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Zhao Q, Hong X, Wang Y, Zhang S, Ding Z, Meng X, Song Q, Hong Q, Jiang W, Shi X, Cai T, Cong Y. An immobilized antibody-based affinity grid strategy for on-grid purification of target proteins enables high-resolution cryo-EM. Commun Biol 2024; 7:715. [PMID: 38858498 PMCID: PMC11164986 DOI: 10.1038/s42003-024-06406-z] [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: 01/17/2024] [Accepted: 05/31/2024] [Indexed: 06/12/2024] Open
Abstract
In cryo-electron microscopy (cryo-EM), sample preparation poses a critical bottleneck, particularly for rare or fragile macromolecular assemblies and those suffering from denaturation and particle orientation distribution issues related to air-water interface. In this study, we develop and characterize an immobilized antibody-based affinity grid (IAAG) strategy based on the high-affinity PA tag/NZ-1 antibody epitope tag system. We employ Pyr-NHS as a linker to immobilize NZ-1 Fab on the graphene oxide or carbon-covered grid surface. Our results demonstrate that the IAAG grid effectively enriches PA-tagged target proteins and overcomes preferred orientation issues. Furthermore, we demonstrate the utility of our IAAG strategy for on-grid purification of low-abundance target complexes from cell lysates, enabling atomic resolution cryo-EM. This approach greatly streamlines the purification process, reduces the need for large quantities of biological samples, and addresses common challenges encountered in cryo-EM sample preparation. Collectively, our IAAG strategy provides an efficient and robust means for combined sample purification and vitrification, feasible for high-resolution cryo-EM. This approach holds potential for broader applicability in both cryo-EM and cryo-electron tomography (cryo-ET).
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Affiliation(s)
- Qiaoyu Zhao
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xiaoyu Hong
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Yanxing Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Shaoning Zhang
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 200050, Shanghai, China
| | - Zhanyu Ding
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Xueming Meng
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Qianqian Song
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Qin Hong
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China
| | - Wanying Jiang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Xiangyi Shi
- Shanghai Nanoport, Thermo Fisher Scientific, Shanghai, China
| | - Tianxun Cai
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 200050, Shanghai, China
| | - Yao Cong
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
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2
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Ramlaul K, Feng Z, Canavan C, de Martín Garrido N, Carreño D, Crone M, Jensen KE, Li B, Barnett H, Riglar DT, Freemont PS, Miller D, Aylett CHS. A 3D-printed flow-cell for on-grid purification of electron microscopy samples directly from lysate. J Struct Biol 2023; 215:107999. [PMID: 37451560 DOI: 10.1016/j.jsb.2023.107999] [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: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
While recent advances in cryo-EM, coupled with single particle analysis, have the potential to allow structure determination in a near-native state from vanishingly few individual particles, this vision has yet to be realised in practise. Requirements for particle numbers that currently far exceed the theoretical lower limits, challenges with the practicalities of achieving high concentrations for difficult-to-produce samples, and inadequate sample-dependent imaging conditions, all result in significant bottlenecks preventing routine structure determination using cryo-EM. Therefore, considerable efforts are being made to circumvent these bottlenecks by developing affinity purification of samples on-grid; at once obviating the need to produce large amounts of protein, as well as more directly controlling the variable, and sample-dependent, process of grid preparation. In this proof-of-concept study, we demonstrate a further practical step towards this paradigm, developing a 3D-printable flow-cell device to allow on-grid affinity purification from raw inputs such as whole cell lysates, using graphene oxide-based affinity grids. Our flow-cell device can be interfaced directly with routinely-used laboratory equipment such as liquid chromatographs, or peristaltic pumps, fitted with standard chromatographic (1/16") connectors, and can be used to allow binding of samples to affinity grids in a controlled environment prior to the extensive washing required to remove impurities. Furthermore, by designing a device which can be 3D printed and coupled to routinely used laboratory equipment, we hope to increase the accessibility of the techniques presented herein to researchers working towards single-particle macromolecular structures.
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Affiliation(s)
- Kailash Ramlaul
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ziyi Feng
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Caoimhe Canavan
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Natàlia de Martín Garrido
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - David Carreño
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Michael Crone
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Kirsten E Jensen
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Bing Li
- Hamlyn Centre, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Harry Barnett
- Imperial College Advanced Hackspace, Imperial College London, London, United Kingdom
| | - David T Riglar
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom; The Francis Crick Institute, London, United Kingdom
| | - Paul S Freemont
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - David Miller
- Imperial College Advanced Hackspace, Imperial College London, London, United Kingdom.
| | - Christopher H S Aylett
- Section for Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, United Kingdom.
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3
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Ahn E, Kim B, Park S, Erwin AL, Sung SH, Hovden R, Mosalaganti S, Cho US. Batch Production of High-Quality Graphene Grids for Cryo-EM: Cryo-EM Structure of Methylococcus capsulatus Soluble Methane Monooxygenase Hydroxylase. ACS NANO 2023; 17:6011-6022. [PMID: 36926824 PMCID: PMC10062032 DOI: 10.1021/acsnano.3c00463] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) has become a widely used tool for determining the protein structure. Despite recent technical advances, sample preparation remains a major bottleneck for several reasons, including protein denaturation at the air-water interface, the presence of preferred orientations, nonuniform ice layers, etc. Graphene, a two-dimensional allotrope of carbon consisting of a single atomic layer, has recently gained attention as a near-ideal support film for cryo-EM that can overcome these challenges because of its superior properties, including mechanical strength and electrical conductivity. Here, we introduce a reliable, easily implemented, and reproducible method to produce 36 graphene-coated grids within 1.5 days. To demonstrate their practical application, we determined the cryo-EM structure of Methylococcus capsulatus soluble methane monooxygenase hydroxylase (sMMOH) at resolutions of 2.9 and 2.5 Å using Quantifoil and graphene-coated grids, respectively. We found that the graphene-coated grid has several advantages, including a smaller amount of protein required and avoiding protein denaturation at the air-water interface. By comparing the cryo-EM structure of sMMOH with its crystal structure, we identified subtle yet significant geometrical changes at the nonheme diiron center, which may better indicate the active site configuration of sMMOH in the resting/oxidized state.
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Affiliation(s)
- Eungjin Ahn
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Byungchul Kim
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Soyoung Park
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Fine Chemistry, Seoul National University
of Science and Technology, Seoul 139-743, Korea
| | - Amanda L. Erwin
- Department
of Cell and Developmental Biology, University
of Michigan, Ann Arbor, Michigan 48109, United
States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Suk Hyun Sung
- Department
of Materials Science and Engineering, University
of Michigan, Ann Arbor, Michigan 48105, United
States
| | - Robert Hovden
- Department
of Materials Science and Engineering, University
of Michigan, Ann Arbor, Michigan 48105, United
States
- Applied
Physics Program, University of Michigan, Ann Arbor, Michigan 48105, United States
| | - Shyamal Mosalaganti
- Department
of Cell and Developmental Biology, University
of Michigan, Ann Arbor, Michigan 48109, United
States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Uhn-Soo Cho
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Fernandez A, Krishna J, Anson F, Dinsmore AD, Thayumanavan S. Consequences of Noncovalent Interfacial Contacts between Nanoparticles and Giant Vesicles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/anie.202208616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ann Fernandez
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Jithu Krishna
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Francesca Anson
- Department of Chemistry University of Massachusetts Amherst Amherst MA 01003 USA
| | - Anthony D. Dinsmore
- Department of Physics University of Massachusetts Amherst Amherst MA 01003 USA
| | - S. Thayumanavan
- Department of Chemistry Department of Biomedical Engineering Center for Bioactive Delivery Institute for Applied Life Sciences University of Massachusetts Amherst Amherst MA 01003 USA
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5
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Fernandez A, Krishna J, Anson F, Dinsmore AD, Thayumanavan S. Consequences of Noncovalent Interfacial Contacts between Nanoparticles and Giant Vesicles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ann Fernandez
- University of Massachusetts Amherst Chemistry UNITED STATES
| | - Jithu Krishna
- University of Massachusetts Amherst Chemistry UNITED STATES
| | | | | | - Sankaran Thayumanavan
- University of Massachusetts Amherst Department of Chemistry 710 N. Pleasant Street 01003 Amherst UNITED STATES
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6
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Hoq MR, Vago FS, Li K, Kovaliov M, Nicholas RJ, Huryn DM, Wipf P, Jiang W, Thompson DH. Affinity Capture of p97 with Small-Molecule Ligand Bait Reveals a 3.6 Å Double-Hexamer Cryoelectron Microscopy Structure. ACS NANO 2021; 15:8376-8385. [PMID: 33900731 DOI: 10.1021/acsnano.0c10185] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recent progress in the development of affinity grids for cryoelectron microscopy (cryo-EM) typically employs genetic engineering of the protein sample such as histidine or Spy tagging, immobilized antibody capture, or nonselective immobilization via electrostatic interactions or Schiff base formation. We report a powerful and flexible method for the affinity capture of target proteins for cryo-EM analysis that utilizes small-molecule ligands as bait for concentrating human target proteins directly onto the grid surface for single-particle reconstruction. This approach is demonstrated for human p97, captured using two different small-molecule high-affinity ligands of this AAA+ ATPase. Four electron density maps are revealed, each representing a p97 conformational state captured from solution, including a double-hexamer structure resolved to 3.6 Å. These results demonstrate that the noncovalent capture of protein targets on EM grids modified with high-affinity ligands can enable the structure elucidation of multiple configurational states of the target and potentially inform structure-based drug design campaigns.
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Affiliation(s)
- Md Rejaul Hoq
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Frank S Vago
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kunpeng Li
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
| | - Marina Kovaliov
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Robert J Nicholas
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Donna M Huryn
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Peter Wipf
- University of Pittsburgh Chemical Diversity Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Wen Jiang
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, West Lafayette, Indiana 47907, United States
| | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, West Lafayette, Indiana 47907, United States
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7
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General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Proc Natl Acad Sci U S A 2020; 117:24269-24273. [PMID: 32913054 PMCID: PMC7533693 DOI: 10.1073/pnas.2009707117] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Despite the increasing efforts in developing affinity grids to facilitate sample preparation for challenging systems and dynamic complexes, they are not widely used in cryo-electron microscopy (EM) owing to concerns of limiting resolution. We show that our affinity grids extract proteins through covalent bonding with 3.3-Å reconstruction. To our knowledge, no example of small proteins (<200 KDa) has been successfully tested with other affinity grids. With encouraging results further from a mixture sample, we believe that the strategy described here is highly applicable to a broad array of challenging macromolecules and thus is a method of broad interest to the cryo-EM community. The dramatic improvement in cryo-EM sample preparation outlined here paves the way to “purification on the grid.” Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids over the past decades, no single strategy has demonstrated general utility. Here we chemically functionalize cryo-EM grids coated with mostly one or two layers of graphene oxide to facilitate affinity capture. The protein of interest is tagged using a system that rapidly forms a highly specific covalent bond to its cognate catcher linked to the grid via a polyethylene glycol (PEG) spacer. Importantly, the spacer keeps particles away from both the air–water interface and the graphene oxide surface, protecting them from potential denaturation and rendering them sufficiently flexible to avoid preferential sample orientation concerns. Furthermore, the PEG spacer successfully reduces nonspecific binding, enabling high-resolution reconstructions from a much cruder lysate sample.
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8
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Brillault L, Landsberg MJ. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy. Methods Mol Biol 2020; 2073:221-246. [PMID: 31612445 DOI: 10.1007/978-1-4939-9869-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.
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Affiliation(s)
- Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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9
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Nakanishi A, Kishikawa JI, Mitsuoka K, Yokoyama K. Cryo-EM studies of the rotary H +-ATPase/synthase from Thermus thermophilus. Biophys Physicobiol 2019; 16:140-146. [PMID: 31660281 PMCID: PMC6812961 DOI: 10.2142/biophysico.16.0_140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
Proton-translocating rotary ATPases couple proton influx across the membrane domain and ATP hydrolysis/synthesis in the soluble domain through rotation of the central rotor axis against the surrounding peripheral stator apparatus. It is a significant challenge to determine the structure of rotary ATPases due to their intrinsic conformational heterogeneity and instability. Recent progress of single particle analysis of protein complexes using cryogenic electron microscopy (cryo-EM) has enabled the determination of whole rotary ATPase structures and made it possible to classify different rotational states of the enzymes at a near atomic resolution. Three cryo-EM maps corresponding to different rotational states of the V/A type H+-rotary ATPase from a bacterium Thermus thermophilus provide insights into the rotation of the whole complex, which allow us to determine the movement of each subunit during rotation. In addition, this review describes methodological developments to determine higher resolution cryo-EM structures, such as specimen preparation, to improve the image contrast of membrane proteins.
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Affiliation(s)
- Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Jun-Ichi Kishikawa
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, Ibaraki, Osaka 567-0047 Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kyoto 603-8555, Japan
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10
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Lee JH, Lee JH, Xiao J, Desai MS, Zhang X, Lee SW. Vertical Self-Assembly of Polarized Phage Nanostructure for Energy Harvesting. NANO LETTERS 2019; 19:2661-2667. [PMID: 30875472 DOI: 10.1021/acs.nanolett.9b00569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Controlling the shape, geometry, density, and orientation of nanomaterials is critical to fabricate functional devices. However, there is limited control over the morphological and directional characteristics of presynthesized nanomaterials, which makes them unsuitable for developing devices for practical applications. Here, we address this challenge by demonstrating vertically aligned and polarized piezoelectric nanostructures from presynthesized biological piezoelectric nanofibers, M13 phage, with control over the orientation, polarization direction, microstructure morphology, and density using genetic engineering and template-assisted self-assembly process. The resulting vertically ordered structures exhibit strong unidirectional polarization with three times higher piezoelectric constant values than that of in-plane aligned structures, supported by second harmonic generation and piezoelectric force microscopy measurements. The resulting vertically self-assembled phage-based piezoelectric energy harvester (PEH) produces up to 2.8 V of potential, 120 nA of current, and 236 nW of power upon 17 N of force. In addition, five phage-based PEH integrated devices produce an output voltage of 12 V and an output current of 300 nA, simply by pressing with a finger. The resulting device can operate light-emitting diode backlights on a liquid crystal display. Our approach will be useful for assembling many other presynthesized nanomaterials into high-performance devices for various applications.
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Affiliation(s)
- Ju-Hyuck Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Ju Hun Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jun Xiao
- Nanoscale Science and Engineering Center , University of California , Berkeley , California 94720 , United States
| | - Malav S Desai
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Xiang Zhang
- Nanoscale Science and Engineering Center , University of California , Berkeley , California 94720 , United States
- Materials Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Seung-Wuk Lee
- Department of Bioengineering , University of California , Berkeley , California 94720 , United States
- Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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11
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Liu N, Zhang J, Chen Y, Liu C, Zhang X, Xu K, Wen J, Luo Z, Chen S, Gao P, Jia K, Liu Z, Peng H, Wang HW. Bioactive Functionalized Monolayer Graphene for High-Resolution Cryo-Electron Microscopy. J Am Chem Soc 2019; 141:4016-4025. [DOI: 10.1021/jacs.8b13038] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peng Gao
- Collaborative Innovation Center of Quantum Matter, Beijing 100871, China
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12
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Sgro GG, Costa TRD. Cryo-EM Grid Preparation of Membrane Protein Samples for Single Particle Analysis. Front Mol Biosci 2018; 5:74. [PMID: 30131964 PMCID: PMC6090150 DOI: 10.3389/fmolb.2018.00074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/10/2018] [Indexed: 11/26/2022] Open
Abstract
Recent advances in cryo-electron microscopy (cryo-EM) have made it possible to solve structures of biological macromolecules at near atomic resolution. Development of more stable microscopes, improved direct electron detectors and faster software for image processing has enabled structural solution of not only large macromolecular (megadalton range) complexes but also small (~60 kDa) proteins. As a result of the widespread use of the technique, we have also witnessed new developments of techniques for cryo-EM grid preparation of membrane protein samples. This includes new types of solubilization strategies that better stabilize these protein complexes and the development of new grid supports with proven efficacy in reducing the motion of the molecules during electron beam exposure. Here, we discuss the practicalities and recent challenges of membrane protein sample preparation and vitrification, as well as grid support and foil treatment in the context of the structure determination of protein complexes by single particle cryo-EM.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago R. D. Costa
- Department of Life Sciences, Imperial College London, MRC Centre for Molecular Microbiology and Infection, London, United Kingdom
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13
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Wang H, Han W, Takagi J, Cong Y. Yeast Inner-Subunit PA–NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis. J Mol Biol 2018; 430:1417-1425. [DOI: 10.1016/j.jmb.2018.03.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/14/2018] [Accepted: 03/25/2018] [Indexed: 12/25/2022]
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14
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Gilmore BL, Varano AC, Dearnaley W, Liang Y, Marcinkowski BC, Dukes MJ, Kelly DF. Preparation of Tunable Microchips to Visualize Native Protein Complexes for Single-Particle Electron Microscopy. Methods Mol Biol 2018; 1764:45-58. [PMID: 29605907 DOI: 10.1007/978-1-4939-7759-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent advances in technology have enabled single-particle electron microscopy (EM) to rapidly progress as a preferred tool to study protein assemblies. Newly developed materials and methods present viable alternatives to traditional EM specimen preparation. Improved lipid monolayer purification reagents offer considerable flexibility, while ultrathin silicon nitride films provide superior imaging properties to the structural study of protein complexes. Here, we describe the steps for combining monolayer purification with silicon nitride microchips to create a tunable approach for the EM community.
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Affiliation(s)
| | - A Cameron Varano
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA.,Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, USA
| | | | - Yanping Liang
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA
| | | | | | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, VA, USA. .,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
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15
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Abstract
It has become clear that the standard cartoon, in which macromolecular particles prepared for electron cryo-microscopy are shown to be surrounded completely by vitreous ice, often is not accurate. In particular, the standard picture does not include the fact that diffusion to the air-water interface, followed by adsorption and possibly denaturation, can occur on the time scale that normally is required to make thin specimens. The extensive literature on interaction of proteins with the air-water interface suggests that many proteins can bind to the interface, either directly or indirectly via a sacrificial layer of already-denatured protein. In the process, the particles of interest can, in some cases, become preferentially oriented, and in other cases they can be damaged and/or aggregated at the surface. Thus, although a number of methods and recipes have evolved for dealing with protein complexes that prove to be difficult, making good cryo-grids can still be a major challenge for each new type of specimen. Recognition that the air-water interface is a very dangerous place to be has inspired work on some novel approaches for preparing cryo-grids. At the moment, two of the most promising ones appear to be: (1) thin and vitrify the specimen much faster than is done currently or (2) immobilize the particles onto a structure-friendly support film so that they cannot diffuse to the air-water interface.
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Affiliation(s)
- Robert M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94705
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16
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Karlova MG, Volokh OI, Chertkov OV, Kirpichnikov MP, Studitsky VM, Sokolova OS. Purification and concentration of RNA polymerase on Ni-lipid monolayers. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s1068162017060048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Jiang W, Tang L. Atomic cryo-EM structures of viruses. Curr Opin Struct Biol 2017; 46:122-129. [PMID: 28787658 PMCID: PMC5683926 DOI: 10.1016/j.sbi.2017.07.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/12/2017] [Accepted: 07/19/2017] [Indexed: 01/30/2023]
Abstract
During the development of single particle cryo-EM in past five decades, icosahedral viruses have led the resolution progress owing to their large mass and high symmetry. Many technical advances in cryo-EM were first established with viruses. Since reaching ∼4Å resolution in 2008, it has become a relatively routine task to solve the atomic structure of isolated viruses. The future of structural virology will be increasingly focused on remaining challenges including solving structures of jumbo viruses, intermediate functional states during assembly, maturation, and infection, and in situ structures. Recent demonstrations of near-atomic resolution structure with electron tomography and sub-tomogram averaging opens a new direction for high resolution studies of pleomorphic viruses and the pleomorphic states of icosahedral viruses that have defied past efforts using the single particle cryo-EM approach.
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Affiliation(s)
- Wen Jiang
- Department of Biological Sciences, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Department of Chemistry, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Markey Center for Structural Biology, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, 240 S. Martin Jischke Drive, West Lafayette, IN 47907, USA.
| | - Liang Tang
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA.
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18
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Yu G, Li K, Huang P, Jiang X, Jiang W. Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution. Structure 2017; 24:1984-1990. [PMID: 27806259 DOI: 10.1016/j.str.2016.09.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/16/2016] [Accepted: 09/30/2016] [Indexed: 02/02/2023]
Abstract
The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.
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Affiliation(s)
- Guimei Yu
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kunpeng Li
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Pengwei Huang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Wen Jiang
- Department of Biological Science, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.
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19
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Benjamin CJ, Wright KJ, Bolton SC, Hyun SH, Krynski K, Grover M, Yu G, Guo F, Kinzer-Ursem TL, Jiang W, Thompson DH. Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide. Sci Rep 2016; 6:32500. [PMID: 27748364 PMCID: PMC5066248 DOI: 10.1038/srep32500] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/08/2016] [Indexed: 01/02/2023] Open
Abstract
We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with Nα, Nα-dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His6-T7 bacteriophage and His6-GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His6-GroEL obtained from clarified E. coli lysates. Single particle analysis produced a 3D map with a gold standard resolution of 8.1 Å. We infer from these findings that TEM grids modified with GO-NTA are a useful tool that reduces background and improves both the speed and simplicity of biological sample preparation for high-resolution structure elucidation by cryo-EM.
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Affiliation(s)
| | - Kyle J Wright
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Scott C Bolton
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Seok-Hee Hyun
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Kyle Krynski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Mahima Grover
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Guimei Yu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Fei Guo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Tamara L Kinzer-Ursem
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Wen Jiang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA.,Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
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20
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Yu G, Li K, Jiang W. Antibody-based affinity cryo-EM grid. Methods 2016; 100:16-24. [PMID: 26804563 DOI: 10.1016/j.ymeth.2016.01.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 12/01/2022] Open
Abstract
The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
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21
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Benjamin CJ, Wright KJ, Hyun SH, Krynski K, Yu G, Bajaj R, Guo F, Stauffacher CV, Jiang W, Thompson DH. Nonfouling NTA-PEG-Based TEM Grid Coatings for Selective Capture of Histidine-Tagged Protein Targets from Cell Lysates. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:551-9. [PMID: 26726866 PMCID: PMC5310270 DOI: 10.1021/acs.langmuir.5b03445] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We report the preparation and performance of TEM grids bearing stabilized nonfouling lipid monolayer coatings. These films contain NTA capture ligands of controllable areal density at the distal end of a flexible poly(ethylene glycol) 2000 (PEG2000) spacer to avoid preferred orientation of surface-bound histidine-tagged (His-tag) protein targets. Langmuir-Schaefer deposition at 30 mN/m of mixed monolayers containing two novel synthetic lipids-1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[(5-amido-1-carboxypentyl)iminodiacetic acid]polyethylene glycolamide 2000) (NTA-PEG2000-DSPE) and 1,2-(tricosa-10',12'-diynoyl)-sn-glycero-3-phosphoethanolamine-N-(methoxypolyethylene glycolamide 350) (mPEG350-DTPE)-in 1:99 and 5:95 molar ratios prior to treatment with a 5 min, 254 nm light exposure was used for grid fabrication. These conditions were designed to limit nonspecific protein adsorption onto the stabilized lipid coating by favoring the formation of a mPEG350 brush layer below a flexible, mushroom conformation of NTA-PEG2000 at low surface density to enable specific immobilization and random orientation of the protein target on the EM grid. These grids were then used to capture His6-T7 bacteriophage and RplL from cell lysates, as well as purified His8-green fluorescent protein (GFP) and nanodisc solubilized maltose transporter, His6-MalFGK2. Our findings indicate that TEM grid supported, polymerized NTA lipid monolayers are capable of capturing His-tag protein targets in a manner that controls their areal densities, while efficiently blocking nonspecific adsorption and limiting film degradation, even upon prolonged detergent exposure.
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Affiliation(s)
- Christopher J Benjamin
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Kyle J Wright
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Seok-Hee Hyun
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Kyle Krynski
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Guimei Yu
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Ruchika Bajaj
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Fei Guo
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Cynthia V Stauffacher
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - Wen Jiang
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
| | - David H Thompson
- Department of Chemistry and ‡Department of Biological Sciences, Purdue University , West Lafayette, Indiana 47907, United States
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22
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Abstract
About 20 years ago, the first three-dimensional (3D) reconstructions at subnanometer (<10-Å) resolution of an icosahedral virus assembly were obtained by cryogenic electron microscopy (cryo-EM) and single-particle analysis. Since then, thousands of structures have been determined to resolutions ranging from 30 Å to near atomic (<4 Å). Almost overnight, the recent development of direct electron detectors and the attendant improvement in analysis software have advanced the technology considerably. Near-atomic-resolution reconstructions can now be obtained, not only for megadalton macromolecular complexes or highly symmetrical assemblies but also for proteins of only a few hundred kilodaltons. We discuss the developments that led to this breakthrough in high-resolution structure determination by cryo-EM and point to challenges that lie ahead.
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Affiliation(s)
- Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia;
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23
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van den Ent F, Izoré T, Bharat TAM, Johnson CM, Löwe J. Bacterial actin MreB forms antiparallel double filaments. eLife 2014; 3:e02634. [PMID: 24843005 PMCID: PMC4051119 DOI: 10.7554/elife.02634] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Filaments of all actin-like proteins known to date are assembled from pairs of protofilaments that are arranged in a parallel fashion, generating polarity. In this study, we show that the prokaryotic actin homologue MreB forms pairs of protofilaments that adopt an antiparallel arrangement in vitro and in vivo. We provide an atomic view of antiparallel protofilaments of Caulobacter MreB as apparent from crystal structures. We show that a protofilament doublet is essential for MreB's function in cell shape maintenance and demonstrate by in vivo site-specific cross-linking the antiparallel orientation of MreB protofilaments in E. coli. 3D cryo-EM shows that pairs of protofilaments of Caulobacter MreB tightly bind to membranes. Crystal structures of different nucleotide and polymerisation states of Caulobacter MreB reveal conserved conformational changes accompanying antiparallel filament formation. Finally, the antimicrobial agents A22/MP265 are shown to bind close to the bound nucleotide of MreB, presumably preventing nucleotide hydrolysis and destabilising double protofilaments.DOI: http://dx.doi.org/10.7554/eLife.02634.001.
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Affiliation(s)
- Fusinita van den Ent
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom,For correspondence:
| | - Thierry Izoré
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Tanmay AM Bharat
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Christopher M Johnson
- Protein and Nucleic Acid Chemistry Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Jan Löwe
- Structural Studies Division, Medical Research Council - Laboratory of Molecular Biology, Cambridge, United Kingdom
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24
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Yu G, Vago F, Zhang D, Snyder JE, Yan R, Zhang C, Benjamin C, Jiang X, Kuhn RJ, Serwer P, Thompson DH, Jiang W. Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies. J Struct Biol 2014; 187:1-9. [PMID: 24780590 DOI: 10.1016/j.jsb.2014.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/18/2022]
Abstract
Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures.
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Affiliation(s)
- Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Frank Vago
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Dongsheng Zhang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jonathan E Snyder
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Ci Zhang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | | | - Xi Jiang
- Divisions of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Richard J Kuhn
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA
| | - Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David H Thompson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN, USA.
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25
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Beck M, Glavy JS. Toward understanding the structure of the vertebrate nuclear pore complex. Nucleus 2014; 5:119-23. [PMID: 24699243 DOI: 10.4161/nucl.28739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear pore complexes are large macromolecular assemblies that facilitate the nucleocytoplasmic exchange of macromolecules. Because of their intricate composition, membrane association, and sheer size, the integration of various, complementary structure determination approaches is a prerequisite for elucidating their structure. We have recently employed such an integrated strategy to analyze the scaffold structure of the cytoplasmic and nuclear rings of the human nuclear pore complex. In this extra view, we highlight two specific aspects of this work: the power of electron microscopy for bridging different resolution regimes and the importance of post-translational modifications for regulating nucleoporin interactions. We review recent technological developments and give a perspective toward future structure determination approaches.
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Affiliation(s)
- Martin Beck
- European Molecular Biology Laboratory; Structural and Computational Biology Unit; Heidelberg, Germany; Stevens Institute of Technology; Department of Chemistry, Chemical Biology, and Biomedical Engineering; Hoboken, NJ USA
| | - Joseph S Glavy
- European Molecular Biology Laboratory; Structural and Computational Biology Unit; Heidelberg, Germany; Stevens Institute of Technology; Department of Chemistry, Chemical Biology, and Biomedical Engineering; Hoboken, NJ USA
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26
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Anthony KC, You C, Piehler J, Pomeranz Krummel DA. High-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies. Structure 2014; 22:628-35. [PMID: 24560806 DOI: 10.1016/j.str.2014.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 01/08/2014] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
There is significant demand for experimental approaches to aid protein localization in electron microscopy micrographs and ultimately in three-dimensional reconstructions of macromolecular assemblies. We report preparation and use of a reagent consisting of tris-nitrilotriacetic acid (tris-NTA) conjugated with a monofunctional gold nanoparticle ((AuNP)tris-NTA) for site-specific, non-covalent labeling of protein termini fused to a histidine-tag (His-tag). Multivalent binding of tris-NTA to a His-tag via complexed Ni(II) ions results in subnanomolar affinity and a defined 1:1 stoichiometry. Precise localization of (AuNP)tris-NTA labeled proteins by electron microscopy is further ensured by the reagent's short conformationally restricted linker. We used (AuNP)tris-NTA to localize His-tagged proteins in an oligomeric ATPase and in the bacterial 50S ribosomal subunit. (AuNP)tris-NTA can specifically bind to the target proteins in these assemblies and is clearly discernible. Our labeling reagent should find broad application in noncovalent, site-specific labeling of protein termini to pinpoint their location in macromolecular assemblies.
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Affiliation(s)
- Kelsey C Anthony
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Changjiang You
- Department of Biology, University of Osnabrück, Barbarastraße 11, Osnabrück 49076, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, Osnabrück 49076, Germany.
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27
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Kiss G, Chen X, Brindley MA, Campbell P, Afonso CL, Ke Z, Holl JM, Guerrero-Ferreira RC, Byrd-Leotis LA, Steel J, Steinhauer DA, Plemper RK, Kelly DF, Spearman PW, Wright ER. Capturing enveloped viruses on affinity grids for downstream cryo-electron microscopy applications. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2014; 20:164-74. [PMID: 24279992 PMCID: PMC4073796 DOI: 10.1017/s1431927613013937] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Electron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.
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Affiliation(s)
- Gabriella Kiss
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
| | - Xuemin Chen
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
| | - Melinda A. Brindley
- Center for Inflammation, Immunity & Infection. Georgia State University. Atlanta, GA 30303
| | - Patricia Campbell
- Department of Microbiology and Immunology. Emory University School of Medicine. GA 30322
| | - Claudio L. Afonso
- USDA, ARS, Southeast Poultry Research Laboratory, Athens, Georgia, USA
| | - Zunlong Ke
- School of Biology, Georgia Institute of Technology, Atlanta GA 30332
| | - Jens M. Holl
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
| | - Ricardo C. Guerrero-Ferreira
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
| | - Lauren A. Byrd-Leotis
- Department of Microbiology and Immunology. Emory University School of Medicine. GA 30322
| | - John Steel
- Department of Microbiology and Immunology. Emory University School of Medicine. GA 30322
| | - David A. Steinhauer
- Department of Microbiology and Immunology. Emory University School of Medicine. GA 30322
| | - Richard K. Plemper
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
- Center for Inflammation, Immunity & Infection. Georgia State University. Atlanta, GA 30303
| | | | - Paul W. Spearman
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
| | - Elizabeth R. Wright
- Division of Pediatric Infectious Diseases. Department of Pediatrics. Emory University School of Medicine. Children’s Healthcare of Atlanta. Atlanta, GA 30322
- To whom correspondence should be addressed. ; Tel. (+1) 404-727-4665; Fax (+1) 404-727-9223
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28
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Llaguno MC, Xu H, Shi L, Huang N, Zhang H, Liu Q, Jiang QX. Chemically functionalized carbon films for single molecule imaging. J Struct Biol 2014; 185:405-17. [PMID: 24457027 DOI: 10.1016/j.jsb.2014.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 01/08/2014] [Accepted: 01/11/2014] [Indexed: 11/25/2022]
Abstract
Many biological complexes are naturally low in abundance and pose a significant challenge to their structural and functional studies. Here we describe a new method that utilizes strong oxidation and chemical linkage to introduce a high density of bioactive ligands onto nanometer-thick carbon films and enable selective enrichment of individual macromolecular complexes at subnanogram levels. The introduced ligands are physically separated. Ni-NTA, Protein G and DNA/RNA oligonucleotides were covalently linked to the carbon surface. They embody negligible mass and their stability makes the functionalized films able to survive long-term storage and tolerate variations in pH, temperature, salts, detergents, and solvents. We demonstrated the application of the new method to the electron microscopic imaging of the substrate-bound C3PO, an RNA-processing enzyme important for the RNA interference pathway. On the ssRNA-linked carbon surface, the formation of C3PO oligomers at subnanomolar concentrations likely mimics their assembly onto ssRNA substrates presented by their native partners. Interestingly, the 3D reconstructions by negative stain EM reveal a side port in the C3PO/ssRNA complex, and the 15Å cryoEM map showed extra density right above the side port, which probably represents the ssRNA. These results suggest a new way for ssRNAs to interact with the active sites of the complex. Together our data demonstrate that the surface-engineered carbon films are suitable for selectively enriching low-abundance biological complexes at nanomolar level and for developing novel applications on a large number of surface-presented molecules.
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Affiliation(s)
- Marc C Llaguno
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Hui Xu
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Liang Shi
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Nian Huang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Biophysics, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Hong Zhang
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA; Department of Biophysics, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Qinghua Liu
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA
| | - Qiu-Xing Jiang
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX 75390, USA.
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29
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Yang X, Li Z, Li M, Ren J, Qu X. Fluorescent Protein Capped Mesoporous Nanoparticles for Intracellular Drug Delivery and Imaging. Chemistry 2013; 19:15378-83. [DOI: 10.1002/chem.201302026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/29/2013] [Indexed: 11/06/2022]
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30
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Fotinou C, Aittoniemi J, de Wet H, Polidori A, Pucci B, Sansom MSP, Vénien-Bryan C, Ashcroft FM. Tetrameric structure of SUR2B revealed by electron microscopy of oriented single particles. FEBS J 2013; 280:1051-63. [PMID: 23253866 PMCID: PMC3599479 DOI: 10.1111/febs.12097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 11/26/2012] [Accepted: 12/03/2012] [Indexed: 12/25/2022]
Abstract
The ATP-sensitive potassium (KATP) channel is a hetero-octameric complex that links cell metabolism to membrane electrical activity in many cells, thereby controlling physiological functions such as insulin release, muscle contraction and neuronal activity. It consists of four pore-forming Kir6.2 and four regulatory sulfonylurea receptor (SUR) subunits. SUR2B serves as the regulatory subunit in smooth muscle and some neurones. An integrative approach, combining electron microscopy and homology modelling, has been used to obtain information on the structure of this large (megadalton) membrane protein complex. Single-particle electron microscopy of purified SUR2B tethered to a lipid monolayer revealed that it assembles as a tetramer of four SUR2B subunits surrounding a central hole. In the absence of an X-ray structure, a homology model for SUR2B based on the X-ray structure of the related ABC transporter Sav1866 was used to fit the experimental images. The model indicates that the central hole can readily accommodate the transmembrane domains of the Kir tetramer, suggests a location for the first transmembrane domains of SUR2B (which are absent in Sav1866) and suggests the relative orientation of the SUR and Kir6.2 subunits.
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Affiliation(s)
- Constantina Fotinou
- Department of Physiology, Henry Wellcome Centre for Gene Function, University of Oxford, Oxford, UK
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31
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Affinity grid-based cryo-EM of PKC binding to RACK1 on the ribosome. J Struct Biol 2012; 181:190-4. [PMID: 23228487 DOI: 10.1016/j.jsb.2012.11.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 11/23/2022]
Abstract
Affinity grids (AG) are specialized EM grids that bind macromolecular complexes containing tagged proteins to obtain maximum occupancy for structural analysis through single-particle EM. In this study, utilizing AG, we show that His-tagged activated PKC βII binds to the small ribosomal subunit (40S). We reconstructed a cryo-EM map which shows that PKC βII interacts with RACK1, a seven-bladed β-propeller protein present on the 40S and binds in two different regions close to blades 3 and 4 of RACK1. This study is a first step in understanding the molecular framework of PKC βII/RACK1 interaction and its role in translation.
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32
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Han BG, Walton RW, Song A, Hwu P, Stubbs MT, Yannone SM, Arbeláez P, Dong M, Glaeser RM. Electron microscopy of biotinylated protein complexes bound to streptavidin monolayer crystals. J Struct Biol 2012; 180:249-53. [PMID: 22584152 DOI: 10.1016/j.jsb.2012.04.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/07/2012] [Accepted: 04/23/2012] [Indexed: 11/30/2022]
Abstract
Chemical biotinylation of protein complexes followed by binding to two-dimensional (monolayer) crystals of streptavidin is shown to be an effective way to prepare cryo-EM specimens from samples at low protein concentration. Three different multiprotein complexes are used to demonstrate the generality of this method. In addition, native thermosomes, purified from Sulfolobus solfataricus P2, are used to demonstrate that a uniform distribution of Euler angles is produced, even though this particle is known to adopt a preferred orientation when other methods of cryo-EM specimen preparation are used.
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Affiliation(s)
- Bong-Gyoon Han
- Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
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33
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Tanner JR, Degen K, Gilmore BL, Kelly DF. Capturing RNA-dependent pathways for cryo-EM analysis. Comput Struct Biotechnol J 2012; 1:e201204003. [PMID: 24688633 PMCID: PMC3962177 DOI: 10.5936/csbj.201204003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/08/2012] [Accepted: 02/11/2012] [Indexed: 01/14/2023] Open
Abstract
Cryo-Electron Microscopy (EM) is a powerful technique to visualize biological processes at nanometer resolution. Structural studies of macromolecular assemblies are typically performed on individual complexes that are biochemically isolated from their cellular context. Here we present a molecular imaging platform to capture and view multiple components of cellular pathways within a functionally relevant framework. We utilized the bacterial protein synthesis machinery as a model system to develop our approach. By using modified Affinity Grid surfaces, we were able to recruit multiple protein assemblies bound to nascent strands of mRNA. The combined use of Affinity Capture technology and single particle electron microscopy provide the basis for visualizing RNA-dependent pathways in a remarkable new way.
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Affiliation(s)
- Justin R Tanner
- Virginia Tech Carilion Research Institute, Roanoke, VA, 24016, USA
| | - Katherine Degen
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, 22908, USA
| | - Brian L Gilmore
- Virginia Tech Carilion Research Institute, Roanoke, VA, 24016, USA
| | - Deborah F Kelly
- Virginia Tech Carilion Research Institute, Roanoke, VA, 24016, USA
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34
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Degen K, Dukes M, Tanner JR, Kelly DF. The development of affinity capture devices—a nanoscale purification platform for biological in situ transmission electron microscopy. RSC Adv 2012. [DOI: 10.1039/c2ra01163h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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35
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Pantelic RS, Suk JW, Hao Y, Ruoff RS, Stahlberg H. Oxidative doping renders graphene hydrophilic, facilitating its use as a support in biological TEM. NANO LETTERS 2011; 11:4319-4323. [PMID: 21910506 DOI: 10.1021/nl202386p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Graphene represents the first practical realization of crystalline supports in biological transmission electron microscopy (TEM) since their introduction over 30 years ago. The high transparency, minimal inelastic cross-section, and electrical conductivity of graphene are highly desirable characteristics for a TEM support. However, without a suitable method for rendering graphene supports, hydrophilic applications are limited. This work describes the in situ functionalization of graphene with minimal structural degradation, rendering TEM supports sufficiently hydrophilic for the mounting of biological samples.
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Affiliation(s)
- Radosav S Pantelic
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel , Basel, Switzerland
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36
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Salje J, van den Ent F, de Boer P, Löwe J. Direct membrane binding by bacterial actin MreB. Mol Cell 2011; 43:478-87. [PMID: 21816350 PMCID: PMC3163269 DOI: 10.1016/j.molcel.2011.07.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 05/17/2011] [Accepted: 07/18/2011] [Indexed: 11/28/2022]
Abstract
Bacterial actin MreB is one of the key components of the bacterial cytoskeleton. It assembles into short filaments that lie just underneath the membrane and organize the cell wall synthesis machinery. Here we show that MreB from both T. maritima and E. coli binds directly to cell membranes. This function is essential for cell shape determination in E. coli and is proposed to be a general property of many, if not all, MreBs. We demonstrate that membrane binding is mediated by a membrane insertion loop in TmMreB and by an N-terminal amphipathic helix in EcMreB and show that purified TmMreB assembles into double filaments on a membrane surface that can induce curvature. This, the first example of a membrane-binding actin filament, prompts a fundamental rethink of the structure and dynamics of MreB filaments within cells.
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Affiliation(s)
- Jeanne Salje
- MRC Laboratory of Molecular Biology, Cambridge, UK
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37
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Chiu PL, Kelly DF, Walz T. The use of trehalose in the preparation of specimens for molecular electron microscopy. Micron 2011; 42:762-72. [PMID: 21752659 DOI: 10.1016/j.micron.2011.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/09/2011] [Accepted: 06/10/2011] [Indexed: 11/29/2022]
Abstract
Biological specimens have to be prepared for imaging in the electron microscope in a way that preserves their native structure. Two-dimensional (2D) protein crystals to be analyzed by electron crystallography are best preserved by sugar embedding. One of the sugars often used to embed 2D crystals is trehalose, a disaccharide used by many organisms for protection against stress conditions. Sugars such as trehalose can also be added to negative staining solutions used to prepare proteins and macromolecular complexes for structural studies by single-particle electron microscopy (EM). In this review, we describe trehalose and its characteristics that make it so well suited for preparation of EM specimens and we review specimen preparation methods with a focus on the use of trehalose.
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Affiliation(s)
- Po-Lin Chiu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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38
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Norville JE, Kelly DF, Knight TF, Belcher AM, Walz T. Fast and easy protocol for the purification of recombinant S-layer protein for synthetic biology applications. Biotechnol J 2011; 6:807-11. [PMID: 21681963 DOI: 10.1002/biot.201100024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 04/19/2011] [Accepted: 05/24/2011] [Indexed: 12/24/2022]
Abstract
A goal of synthetic biology is to make biological systems easier to engineer. One of the aims is to design, with nanometer-scale precision, biomaterials with well-defined properties. The surface-layer protein SbpA forms 2D arrays naturally on the cell surface of Lysinibacillus sphaericus, but also as the purified protein in solution upon the addition of divalent cations. The high propensity of SbpA to form crystalline arrays, which can be simply controlled by divalent cations, and the possibility to genetically alter the protein, make SbpA an attractive molecule for synthetic biology. To be a useful tool, however, it is important that a simple protocol can be used to produce recombinant wild-type and modified SbpA in large quantities and in a biologically active form. The present study addresses this requirement by introducing a mild and non-denaturing purification protocol to produce milligram quantities of recombinant, active SbpA.
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Affiliation(s)
- Julie E Norville
- Synthetic Biology Working Group, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.
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39
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Norville JE, Derda R, Gupta S, Drinkwater KA, Belcher AM, Leschziner AE, Knight TF. Introduction of customized inserts for s-treamlined assembly and optimization of BioBrick synthetic genetic circuits. J Biol Eng 2010; 4:17. [PMID: 21172029 PMCID: PMC3022552 DOI: 10.1186/1754-1611-4-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 12/20/2010] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND BioBrick standard biological parts are designed to make biological systems easier to engineer (e.g. assemble, manipulate, and modify). There are over 5,000 parts available in the Registry of Standard Biological Parts that can be easily assembled into genetic circuits using a standard assembly technique. The standardization of the assembly technique has allowed for wide distribution to a large number of users -- the parts are reusable and interchangeable during the assembly process. The standard assembly process, however, has some limitations. In particular it does not allow for modification of already assembled biological circuits, addition of protein tags to pre-existing BioBrick parts, or addition of non-BioBrick parts to assemblies. RESULTS In this paper we describe a simple technique for rapid generation of synthetic biological circuits using introduction of customized inserts. We demonstrate its use in Escherichia coli (E. coli) to express green fluorescent protein (GFP) at pre-calculated relative levels and to add an N-terminal tag to GFP. The technique uses a new BioBrick part (called a BioScaffold) that can be inserted into cloning vectors and excised from them to leave a gap into which other DNA elements can be placed. The removal of the BioScaffold is performed by a Type IIB restriction enzyme (REase) that recognizes the BioScaffold but cuts into the surrounding sequences; therefore, the placement and removal of the BioScaffold allows the creation of seamless connections between arbitrary DNA sequences in cloning vectors. The BioScaffold contains a built-in red fluorescent protein (RFP) reporter; successful insertion of the BioScaffold is, thus, accompanied by gain of red fluorescence and its removal is manifested by disappearance of the red fluorescence. CONCLUSIONS The ability to perform targeted modifications of existing BioBrick circuits with BioScaffolds (1) simplifies and speeds up the iterative design-build-test process through direct reuse of existing circuits, (2) allows incorporation of sequences incompatible with BioBrick assembly into BioBrick circuits (3) removes scar sequences between standard biological parts, and (4) provides a route to adapt synthetic biology innovations to BioBrick assembly through the creation of new parts rather than new assembly standards or parts collections.
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Affiliation(s)
- Julie E Norville
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Saurabh Gupta
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kelly A Drinkwater
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Angela M Belcher
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andres E Leschziner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas F Knight
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ginkgo BioWorks, 7 Tide St., Unit 2B, Boston, MA 02210, USA
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40
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Dezi M, Fribourg PF, Cicco AD, Jault JM, Chami M, Lévy D. Binding, reconstitution and 2D crystallization of membrane or soluble proteins onto functionalized lipid layer observed in situ by reflected light microscopy. J Struct Biol 2010; 174:307-14. [PMID: 21163357 DOI: 10.1016/j.jsb.2010.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/06/2010] [Accepted: 12/08/2010] [Indexed: 12/20/2022]
Abstract
Monolayer of functionalized lipid spread at the air/water interface is used for the structural analysis of soluble and membrane proteins by electron crystallography and single particle analysis. This powerful approach lacks of a method for the screening of the binding of proteins to the surface of the lipid layer. Here, we described an optical method based on the use of reflected light microscopy to image, without the use of any labeling, the lipid layer at the surface of buffers in the Teflon wells used for 2D crystallization. Images revealed that the lipid layer was made of a monolayer coexisting with liposomes or aggregates of lipids floating at the surface. Protein binding led to an increase of the contrast and the decrease of the fluidity of the lipid surface, as demonstrated with the binding of soluble Shiga toxin B subunit, of purple membrane and of solubilized His-BmrA, a bacterial ABC transporter. Moreover the reconstitution of membrane proteins bound to the lipidic surface upon detergent removal can be followed through the appearance of large recognizable domains at the surface. Proteins binding and reconstitution were further confirmed by electron microcopy. Overall, this method provides a quick evaluation of the monolayer trials, a significant reduction in screening by transmission electron microscopy and new insights in the proteins binding and 2D crystallogenesis at the lipid surface.
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Affiliation(s)
- Manuela Dezi
- Institut Curie, Centre de Recherche, Paris F-75231, France
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41
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Pantelic RS, Suk JW, Magnuson CW, Meyer JC, Wachsmuth P, Kaiser U, Ruoff RS, Stahlberg H. Graphene: Substrate preparation and introduction. J Struct Biol 2010; 174:234-8. [PMID: 20937392 DOI: 10.1016/j.jsb.2010.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 09/29/2010] [Accepted: 10/04/2010] [Indexed: 11/26/2022]
Abstract
This technical note describes the transfer of continuous, single-layer, pristine graphene to standard Quantifoil TEM grids. We compare the transmission properties of pristine graphene substrates to those of graphene oxide and thin amorphous carbon substrates. Positively stained DNA imaged across amorphous carbon is typically indiscernible and requires metal shadowing for sufficient contrast. However, in a practical illustration of the new substrates properties, positively stained DNA is imaged across pristine graphene in striking contrast without the need of metal shadowing. We go onto discuss technical considerations and the potential applications of pristine graphene substrates as well as their ongoing development.
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Affiliation(s)
- Radosav S Pantelic
- Center for Cellular Imaging and Nano Analytics, Biozentrum, University of Basel, Basel, Switzerland
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42
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Dezi M, Fribourg PF, Di Cicco A, Arnaud O, Marco S, Falson P, Di Pietro A, Lévy D. The multidrug resistance half-transporter ABCG2 is purified as a tetramer upon selective extraction from membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1798:2094-101. [PMID: 20691149 DOI: 10.1016/j.bbamem.2010.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 07/27/2010] [Accepted: 07/27/2010] [Indexed: 01/07/2023]
Abstract
ABCG2 is a human membrane ATP-binding cassette half-transporter that hydrolyzes ATP to efflux a large number of chemotherapeutic agents. Several oligomeric states of ABCG2 from homodimers to dodecamers have been reported depending on the overexpression systems and/or the protocols used for purification. Here, we compared the oligomeric state of His(6)-ABCG2 expressed in Sf9 insect cells and in human Flp-In-293/ABCG2 cells after solubilization in mild detergents. His(6)-ABCG2 was purified through a new approach involving its specific recognition onto a functionalized lipid layer containing a Ni-NTA lipid. This approach allowed the purification of His-ABCG2 in presence of all solubilized membrane components that might be involved in the stabilisation of native oligomers and without requiring any additional washing or concentration passages. ABCG2 purified onto the NiNTA lipid surfaces were directly analyzed by electron microscopy and by biochemical assays. Altogether, our data are consistent with a tetrameric organization of ABCG2 when expressed in either heterologous Sf9 insect cells or in human homologous cells.
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Affiliation(s)
- Manuela Dezi
- Institut Curie, Centre de Recherche, Paris, F-75231, France
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43
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Schmidt-Krey I, Rubinstein JL. Electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles. Micron 2010; 42:107-16. [PMID: 20678942 DOI: 10.1016/j.micron.2010.07.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 07/08/2010] [Accepted: 07/11/2010] [Indexed: 01/08/2023]
Abstract
Membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-EM) methods: electron crystallography of two-dimensional (2D) crystals and single particle analysis of detergent-solubilized protein complexes. To obtain the highest-possible resolution data from membrane proteins, whether prepared as 2D crystals or single particles, cryo-EM samples must be vitrified with great care. Grid preparation for cryo-EM of 2D crystals is possible by back-injection, the carbon sandwich technique, drying in sugars before cooling in the electron microscope, or plunge-freezing. Specimen grids for single particle cryo-EM studies of membrane proteins are usually produced by plunge-freezing protein solutions, supported either by perforated or a continuous carbon film substrate. This review outlines the different techniques available and the suitability of each method for particular samples and studies. Experimental considerations in sample preparation and preservation include the protein itself and the presence of lipid or detergent. The appearance of cryo-EM samples in different conditions is also discussed.
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Affiliation(s)
- Ingeborg Schmidt-Krey
- Georgia Institute of Technology, School of Biology, School of Chemistry and Biochemistry, 310 Ferst Drive, Rm. A118, Atlanta, GA 30332-0230, USA.
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44
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Kelly DF, Dukovski D, Walz T. Strategy for the use of affinity grids to prepare non-His-tagged macromolecular complexes for single-particle electron microscopy. J Mol Biol 2010; 400:675-81. [PMID: 20562026 DOI: 10.1016/j.jmb.2010.05.045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 05/11/2010] [Accepted: 05/18/2010] [Indexed: 11/24/2022]
Abstract
Affinity Grids are electron microscopy (EM) grids with a pre-deposited lipid monolayer containing functionalized nickel-nitrilotriacetic acid lipids. Affinity Grids can be used to prepare His-tagged proteins for single-particle EM from impure solutions or even directly from cell extracts. Here, we introduce the concept of His-tagged adaptor molecules, which eliminate the need for the target protein or complex to be His-tagged. The use of His-tagged protein A as adaptor molecule allows Affinity Grids to be used for the preparation of virtually any protein or complex provided that a specific antibody is available or can be raised against the target protein. The principle is that the Affinity Grid is coated with a specific antibody that is recruited to the grid by His-tagged protein A. The antibody-decorated Affinity Grid can then be used to isolate the target protein directly from a cell extract. We first established this approach by preparing negatively stained specimens of both native ribosomal complexes and ribosomal complexes carrying different purification tags directly from HEK-293T cell extract. We then used the His-tagged protein A/antibody strategy to isolate RNA polymerase II, still bound to native DNA, from HEK-293T cell extract, allowing us to calculate a 25-A-resolution density map by single-particle cryo-EM.
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Affiliation(s)
- Deborah F Kelly
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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45
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Kelly DF, Lake RJ, Middelkoop TC, Fan HY, Artavanis-Tsakonas S, Walz T. Molecular structure and dimeric organization of the Notch extracellular domain as revealed by electron microscopy. PLoS One 2010; 5:e10532. [PMID: 20479883 PMCID: PMC2866536 DOI: 10.1371/journal.pone.0010532] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 04/16/2010] [Indexed: 11/18/2022] Open
Abstract
Background The Notch receptor links cell fate decisions of one cell to that of the immediate cellular neighbor. In humans, malfunction of Notch signaling results in diseases and congenital disorders. Structural information is essential for gaining insight into the mechanism of the receptor as well as for potentially interfering with its function for therapeutic purposes. Methodology/Principal Findings We used the Affinity Grid approach to prepare specimens of the Notch extracellular domain (NECD) of the Drosophila Notch and human Notch1 receptors suitable for analysis by electron microscopy and three-dimensional (3D) image reconstruction. The resulting 3D density maps reveal that the NECD structure is conserved across species. We show that the NECD forms a dimer and adopts different yet defined conformations, and we identify the membrane-proximal region of the receptor and its ligand-binding site. Conclusions/Significance Our results provide direct and unambiguous evidence that the NECD forms a dimer. Our studies further show that the NECD adopts at least three distinct conformations that are likely related to different functional states of the receptor. These findings open the way to now correlate mutations in the NECD with its oligomeric state and conformation.
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Affiliation(s)
- Deborah F. Kelly
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert J. Lake
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Teije C. Middelkoop
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hua-Ying Fan
- Epigenetics and Progenitor Cells Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Spyros Artavanis-Tsakonas
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SA-T); (TW)
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SA-T); (TW)
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46
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Abstract
Lipid monolayers have traditionally been used in electron microscopy (EM) to form two-dimensional (2D) protein arrays for structural studies by electron crystallography. More recently, monolayers containing Nickel-nitrilotriacetic acid (Ni-NTA) lipids have been used to combine the purification and preparation of single-particle EM specimens of His-tagged proteins into a single, convenient step. This monolayer purification technique was further simplified by introducing the Affinity Grid, an EM grid that features a predeposited Ni-NTA lipid-containing monolayer. In this contribution, we provide a detailed description for the use of monolayer purification and Affinity Grids, discuss their advantages and limitations, and present examples to illustrate specific applications of the methods.
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47
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Pierson J, Sani M, Tomova C, Godsave S, Peters PJ. Toward visualization of nanomachines in their native cellular environment. Histochem Cell Biol 2009; 132:253-62. [PMID: 19649648 PMCID: PMC2729413 DOI: 10.1007/s00418-009-0622-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2009] [Indexed: 11/01/2022]
Abstract
The cellular nanocosm is made up of numerous types of macromolecular complexes or biological nanomachines. These form functional modules that are organized into complex subcellular networks. Information on the ultra-structure of these nanomachines has mainly been obtained by analyzing isolated structures, using imaging techniques such as X-ray crystallography, NMR, or single particle electron microscopy (EM). Yet there is a strong need to image biological complexes in a native state and within a cellular environment, in order to gain a better understanding of their functions. Emerging methods in EM are now making this goal reachable. Cryo-electron tomography bypasses the need for conventional fixatives, dehydration and stains, so that a close-to-native environment is retained. As this technique is approaching macromolecular resolution, it is possible to create maps of individual macromolecular complexes. X-ray and NMR data can be 'docked' or fitted into the lower resolution particle density maps to create a macromolecular atlas of the cell under normal and pathological conditions. The majority of cells, however, are too thick to be imaged in an intact state and therefore methods such as 'high pressure freezing' with 'freeze-substitution followed by room temperature plastic sectioning' or 'cryo-sectioning of unperturbed vitreous fully hydrated samples' have been introduced for electron tomography. Here, we review methodological considerations for visualizing nanomachines in a close-to-physiological, cellular context. EM is in a renaissance, and further innovations and training in this field should be fully supported.
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Affiliation(s)
- Jason Pierson
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Musa Sani
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Cveta Tomova
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Susan Godsave
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
| | - Peter J. Peters
- Division of Cell Biology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121 B6, 1066 CX Amsterdam, The Netherlands
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48
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Abstract
Single-particle electron microscopy (EM) can provide structural information for a large variety of biological molecules, ranging from small proteins to large macromolecular assemblies, without the need to produce crystals. The year 2008 has become a landmark year for single-particle EM as for the first time density maps have been produced at a resolution that made it possible to trace protein backbones or even to build atomic models. In this review, we highlight some of the recent successes achieved by single-particle EM and describe the individual steps involved in producing a density map by this technique. We also discuss some of the remaining challenges and areas, in which further advances would have a great impact on the results that can be achieved by single-particle EM.
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Affiliation(s)
- Yifan Cheng
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California-San Francisco, CA 94158, USA.
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49
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Dukovski D, Li Z, Kelly DF, Mack E, Walz T. Structural and functional studies on the stalk of the transferrin receptor. Biochem Biophys Res Commun 2009; 381:712-6. [PMID: 19258014 DOI: 10.1016/j.bbrc.2009.02.133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 02/24/2009] [Indexed: 10/21/2022]
Abstract
Transferrin (Tf) is an iron carrier protein that consists of two lobes, the N- and C-lobes, which can each bind a Fe(3+) ion. Tf binds to its receptor (TfR), which mediates iron delivery to cells through an endocytotic pathway. Receptor binding facilitates iron release from the Tf C-lobe, but impedes iron release from the N-lobe. An atomic model of the Tf-TfR complex based on single particle electron microscopy (EM) indicated that receptor binding is indeed likely to hinder opening of the N-lobe, thus interfering with its iron release. The atomic model also suggested that the TfR stalks could form additional contacts with the Tf N-lobes, thus potentially further slowing down its iron release. Here, we show that the TfR stalks are unlikely to make strong interactions with the Tf N-lobes and that the stalks have no effect on iron release from the N-lobes of receptor-bound Tf.
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Affiliation(s)
- Danijela Dukovski
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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50
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Hussein WM, Ross BP, Landsberg MJ, Lévy D, Hankamer B, McGeary RP. Synthesis of Nickel-Chelating Fluorinated Lipids for Protein Monolayer Crystallizations. J Org Chem 2009; 74:1473-9. [DOI: 10.1021/jo802651p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Waleed M. Hussein
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Benjamin P. Ross
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Michael J. Landsberg
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Daniel Lévy
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Ben Hankamer
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
| | - Ross P. McGeary
- The University of Queensland, School of Molecular & Microbial Sciences, Institute for Molecular Bioscience, and School of Pharmacy QLD 4072, Australia, and Institut Curie, UMR CNRS 168, 11 rue P.M.Curie, F-75231 Paris, France
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