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Remis J, Petrov PN, Zhang JT, Axelrod JJ, Cheng H, Sandhaus S, Mueller H, Glaeser RM. Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.04.606536. [PMID: 39149370 PMCID: PMC11326166 DOI: 10.1101/2024.08.04.606536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Apoferritin (apoF) is commonly used as a test specimen in single-particle electron cryo-microscopy (cryo-EM), since it consistently produces density maps that go to 3 Å resolution or higher. When we imaged apoF with a laser phase plate (LPP), however, we observed more severe particle-to-particle variation in the images than we had previously thought to exist. Similarly, we found that images of ribulose bisphosphate carboxylase/oxygenase (rubisco) also exhibited a much greater amount of heterogeneity than expected. By comparison to simulations of images, we verified that the heterogeneity is not explained by the known features of the LPP, shot noise, or differences in particle orientation. We also demonstrate that our specimens are comparable to those previously used in the literature, based on using the final-reconstruction resolution as the metric for evaluation. All of this leads us to the hypothesis that the heterogeneity is due to damage that has occurred either during purification of the specimen or during preparation of the grids. It is not, however, our goal to explain the causes of heterogeneity; rather, we report that using the LPP has made the apparent damage too obvious to be ignored. In hindsight, similar heterogeneity can be seen in images of apoF and the 20S proteasome which others had recorded with a Volta phase plate. We therefore conclude that the increased contrast of phase-plate images (at low spatial frequencies) should also make it possible to visualize, on a single-particle basis, various forms of biologically functional heterogeneity in structure that had previously gone unnoticed.
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Affiliation(s)
- Jonathan Remis
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Petar N. Petrov
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jessie T, Zhang
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Jeremy J. Axelrod
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Hang Cheng
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Shahar Sandhaus
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Holger Mueller
- Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Zhu D, Cao W, Li J, Wu C, Cao D, Zhang X. Correction of preferred orientation-induced distortion in cryo-electron microscopy maps. SCIENCE ADVANCES 2024; 10:eadn0092. [PMID: 39058771 DOI: 10.1126/sciadv.adn0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/06/2024] [Indexed: 07/28/2024]
Abstract
Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weili Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Junxi Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Chunling Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
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Han BG, Avila-Sakar A, Remis J, Glaeser RM. Challenges in making ideal cryo-EM samples. Curr Opin Struct Biol 2023; 81:102646. [PMID: 37392555 DOI: 10.1016/j.sbi.2023.102646] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/03/2023]
Abstract
Recognizing that interaction with the air-water interface (AWI) is a major challenge for cryo-EM, we first review current approaches designed to avoid it. Of these, immobilizing particles on affinity grids is arguably the most promising. In addition, we review efforts to gain more reliable control of the sample thicknesses, not the least important reason being to prevent immobilized particles from coming in contact with the AWI of the remaining buffer. It is emphasized that avoiding such a contact is as important for cryo-ET as for single-particle cryo-EM. Finally, looking to the future, it is proposed that immobilized samples might be used to perform time-resolved biochemical experiments directly on EM grids rather than just in test tubes or cuvettes.
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Affiliation(s)
- Bong-Gyoon Han
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Agustin Avila-Sakar
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
| | - Jonathan Remis
- Department of Physics, University of California, Berkeley, CA 94720, USA
| | - Robert M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA.
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Liu N, Wang HW. Better Cryo-EM Specimen Preparation: How to Deal with the Air-Water Interface? J Mol Biol 2022; 435:167926. [PMID: 36563741 DOI: 10.1016/j.jmb.2022.167926] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is now one of the most powerful and widely used methods to determine high-resolution structures of macromolecules. A major bottleneck of cryo-EM is to prepare high-quality vitrified specimen, which still faces many practical challenges. During the conventional vitrification process, macromolecules tend to adsorb at the air-water interface (AWI), which is known unfriendly to biological samples. In this review, we outline the nature of AWI and the problems caused by it, such as unpredictable or uneven particle distribution, protein denaturation, dissociation of complex and preferential orientation. We review and discuss the approaches and underlying mechanisms to deal with AWI: 1) Additives, exemplified by detergents, forming a protective layer at AWI and thus preserving the native folds of target macromolecules. 2) Fast vitrification devices based on the idea to freeze in-solution macromolecules before their touching of AWI. 3) Thin layer of continuous supporting films to adsorb macromolecules, and when functionalized with affinity ligands, to specifically anchor the target particles away from the AWI. Among these supporting films, graphene, together with its derivatives, with negligible background noise and mechanical robustness, has emerged as a new generation of support. These strategies have been proven successful in various cases and enable us a better handling of the problems caused by the AWI in cryo-EM specimen preparation.
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Affiliation(s)
- Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structures, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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Han BG, Armstrong M, Fletcher DA, Glaeser RM. Perspective: Biochemical and Physical Constraints Associated With Preparing Thin Specimens for Single-Particle Cryo-EM. Front Mol Biosci 2022; 9:864829. [PMID: 35573724 PMCID: PMC9100935 DOI: 10.3389/fmolb.2022.864829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
While many aspects of single-particle electron cryo-microscopy (cryo-EM) of biological macromolecules have reached a sophisticated level of development, this is not yet the case when it comes to preparing thin samples on specimen grids. As a result, there currently is considerable interest in achieving better control of both the sample thickness and the amount of area that is useful, but this is only one aspect in which improvement is needed. This Perspective addresses the further need to prevent the macromolecular particles from making contact with the air-water interface, something that can result in preferential orientation and even structural disruption of macromolecular particles. This unwanted contact can occur either as the result of free diffusion of particles during the interval between application, thinning and vitrification of the remaining buffer, or-when particles have been immobilized-by the film of buffer becoming too thin prior to vitrification. An opportunity now exists to apply theoretical and practical insights from the fields of thin-film physical chemistry and interfacial science, in an effort to bring cryo-EM sample preparation to a level of sophistication that is comparable to that of current data collection and analysis.
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Affiliation(s)
- Bong-Gyoon Han
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Max Armstrong
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Daniel A. Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,Chan Zuckerberg Biohub, San Francisco, CA, United States
| | - Robert M. Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States,*Correspondence: Robert M. Glaeser,
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