
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Zijuan Zou
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Wei Li
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Xu Dong
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Yi Chen
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Yan Lu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Mingyue Zhu
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China
| | - Mengsen Li
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China; Institution of Tumor, Hainan Medical University, Haikou, 570102, Hainan Province, PR China.
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, 571199, Hainan Province, PR China.
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11
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Abe KM, Lim CJ. Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579238. [PMID: 38370693 PMCID: PMC10871254 DOI: 10.1101/2024.02.06.579238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis Abundant (LEA) proteins, which naturally bind to AWI, can protect samples from AWI damage during plunge freezing. This protection is demonstrated with two LEA proteins from nematodes and tardigrades, which rescued the cryo-EM structural determination outcome of two fragile multisubunit protein complexes.
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Affiliation(s)
- Kaitlyn M. Abe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
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12
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Bhattacharjee S, Feng X, Maji S, Dadhwal P, Zhang Z, Brown ZP, Frank J. Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling. Cell 2024; 187:782-796.e23. [PMID: 38244547 PMCID: PMC10872292 DOI: 10.1016/j.cell.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024]
Abstract
The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-pathway intermediates have been trapped using chemical modifications or reduced temperature, giving limited insights. Here, we introduce a time-resolved cryo-EM method using a reusable PDMS-based microfluidic chip assembly with high reactant mixing efficiency. Coating of PDMS walls with SiO2 virtually eliminates non-specific sample adsorption and ensures maintenance of the stoichiometry of the reaction, rendering it highly reproducible. In an operating range from 10 to 1,000 ms, the device allows us to follow in vitro reactions of biological molecules at resolution levels in the range of 3 Å. By employing this method, we show the mechanism of progressive HflX-mediated splitting of the 70S E. coli ribosome in the presence of the GTP via capture of three high-resolution reaction intermediates within 140 ms.
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Affiliation(s)
- Sayan Bhattacharjee
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Xiangsong Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA.
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Prikshat Dadhwal
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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13
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Xu J, Gao X, Zheng L, Jia X, Xu K, Ma Y, Wei X, Liu N, Peng H, Wang HW. Graphene sandwich-based biological specimen preparation for cryo-EM analysis. Proc Natl Acad Sci U S A 2024; 121:e2309384121. [PMID: 38252835 PMCID: PMC10835136 DOI: 10.1073/pnas.2309384121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
High-quality specimen preparation plays a crucial role in cryo-electron microscopy (cryo-EM) structural analysis. In this study, we have developed a reliable and convenient technique called the graphene sandwich method for preparing cryo-EM specimens. This method involves using two layers of graphene films that enclose macromolecules on both sides, allowing for an appropriate ice thickness for cryo-EM analysis. The graphene sandwich helps to mitigate beam-induced charging effect and reduce particle motion compared to specimens prepared using the traditional method with graphene support on only one side, therefore improving the cryo-EM data quality. These advancements may open new opportunities to expand the use of graphene in the field of biological electron microscopy.
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Affiliation(s)
- Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Xiaoyin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Liming Zheng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
| | - Xia Jia
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Kui Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Yuwei Ma
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Xiaoding Wei
- State Key Laboratory for Turbulence and Complex System, Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing100871, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Hailin Peng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing100871, China
- Beijing Graphene Institute, Beijing100095, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing100084, China
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing100084, China
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14
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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15
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Zhu J, Zhang Q, Zhang H, Shi Z, Hu M, Bao C. A minority of final stacks yields superior amplitude in single-particle cryo-EM. Nat Commun 2023; 14:7822. [PMID: 38072910 PMCID: PMC10711021 DOI: 10.1038/s41467-023-43555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Cryogenic electron microscopy (cryo-EM) is widely used to determine near-atomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a crucial question in the field of cryo-EM remains unanswered: how close can we get to the minimum number of particles required to reach a specific resolution in practice? The absence of an answer to this question has impeded progress in understanding sample behavior and the performance of sample preparation methods. To address this issue, we develop an iterative particle sorting and/or sieving method called CryoSieve. Extensive experiments demonstrate that CryoSieve outperforms other cryo-EM particle sorting algorithms, revealing that most particles are unnecessary in final stacks. The minority of particles remaining in the final stacks yield superior high-resolution amplitude in reconstructed density maps. For some datasets, the size of the finest subset approaches the theoretical limit.
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Affiliation(s)
- Jianying Zhu
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China
| | - Qi Zhang
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China
- School of Life Science, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China
- Beijing Frontier Research Center for Biological Structure, Beijing, China
| | - Hui Zhang
- Qiuzhen College, Tsinghua University, Beijing, China
| | - Zuoqiang Shi
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
| | - Mingxu Hu
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.
- School of Life Science, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology, Beijing, China.
- Beijing Frontier Research Center for Biological Structure, Beijing, China.
- Shenzhen Academy of Research and Translation, Shenzhen, China.
| | - Chenglong Bao
- Yau Mathematical Sciences Center, Tsinghua University, Beijing, China.
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing, China.
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, China.
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16
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Ma H, Yan S, Lu X, Bao YF, Liu J, Liao L, Dai K, Cao M, Zhao X, Yan H, Wang HL, Peng X, Chen N, Feng H, Zhu L, Yao G, Fan C, Wu DY, Wang B, Wang X, Ren B. Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy. SCIENCE ADVANCES 2023; 9:eadh8362. [PMID: 37992170 PMCID: PMC10665000 DOI: 10.1126/sciadv.adh8362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/23/2023] [Indexed: 11/24/2023]
Abstract
Despite great advances in protein structure analysis, label-free and ultrasensitive methods to obtain the natural and dynamic three-dimensional (3D) structures are still urgently needed. Surface-enhanced Raman spectroscopy (SERS) can be a good candidate, whereas the complexity originated from the interactions between the protein and the gradient surface electric field makes it extremely challenging to determine the protein structure. Here, we propose a deciphering strategy for accurate determination of 3D protein structure from experimental SERS spectra in seconds by simply summing SERS spectra of isolated amino acids in electric fields of different strength with their orientations in protein. The 3D protein structure can be reconstructed by comparing the experimental spectra obtained in a well-defined gap-mode SERS configuration with the simulated spectra. The gradient electric field endows SERS with a unique advantage to section biomolecules with atomic precision, which makes SERS a competent tool for monitoring biomolecular events under physiological conditions.
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Affiliation(s)
- Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Sen Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Xinyu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Yi-Fan Bao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Jia Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Langxing Liao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Kun Dai
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Maofeng Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Xiaojiao Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Hao Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hai-Long Wang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Xiaohui Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Ningyu Chen
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Huishu Feng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Lilin Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Guangbao Yao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xiang Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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17
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Basanta B, Chen W, Pride DE, Lander GC. Fabrication of Monolayer Graphene-Coated Grids for Cryoelectron Microscopy. J Vis Exp 2023:10.3791/65702. [PMID: 37747197 PMCID: PMC11141527 DOI: 10.3791/65702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Cryogenic electron microscopy (cryoEM) has emerged as a powerful technique for probing the atomic structure of macromolecular complexes. Sample preparation for cryoEM requires preserving specimens in a thin layer of vitreous ice, typically suspended within the holes of a fenestrated support film. However, all commonly used sample preparation approaches for cryoEM studies expose the specimen to the air-water interface, introducing a strong hydrophobic effect on the specimen that often results in denaturation, aggregation, and complex dissociation. Further, preferred hydrophobic interactions between regions of the specimen and the air-water interface impact the orientations adopted by the macromolecules, resulting in 3D reconstructions with anisotropic directional resolution. Adsorption of cryoEM specimens to a monolayer of graphene has been shown to help mitigate interactions with the air-water interface while minimizing the introduction of background noise. Graphene supports also offer the benefit of substantially lowering the required concentration of proteins required for cryoEM imaging. Despite the advantages of these supports, graphene-coated grids are not widely used by the cryoEM community due to the prohibitive expense of commercial options and the challenges associated with large-scale in-house production. This paper describes an efficient method for preparing batches of cryoEM grids that have nearly full coverage of monolayer graphene.
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Affiliation(s)
- Benjamin Basanta
- Department of Structural and Computational Biology, Scripps Research
| | - Wenqian Chen
- Department of Structural and Computational Biology, Scripps Research
| | - Daniel E Pride
- Department of Structural and Computational Biology, Scripps Research
| | - Gabriel C Lander
- Department of Structural and Computational Biology, Scripps Research;
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18
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Zhang Y, van Schayck JP, Pedrazo-Tardajos A, Claes N, Noteborn WEM, Lu PH, Duimel H, Dunin-Borkowski RE, Bals S, Peters PJ, Ravelli RBG. Charging of Vitreous Samples in Cryogenic Electron Microscopy Mitigated by Graphene. ACS NANO 2023; 17:15836-15846. [PMID: 37531407 PMCID: PMC10448747 DOI: 10.1021/acsnano.3c03722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
Cryogenic electron microscopy can provide high-resolution reconstructions of macromolecules embedded in a thin layer of ice from which atomic models can be built de novo. However, the interaction between the ionizing electron beam and the sample results in beam-induced motion and image distortion, which limit the attainable resolutions. Sample charging is one contributing factor of beam-induced motions and image distortions, which is normally alleviated by including part of the supporting conducting film within the beam-exposed region. However, routine data collection schemes avoid strategies whereby the beam is not in contact with the supporting film, whose rationale is not fully understood. Here we characterize electrostatic charging of vitreous samples, both in imaging and in diffraction mode. We mitigate sample charging by depositing a single layer of conductive graphene on top of regular EM grids. We obtained high-resolution single-particle analysis (SPA) reconstructions at 2 Å when the electron beam only irradiates the middle of the hole on graphene-coated grids, using data collection schemes that previously failed to produce sub 3 Å reconstructions without the graphene layer. We also observe that the SPA data obtained with the graphene-coated grids exhibit a higher b factor and reduced particle movement compared to data obtained without the graphene layer. This mitigation of charging could have broad implications for various EM techniques, including SPA and cryotomography, and for the study of radiation damage and the development of future sample carriers. Furthermore, it may facilitate the exploration of more dose-efficient, scanning transmission EM based SPA techniques.
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Affiliation(s)
- Yue Zhang
- Maastricht
MultiModal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - J. Paul van Schayck
- Maastricht
MultiModal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Adrián Pedrazo-Tardajos
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Antwerp 2020, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Nathalie Claes
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Antwerp 2020, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Willem E. M. Noteborn
- Netherlands
Centre for Electron Nanoscopy (NeCEN), Leiden
University, 2300 RS Leiden, The Netherlands
| | - Peng-Han Lu
- Ernst
Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter
Grünberg Institute, Forschungszentrum
Jülich, 52425 Jülich, Germany
| | - Hans Duimel
- Maastricht
MultiModal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Rafal E. Dunin-Borkowski
- Ernst
Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter
Grünberg Institute, Forschungszentrum
Jülich, 52425 Jülich, Germany
| | - Sara Bals
- Electron
Microscopy for Materials Science (EMAT), University of Antwerp, Antwerp 2020, Belgium
- NANOlab
Center of Excellence, University of Antwerp, 2020 Antwerp, Belgium
| | - Peter J. Peters
- Maastricht
MultiModal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Raimond B. G. Ravelli
- Maastricht
MultiModal Molecular Imaging Institute (M4i), Maastricht University, 6200 MD Maastricht, The Netherlands
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19
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.548955. [PMID: 37503021 PMCID: PMC10369999 DOI: 10.1101/2023.07.14.548955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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20
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Cheng H, Zheng L, Liu N, Huang C, Xu J, Lu Y, Cui X, Xu K, Hou Y, Tang J, Zhang Z, Li J, Ni X, Chen Y, Peng H, Wang HW. Dual-Affinity Graphene Sheets for High-Resolution Cryo-Electron Microscopy. J Am Chem Soc 2023; 145:8073-8081. [PMID: 37011903 PMCID: PMC10103130 DOI: 10.1021/jacs.3c00659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
With the development of cryo-electron microscopy (cryo-EM), high-resolution structures of macromolecules can be reconstructed by the single particle method efficiently. However, challenges may still persist during the specimen preparation stage. Specifically, proteins tend to adsorb at the air-water interface and exhibit a preferred orientation in vitreous ice. To overcome these challenges, we have explored dual-affinity graphene (DAG) modified with two different affinity ligands as a supporting material for cryo-EM sample preparation. The ligands can bind to distinct sites on the corresponding tagged particles, which in turn generates various orientation distributions of particles and prevents the adsorption of protein particles onto the air-water interface. As expected, the DAG exhibited high binding specificity and affinity to target macromolecules, resulting in more balanced particle Euler angular distributions compared to single functionalized graphene on two different protein cases, including the SARS -CoV-2 spike glycoprotein. We anticipate that the DAG grids will enable facile and efficient three-dimensional (3D) reconstruction for cryo-EM structural determination, providing a robust and general technique for future studies.
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Affiliation(s)
- Hang Cheng
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Liming Zheng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
| | - Congyuan Huang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye Lu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoya Cui
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
| | - Kui Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Hou
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Junchuan Tang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhong Zhang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jing Li
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Xiaodan Ni
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Yanan Chen
- School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing Graphene Institute (BGI), Beijing 100095, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
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21
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Fujita J, Makino F, Asahara H, Moriguchi M, Kumano S, Anzai I, Kishikawa JI, Matsuura Y, Kato T, Namba K, Inoue T. Epoxidized graphene grid for highly efficient high-resolution cryoEM structural analysis. Sci Rep 2023; 13:2279. [PMID: 36755111 PMCID: PMC9908306 DOI: 10.1038/s41598-023-29396-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Functionalization of graphene is one of the most important fundamental technologies in a wide variety of fields including industry and biochemistry. We have successfully achieved a novel oxidative modification of graphene using photoactivated ClO2· as a mild oxidant and confirmed the oxidized graphene grid is storable with its functionality for at least three months under N2 atmosphere. Subsequent chemical functionalization enabled us to develop an epoxidized graphene grid (EG-grid™), which effectively adsorbs protein particles for electron cryomicroscopy (cryoEM) image analysis. The EG-grid dramatically improved the particle density and orientation distribution. The density maps of GroEL and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) were reconstructed at 1.99 and 2.16 Å resolution from only 504 and 241 micrographs, respectively. A sample solution of 0.1 mg ml-1 was sufficient to reconstruct a 3.10 Å resolution map of SARS-CoV-2 spike protein from 1163 micrographs. The map resolutions of β-galactosidase and apoferritin easily reached 1.81 Å and 1.29 Å resolution, respectively, indicating its atomic-resolution imaging capability. Thus, the EG-grid will be an extremely powerful tool for highly efficient high-resolution cryoEM structural analysis of biological macromolecules.
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Affiliation(s)
- Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.,JEOL Ltd, 3-2-1 Musashino, Akishima, Tokyo, 196-8558, Japan
| | - Haruyasu Asahara
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Open and Transdisciplinary Research Initiatives, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Maiko Moriguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shota Kumano
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Molecular Biosciences, Kyoto Sangyo University, Motoyama Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Open and Transdisciplinary Research Initiatives, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,dotAqua Inc., 2-1 Yamadaoka, Suita, Osaka, Japan.
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