1
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Yadav S, Vinothkumar KR. Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol 2024; 80:535-550. [PMID: 38935342 PMCID: PMC11220838 DOI: 10.1107/s2059798324005229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
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Affiliation(s)
- Swati Yadav
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
| | - Kutti R. Vinothkumar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
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2
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Esfahani BG, Walia N, Neselu K, Aragon M, Askenasy I, Wei A, Mendez JH, Stroupe ME. Dimerization of assimilatory NADPH-dependent sulfite reductase reveals elements for diflavin reductase binding at a minimal interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599029. [PMID: 38915618 PMCID: PMC11195156 DOI: 10.1101/2024.06.14.599029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Escherichia coli NADPH-dependent assimilatory sulfite reductase is responsible for fixing sulfur for incorporation into sulfur-containing biomolecules. The oxidoreductase is composed of two subunits, an NADPH, FMN, and FAD-binding diflavin reductase and an iron siroheme and Fe4S4-containing oxidase. How they interact has been an unknown for over 50 years because the complex is highly flexible, thus has been intransigent for traditional X-ray or cryo-EM structural analysis. Using a combination of the chameleon plunging system with a fluorinated lipid we overcame the challenge of preserving the minimal dimer between the subunits for high-resolution cryo-EM analysis. Here, we report the first structure of the complex between the reductase and oxidase, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between the pairing of a siroheme-containing oxidase with a diflavin reductase or a ferredoxin partner to channel the six electrons that reduce sulfite to sulfide.
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Affiliation(s)
- Behrouz Ghazi Esfahani
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
| | - Nidhi Walia
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kasahun Neselu
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Mahira Aragon
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Isabel Askenasy
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Alex Wei
- New York Structural Biology Center, New York, NY, 10027, USA
| | | | - M. Elizabeth Stroupe
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
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3
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Gillman C, Bu G, Danelius E, Hattne J, Nannenga BL, Gonen T. Eliminating the missing cone challenge through innovative approaches. J Struct Biol X 2024; 9:100102. [PMID: 38962493 PMCID: PMC11220036 DOI: 10.1016/j.yjsbx.2024.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.
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Affiliation(s)
- Cody Gillman
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guanhong Bu
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Emma Danelius
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
- Department of Physiology, University of California, Los Angeles, CA, USA
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4
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Yang Z, Fan J, Wang J, Fan X, Ouyang Z, Wang HW, Zhou X. Electrospray-assisted cryo-EM sample preparation to mitigate interfacial effects. Nat Methods 2024; 21:1023-1032. [PMID: 38664529 PMCID: PMC11166575 DOI: 10.1038/s41592-024-02247-0] [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: 07/03/2023] [Accepted: 03/17/2024] [Indexed: 06/13/2024]
Abstract
Addressing interfacial effects during specimen preparation in cryogenic electron microscopy remains challenging. Here we introduce ESI-cryoPrep, a specimen preparation method based on electrospray ionization in native mass spectrometry, designed to alleviate issues associated with protein denaturation or preferred orientation induced by macromolecule adsorption at interfaces. Through fine-tuning spraying parameters, we optimized protein integrity preservation and achieved the desired ice thickness for analyzing target macromolecules. With ESI-cryoPrep, we prepared high-quality cryo-specimens of five proteins and obtained three-dimensional reconstructions at near-atomic resolution. Our findings demonstrate that ESI-cryoPrep effectively confines macromolecules within the middle of the thin layer of amorphous ice, facilitating the preparation of blotting-free vitreous samples. The protective mechanism, characterized by the uneven distribution of charged biomolecules of varying sizes within charged droplets, prevents the adsorption of target biomolecules at air-water or graphene-water interfaces, thereby avoiding structural damage to the protein particles or the introduction of dominant orientation issues.
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Affiliation(s)
- Zi Yang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jingjin Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Xiaoyu Zhou
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
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5
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Galaz-Montoya JG. The advent of preventive high-resolution structural histopathology by artificial-intelligence-powered cryogenic electron tomography. Front Mol Biosci 2024; 11:1390858. [PMID: 38868297 PMCID: PMC11167099 DOI: 10.3389/fmolb.2024.1390858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/08/2024] [Indexed: 06/14/2024] Open
Abstract
Advances in cryogenic electron microscopy (cryoEM) single particle analysis have revolutionized structural biology by facilitating the in vitro determination of atomic- and near-atomic-resolution structures for fully hydrated macromolecular complexes exhibiting compositional and conformational heterogeneity across a wide range of sizes. Cryogenic electron tomography (cryoET) and subtomogram averaging are rapidly progressing toward delivering similar insights for macromolecular complexes in situ, without requiring tags or harsh biochemical purification. Furthermore, cryoET enables the visualization of cellular and tissue phenotypes directly at molecular, nanometric resolution without chemical fixation or staining artifacts. This forward-looking review covers recent developments in cryoEM/ET and related technologies such as cryogenic focused ion beam milling scanning electron microscopy and correlative light microscopy, increasingly enhanced and supported by artificial intelligence algorithms. Their potential application to emerging concepts is discussed, primarily the prospect of complementing medical histopathology analysis. Machine learning solutions are poised to address current challenges posed by "big data" in cryoET of tissues, cells, and macromolecules, offering the promise of enabling novel, quantitative insights into disease processes, which may translate into the clinic and lead to improved diagnostics and targeted therapeutics.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, United States
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6
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Odorčić I, Hamed MB, Lismont S, Chávez-Gutiérrez L, Efremov RG. Apo and Aβ46-bound γ-secretase structures provide insights into amyloid-β processing by the APH-1B isoform. Nat Commun 2024; 15:4479. [PMID: 38802343 PMCID: PMC11130327 DOI: 10.1038/s41467-024-48776-2] [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: 08/29/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Deposition of amyloid-β (Aβ) peptides in the brain is a hallmark of Alzheimer's disease. Aβs are generated through sequential proteolysis of the amyloid precursor protein by the γ-secretase complexes (GSECs). Aβ peptide length, modulated by the Presenilin (PSEN) and APH-1 subunits of GSEC, is critical for Alzheimer's pathogenesis. Despite high relevance, mechanistic understanding of the proteolysis of Aβ, and its modulation by APH-1, remain incomplete. Here, we report cryo-EM structures of human GSEC (PSEN1/APH-1B) reconstituted into lipid nanodiscs in apo form and in complex with the intermediate Aβ46 substrate without cross-linking. We find that three non-conserved and structurally divergent APH-1 regions establish contacts with PSEN1, and that substrate-binding induces concerted rearrangements in one of the identified PSEN1/APH-1 interfaces, providing structural basis for APH-1 allosteric-like effects. In addition, the GSEC-Aβ46 structure reveals an interaction between Aβ46 and loop 1PSEN1, and identifies three other H-bonding interactions that, according to functional validation, are required for substrate recognition and efficient sequential catalysis.
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Affiliation(s)
- Ivica Odorčić
- Center for Structural Biology, VIB, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Mohamed Belal Hamed
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Sam Lismont
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Lucía Chávez-Gutiérrez
- VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49 box 602, 3000, Leuven, Belgium.
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Rouslan G Efremov
- Center for Structural Biology, VIB, Brussels, Belgium.
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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7
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Sanchez-Garcia R, Gaullier G, Cuadra-Troncoso JM, Vargas J. Cryo-EM Map Anisotropy Can Be Attenuated by Map Post-Processing and a New Method for Its Estimation. Int J Mol Sci 2024; 25:3959. [PMID: 38612769 PMCID: PMC11012471 DOI: 10.3390/ijms25073959] [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: 02/22/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
One of the most important challenges in cryogenic electron microscopy (cryo-EM) is the substantial number of samples that exhibit preferred orientations, which leads to an uneven coverage of the projection sphere. As a result, the overall quality of the reconstructed maps can be severely affected, as manifested by the presence of anisotropy in the map resolution. Several methods have been proposed to measure the directional resolution of maps in tandem with experimental protocols to address the problem of preferential orientations in cryo-EM. Following these works, in this manuscript we identified one potential limitation that may affect most of the existing methods and we proposed an alternative approach to evaluate the presence of preferential orientations in cryo-EM reconstructions. In addition, we also showed that some of the most recently proposed cryo-EM map post-processing algorithms can attenuate map anisotropy, thus offering alternative visualization opportunities for cases affected by moderate levels of preferential orientations.
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Affiliation(s)
- Ruben Sanchez-Garcia
- Department of Statistics, University of Oxford, 24–29 St Giles’, Oxford OX1 3LB, UK
| | - Guillaume Gaullier
- Department of Chemistry—Ångström, Uppsala University, Box 523, SE 751 20 Uppsala, Sweden;
| | - Jose Manuel Cuadra-Troncoso
- Departamento de Inteligencia Artificial, Universidad Nacional de Educación a Distancia, C. Juan del Rosal 16, 28040 Madrid, Spain;
| | - Javier Vargas
- Departamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040 Madrid, Spain
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8
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Bagde SR, Kim CY. Architecture of full-length type I modular polyketide synthases revealed by X-ray crystallography, cryo-electron microscopy, and AlphaFold2. Nat Prod Rep 2024. [PMID: 38501175 DOI: 10.1039/d3np00060e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Covering: up to the end of 2023Type I modular polyketide synthases construct polyketide natural products in an assembly line-like fashion, where the growing polyketide chain attached to an acyl carrier protein is passed from catalytic domain to catalytic domain. These enzymes have immense potential in drug development since they can be engineered to produce non-natural polyketides by strategically adding, exchanging, and deleting individual catalytic domains. In practice, however, this approach frequently results in complete failures or dramatically reduced product yields. A comprehensive understanding of modular polyketide synthase architecture is expected to resolve these issues. We summarize the three-dimensional structures and the proposed mechanisms of three full-length modular polyketide synthases, Lsd14, DEBS module 1, and PikAIII. We also describe the advantages and limitations of using X-ray crystallography, cryo-electron microscopy, and AlphaFold2 to study intact type I polyketide synthases.
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Affiliation(s)
- Saket R Bagde
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
| | - Chu-Young Kim
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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9
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Hlushko R, Pozharski E, Prabhu VM, Andrianov AK. Directly visualizing individual polyorganophosphazenes and their single-chain complexes with proteins. COMMUNICATIONS MATERIALS 2024; 5:36. [PMID: 38817739 PMCID: PMC11139433 DOI: 10.1038/s43246-024-00476-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/07/2024] [Indexed: 06/01/2024]
Abstract
Polyorganophosphazenes are water-soluble macromolecules with immunoadjuvant activity that self-assemble with proteins to enable biological functionality. Direct imaging by cryogenic electron microscopy uncovers the coil structure of those highly charged macromolecules. The successful visualization of individual polymer chains within the vitrified state is achieved in the absence of additives for contrast enhancement and is attributed to the high mass contrast of the inorganic backbone. Upon assembly with proteins, multiple protein copies bind at the single polymer chain level resulting in structures reminiscent of compact spherical complexes or stiffened coils. The outcome depends on protein characteristics and cannot be deduced by commonly used characterization techniques, such as light scattering, thus revealing direct morphological insights crucial for understanding biological activity. Atomic force microscopy supports the morphology outcomes while advanced analytical techniques confirm protein-polymer binding. The chain visualization methodology provides tools for gaining insights into the processes of supramolecular assembly and mechanistic aspects of polymer enabled vaccine delivery.
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Affiliation(s)
- Raman Hlushko
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
| | - Edwin Pozharski
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
| | - Vivek M. Prabhu
- Materials Science and Engineering Division, Material Measurement Laboratory, National Institute of Standards and Technology‡, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States of America
| | - Alexander K. Andrianov
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, United States of America
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10
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Abe KM, Lim CJ. Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579238. [PMID: 38370693 PMCID: PMC10871254 DOI: 10.1101/2024.02.06.579238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis Abundant (LEA) proteins, which naturally bind to AWI, can protect samples from AWI damage during plunge freezing. This protection is demonstrated with two LEA proteins from nematodes and tardigrades, which rescued the cryo-EM structural determination outcome of two fragile multisubunit protein complexes.
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Affiliation(s)
- Kaitlyn M. Abe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
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11
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González-Rodríguez N, Areán-Ulloa E, Fernández-Leiro R. A web-based dashboard for RELION metadata visualization. Acta Crystallogr D Struct Biol 2024; 80:93-100. [PMID: 38265874 PMCID: PMC10836394 DOI: 10.1107/s2059798323010902] [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: 10/31/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024] Open
Abstract
Cryo-electron microscopy (cryo-EM) has witnessed radical progress in the past decade, driven by developments in hardware and software. While current software packages include processing pipelines that simplify the image-processing workflow, they do not prioritize the in-depth analysis of crucial metadata, limiting troubleshooting for challenging data sets. The widely used RELION software package lacks a graphical native representation of the underlying metadata. Here, two web-based tools are introduced: relion_live.py, which offers real-time feedback on data collection, aiding swift decision-making during data acquisition, and relion_analyse.py, a graphical interface to represent RELION projects by plotting essential metadata including interactive data filtration and analysis. A useful script for estimating ice thickness and data quality during movie pre-processing is also presented. These tools empower researchers to analyse data efficiently and allow informed decisions during data collection and processing.
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Affiliation(s)
- Nayim González-Rodríguez
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Emma Areán-Ulloa
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rafael Fernández-Leiro
- Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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12
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Gillman C, Bu G, Danelius E, Hattne J, Nannenga B, Gonen T. Eliminating the Missing Cone Challenge through Innovative Approaches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575283. [PMID: 38293160 PMCID: PMC10827066 DOI: 10.1101/2024.01.11.575283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If, as is typically the case, the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the grid cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that this method could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop crystallization approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the COVID-19 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting preferred orientations, unlocking new possibilities for structure determination by MicroED.
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13
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Plana-Ruiz S, Gómez-Pérez A, Budayova-Spano M, Foley DL, Portillo-Serra J, Rauch E, Grivas E, Housset D, Das PP, Taheri ML, Nicolopoulos S, Ling WL. High-Resolution Electron Diffraction of Hydrated Protein Crystals at Room Temperature. ACS NANO 2023; 17:24802-24813. [PMID: 37890869 PMCID: PMC10753879 DOI: 10.1021/acsnano.3c05378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Structural characterization is crucial to understanding protein function. Compared with X-ray diffraction methods, electron crystallography can be performed on nanometer-sized crystals and can provide additional information from the resulting Coulomb potential map. Whereas electron crystallography has successfully resolved three-dimensional structures of vitrified protein crystals, its widespread use as a structural biology tool has been limited. One main reason is the fragility of such crystals. Protein crystals can be easily damaged by mechanical stress, change in temperature, or buffer conditions as well as by electron irradiation. This work demonstrates a methodology to preserve these nanocrystals in their natural environment at room temperature for electron diffraction experiments as an alternative to existing cryogenic techniques. Lysozyme crystals in their crystallization solution are hermetically sealed via graphene-coated grids, and their radiation damage is minimized by employing a low-dose data collection strategy in combination with a hybrid-pixel direct electron detector. Diffraction patterns with reflections of up to 3 Å are obtained and successfully indexed using a template-matching algorithm. These results demonstrate the feasibility of in situ protein electron diffraction. The method described will also be applicable to structural studies of hydrated nanocrystals important in many research and technological developments.
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Affiliation(s)
- Sergi Plana-Ruiz
- NanoMegas
SRPL, Rue Emile Claus
49, Brussels 1050, Belgium
- Servei
de Recursos Científics i Tècnics, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
| | | | | | - Daniel L. Foley
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Edgar Rauch
- SIMAP,
Grenoble INP, Université Grenoble Alpes, CNRS, F-38000 Grenoble, France
| | | | | | | | - Mitra L. Taheri
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Wai Li Ling
- Université
Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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14
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling Difficult Cryo-ET Samples: A Study with Primary Neurons from Drosophila melanogaster. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:2127-2148. [PMID: 37966978 PMCID: PMC11168236 DOI: 10.1093/micmic/ozad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/01/2023] [Accepted: 10/18/2023] [Indexed: 11/17/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons having been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA
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15
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Mendez JH, Chua EYD, Paraan M, Potter CS, Carragher B. Automated pipelines for rapid evaluation during cryoEM data acquisition. Curr Opin Struct Biol 2023; 83:102729. [PMID: 37988815 DOI: 10.1016/j.sbi.2023.102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/23/2023]
Abstract
Cryo-electron microscopy (cryoEM) has become a popular method for determining high-resolution structures of biomolecules. However, data processing can be time-consuming, particularly for new researchers entering the field. To improve data quality and increase data collection efficiency, several software packages have been developed for on-the-fly data processing with various degrees of automation. These software packages allow researchers to perform tasks such as motion correction, CTF estimation, 2D classification, and 3D reconstruction in real-time, with minimal human input. On-the-fly data processing can not only improve data collection efficiency but also increase the productivity of instrumentation in high demand. However, the various software packages available differ in their performance, computational requirements, and levels of automation. In this review, we describe the minimal metrics used to assess data quality during data collection, outline the features of an ideal on-the-fly data processing software systems, and provide results from using three of these systems.
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Affiliation(s)
- Joshua H Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y D Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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16
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Westphall MS, Lee KW, Salome AZ, Coon JJ, Grant T. Mass spectrometers as cryoEM grid preparation instruments. Curr Opin Struct Biol 2023; 83:102699. [PMID: 37703606 PMCID: PMC11019453 DOI: 10.1016/j.sbi.2023.102699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/18/2023] [Accepted: 08/15/2023] [Indexed: 09/15/2023]
Abstract
Structure determination by single-particle cryoEM has matured into a core structural biology technique. Despite many methodological advancements, most cryoEM grids are still prepared using the plunge-freezing method developed ∼40 years ago. Embedding samples in thin films and exposing them to the air-water interface often leads to sample damage and preferential orientation of the particles. Using native mass spectrometry to create cryoEM samples, potentially avoids these problems and allows the use of mass spectrometry sample isolation techniques during EM grid creation. We review the recent publications that have demonstrated protein complexes can be ionized, flown through the mass spectrometer, gently landed onto EM grids, imaged, and reconstructed in 3D. Although many uncertainties and challenges remain, the combination of cryoEM and MS has great potential.
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Affiliation(s)
- Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Kenneth W Lee
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Austin Z Salome
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Morgridge Institute for Research, 330 N Orchard Street, Madison, WI 53706, United States.
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17
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Kang JS, Zhou X, Liu YT, Wang K, Zhou ZH. Theoretical framework and experimental solution for the air-water interface adsorption problem in cryoEM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541984. [PMID: 37961330 PMCID: PMC10634880 DOI: 10.1101/2023.05.23.541984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously "disappear" on cryoEM grids, but the reasons for such misbehavior are not well understood, limiting systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air-water interface (AWI) to lower the total potential surface energy - rationalizing the use of surfactant, which is a direct solution to reducing the surface tension of the aqueous solution. By conducting cryogenic electron tomography (cryoET) with the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradual reduction of the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that applicable surfactants do not damage the biological complex, thus suggesting that they might offer a practical, simple, and general solution to the problem for high-resolution cryoEM. Application of this solution to a real-world AWI adsorption problem with a more challenging membrane protein, namely, the ClC-1 channel, has led to its first near-atomic structure using cryoEM.
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18
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Andrianov A, Hlushko R, Pozharski E, Prabhu V. Cryo-EM and AFM visualize linear polyorganophosphazene: individual chains and single-chain assemblies with proteins. RESEARCH SQUARE 2023:rs.3.rs-3411603. [PMID: 37961436 PMCID: PMC10635375 DOI: 10.21203/rs.3.rs-3411603/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Polyorganophosphazenes are biodegradable macromolecules with potent immunoadjuvant activity that self-assemble with protein antigens to provide biological activity. Direct imaging by cryogenic electron microscopy reveals the coil structure of the highly-charged high molecular mass synthetic polyorganophosphazenes within the vitrified state without any additives for contrast enhancement for the first time. Upon mixing with protein antigens under a controlled stoichiometric ratio, multiple proteins bind at the single chain level revealing a structural change reminiscent of compact spherical complexes or stiffened coils depending on the bound protein antigen. The structural outcome depends on the protein charge density that cannot be deduced by methods, such as dynamic light scattering, thus revealing direct morphological insight necessary to understand in vivo biological activity. Complementary atomic force microscopy supports the binding morphology outcomes as well as additional analytical techniques that indicate binding. These observations open opportunities to understand supramolecular assembly of proteins and other biomacromolecules at the single chain level with highly charged polyelectrolytes for vaccines as well as important to developing fields such as polyelectrolyte complex coacervation.
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19
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Ding J, Deme J, Stagno JR, Yu P, Lea S, Wang YX. Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. Nucleic Acids Res 2023; 51:9952-9960. [PMID: 37534568 PMCID: PMC10570017 DOI: 10.1093/nar/gkad651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.
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Affiliation(s)
- Jienyu Ding
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Justin C Deme
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ping Yu
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Susan M Lea
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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20
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Westphall M, Lee KW, Hemme C, Salome AZ, Mertz K, Grant T, Coon JJ. Cryogenic Soft Landing Improves Structural Preservation of Protein Complexes. Anal Chem 2023; 95:15094-15101. [PMID: 37732836 PMCID: PMC10568529 DOI: 10.1021/acs.analchem.3c03228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
We describe an apparatus for the cryogenic landing of particles from the ion beam of a mass spectrometer onto transmission electron microscope grids for cryo-electron microscopy. This system also allows for the controlled formation of thin films of amorphous ice on the grid surface. We demonstrate that as compared to room temperature landings, the use of this cryogenic landing device greatly improves the structural preservation of deposited protein-protein complexes. Furthermore, landing under cryogenic conditions can increase the diversity of particle orientations, allowing for improved 3D structural interpretation. We conclude that this approach allows for the direct coupling of mass spectrometry with cryo-electron microscopy.
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Affiliation(s)
- Michael
S. Westphall
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kenneth W. Lee
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Colin Hemme
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
| | - Austin Z. Salome
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Keaton Mertz
- Department
of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Timothy Grant
- Department
of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
| | - Joshua J. Coon
- Department
of Biomolecular Chemistry, University of
Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge
Institute for Research, Madison, Wisconsin 53715, United States
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21
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Basanta B, Chen W, Pride DE, Lander GC. Fabrication of Monolayer Graphene-Coated Grids for Cryoelectron Microscopy. J Vis Exp 2023:10.3791/65702. [PMID: 37747197 PMCID: PMC11141527 DOI: 10.3791/65702] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
Cryogenic electron microscopy (cryoEM) has emerged as a powerful technique for probing the atomic structure of macromolecular complexes. Sample preparation for cryoEM requires preserving specimens in a thin layer of vitreous ice, typically suspended within the holes of a fenestrated support film. However, all commonly used sample preparation approaches for cryoEM studies expose the specimen to the air-water interface, introducing a strong hydrophobic effect on the specimen that often results in denaturation, aggregation, and complex dissociation. Further, preferred hydrophobic interactions between regions of the specimen and the air-water interface impact the orientations adopted by the macromolecules, resulting in 3D reconstructions with anisotropic directional resolution. Adsorption of cryoEM specimens to a monolayer of graphene has been shown to help mitigate interactions with the air-water interface while minimizing the introduction of background noise. Graphene supports also offer the benefit of substantially lowering the required concentration of proteins required for cryoEM imaging. Despite the advantages of these supports, graphene-coated grids are not widely used by the cryoEM community due to the prohibitive expense of commercial options and the challenges associated with large-scale in-house production. This paper describes an efficient method for preparing batches of cryoEM grids that have nearly full coverage of monolayer graphene.
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Affiliation(s)
- Benjamin Basanta
- Department of Structural and Computational Biology, Scripps Research
| | - Wenqian Chen
- Department of Structural and Computational Biology, Scripps Research
| | - Daniel E Pride
- Department of Structural and Computational Biology, Scripps Research
| | - Gabriel C Lander
- Department of Structural and Computational Biology, Scripps Research;
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22
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Kang JS, Zhou X, Liu YT, Wang K, Zhou ZH. Theoretical framework and experimental solution for the air-water interface adsorption problem in cryoEM. BIOPHYSICS REPORTS 2023; 9:215-229. [PMID: 38516618 PMCID: PMC10951471 DOI: 10.52601/bpr.2023.230008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 10/31/2023] [Indexed: 03/23/2024] Open
Abstract
As cryogenic electron microscopy (cryoEM) gains traction in the structural biology community as a method of choice for determining atomic structures of biological complexes, it has been increasingly recognized that many complexes that behave well under conventional negative-stain electron microscopy tend to have preferential orientation, aggregate or simply mysteriously "disappear" on cryoEM grids. However, the reasons for such misbehavior are not well understood, which limits systematic approaches to solving the problem. Here, we have developed a theoretical formulation that explains these observations. Our formulation predicts that all particles migrate to the air-water interface (AWI) to lower the total potential surface energy-rationalizing the use of surfactant, which is a direct solution to reduce the surface tension of the aqueous solution. By performing cryogenic electron tomography (cryoET) on the widely-tested sample, GroEL, we demonstrate that, in a standard buffer solution, nearly all particles migrate to the AWI. Gradually reducing the surface tension by introducing surfactants decreased the percentage of particles exposed to the surface. By conducting single-particle cryoEM, we confirm that suitable surfactants do not damage the biological complex, thus suggesting that they might provide a practical, simple, and general solution to the problem for high-resolution cryoEM. Applying this solution to a real-world AWI adsorption problem involving a more challenging membrane protein, namely, the ClC-1 channel, has resulted in its near-atomic structure determination using cryoEM.
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Affiliation(s)
- Joon S. Kang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Xueting Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Kaituo Wang
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Z. Hong Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
- California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
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23
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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: 8] [Impact Index Per Article: 8.0] [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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24
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Kim JY, Yang JE, Mitchell JW, English LA, Yang SZ, Tenpas T, Dent EW, Wildonger J, Wright ER. Handling difficult cryo-ET samples: A study with primary neurons from Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548468. [PMID: 37502991 PMCID: PMC10369871 DOI: 10.1101/2023.07.10.548468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cellular neurobiology has benefited from recent advances in the field of cryo-electron tomography (cryo-ET). Numerous structural and ultrastructural insights have been obtained from plunge-frozen primary neurons cultured on electron microscopy grids. With most primary neurons been derived from rodent sources, we sought to expand the breadth of sample availability by using primary neurons derived from 3rd instar Drosophila melanogaster larval brains. Ultrastructural abnormalities were encountered while establishing this model system for cryo-ET, which were exemplified by excessive membrane blebbing and cellular fragmentation. To optimize neuronal samples, we integrated substrate selection, micropatterning, montage data collection, and chemical fixation. Efforts to address difficulties in establishing Drosophila neurons for future cryo-ET studies in cellular neurobiology also provided insights that future practitioners can use when attempting to establish other cell-based model systems.
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Affiliation(s)
- Joseph Y. Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jie E. Yang
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Josephine W. Mitchell
- Department of Chemistry and Biochemistry, Kalamazoo College, Kalamazoo, MI, 49006, USA
| | - Lauren A. English
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Sihui Z. Yang
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tanner Tenpas
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Erik W. Dent
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Jill Wildonger
- Departments of Pediatrics and Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth R. Wright
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Cryo-Electron Microscopy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, 53715, USA
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25
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Michon B, López-Sánchez U, Degrouard J, Nury H, Leforestier A, Rio E, Salonen A, Zoonens M. Role of surfactants in electron cryo-microscopy film preparation. Biophys J 2023; 122:1846-1857. [PMID: 37077048 PMCID: PMC10209149 DOI: 10.1016/j.bpj.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/01/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023] Open
Abstract
Single-particle electron cryo-microscopy (cryo-EM) has become an effective and straightforward approach to determine the structure of membrane proteins. However, obtaining cryo-EM grids of sufficient quality for high-resolution structural analysis remains a major bottleneck. One of the difficulties arises from the presence of detergents, which often leads to a lack of control of the ice thickness. Amphipathic polymers such as amphipols (APols) are detergent substitutes, which have proven to be valuable tools for cryo-EM studies. In this work, we investigate the physico-chemical behavior of APol- and detergent-containing solutions and show a correlation with the properties of vitreous thin films in cryo-EM grids. This study provides new insight on the potential of APols, allowing a better control of ice thickness while limiting protein adsorption at the air-water interface, as shown with the full-length mouse serotonin 5-HT3A receptor whose structure has been solved in APol. These findings may speed up the process of grid optimization to obtain high-resolution structures of membrane proteins.
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Affiliation(s)
- Baptiste Michon
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Paris, France
| | | | - Jéril Degrouard
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Hugues Nury
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Amélie Leforestier
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France.
| | - Emmanuelle Rio
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Anniina Salonen
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, France
| | - Manuela Zoonens
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, UMR 7099, Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le développement de la recherche scientifique, Paris, France.
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26
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Chari A, Stark H. Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. Annu Rev Biophys 2023; 52:391-411. [PMID: 37159297 DOI: 10.1146/annurev-biophys-111622-091300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.
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Affiliation(s)
- Ashwin Chari
- Research Group for Structural Biochemistry and Mechanisms, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany;
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27
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Warmack RA, Maggiolo AO, Orta A, Wenke BB, Howard JB, Rees DC. Structural consequences of turnover-induced homocitrate loss in nitrogenase. Nat Commun 2023; 14:1091. [PMID: 36841829 PMCID: PMC9968304 DOI: 10.1038/s41467-023-36636-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia during the process of biological nitrogen fixation that is essential for sustaining life. The active site FeMo-cofactor contains a [7Fe:1Mo:9S:1C] metallocluster coordinated with an R-homocitrate (HCA) molecule. Here, we establish through single particle cryoEM and chemical analysis of two forms of the Azotobacter vinelandii MoFe-protein - a high pH turnover inactivated species and a ∆NifV variant that cannot synthesize HCA - that loss of HCA is coupled to α-subunit domain and FeMo-cofactor disordering, and formation of a histidine coordination site. We further find a population of the ∆NifV variant complexed to an endogenous protein identified through structural and proteomic approaches as the uncharacterized protein NafT. Recognition by endogenous NafT demonstrates the physiological relevance of the HCA-compromised form, perhaps for cofactor insertion or repair. Our results point towards a dynamic active site in which HCA plays a role in enabling nitrogenase catalysis by facilitating activation of the FeMo-cofactor from a relatively stable form to a state capable of reducing dinitrogen under ambient conditions.
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Affiliation(s)
- Rebeccah A Warmack
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Ailiena O Maggiolo
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Andres Orta
- Biochemistry and Molecular Biophysics Graduate Program, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Belinda B Wenke
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA
| | - James B Howard
- Department of Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Douglas C Rees
- Division of Chemistry and Chemical Engineering 147-75, California Institute of Technology, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
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28
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Rima L, Zimmermann M, Fränkl A, Clairfeuille T, Lauer M, Engel A, Engel HA, Braun T. cryoWriter: a blotting free cryo-EM preparation system with a climate jet and cover-slip injector. Faraday Discuss 2022; 240:55-66. [PMID: 35924676 PMCID: PMC9641993 DOI: 10.1039/d2fd00066k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Electron microscopy (EM) introduced a fast and lasting change to structural and cellular biology. However, the sample preparation is still the bottleneck in the cryogenic electron microscopy (cryo-EM) workflow. Classical specimen preparation methods employ a harsh paper-blotting step, and the protein particles are exposed to a damaging air-water interface. Therefore, improved preparation strategies are urgently needed. Here, we present an amended microfluidic sample preparation method, which entirely avoids paper blotting and allows the passivation of the air-water interface during the preparation process. First, a climate jet excludes oxygen from the sample environment and controls the preparation temperature by varying the relative humidity of the grid environment. Second, the integrated "coverslip injector" allows the modulation of the air-water interface of the thin sample layer with effector molecules. We will briefly discuss the climate jet's effect on the stability and dynamics of the sample thin films. Furthermore, we will address the coverslip injector and demonstrate significant improvement in the sample quality.
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Affiliation(s)
- Luca Rima
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
| | - Michael Zimmermann
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
| | - Andri Fränkl
- Swiss Nanoscience Institute, University of Basel4056 BaselSwitzerland
| | - Thomas Clairfeuille
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070 BaselSwitzerland
| | - Matthias Lauer
- Roche Pharma Research and Early Development, Therapeutic Modalities, Lead Discovery, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd.Grenzacherstrasse 1244070 BaselSwitzerland
| | - Andreas Engel
- cryoWrite Ltd.Klingelbergstrasse 504056 BaselSwitzerland
| | | | - Thomas Braun
- Biozentrum, University of BaselSpitalstrasse 414056 BaselSwitzerland+41 79 7337269
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29
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Halfon Y, Aspinall L, White J, Jackson Hirst I, Wang Y, Darrow MC, Muench SP, Thompson RF. Maintaining the momentum in cryoEM for biological discovery. Faraday Discuss 2022; 240:18-32. [PMID: 36172917 DOI: 10.1039/d2fd00129b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cryo-electron microscopy (cryoEM) has been transformed over the last decade, with continual new hardware and software tools coming online, pushing the boundaries of what is possible and the nature and complexity of projects that can be undertaken. Here we discuss some recent trends and new tools which are creating opportunities to make more effective use of the resources available within facilities (both staff and equipment). We present approaches for the stratification of projects based on risk and known information about the projects, and the impacts this might have on the allocation of microscope time. We show that allocating different resources (microscope time) based on this information can lead to a significant increase in 'successful' use of the microscope, and reduce lead time by enabling projects to 'fail faster'. This model results in more efficient and sustainable cryoEM facility operation.
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Affiliation(s)
- Yehuda Halfon
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Louie Aspinall
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Joshua White
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Isobel Jackson Hirst
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Yiheng Wang
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michele C Darrow
- The Rosalind Franklin Institute, Harwell Campus, Didcot, OX11 0QS, UK.,SPT Labtech Ltd, Melbourn Science Park, Melbourn, SG8 6HB, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Rebecca F Thompson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences & Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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30
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Hrebík D, Gondová M, Valentová L, Füzik T, Přidal A, Nováček J, Plevka P. Polyelectrolyte coating of cryo-EM grids improves lateral distribution and prevents aggregation of macromolecules. Acta Crystallogr D Struct Biol 2022; 78:1337-1346. [DOI: 10.1107/s2059798322009299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/21/2022] [Indexed: 11/06/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) is one of the primary methods used to determine the structures of macromolecules and their complexes. With the increased availability of cryo-electron microscopes, the preparation of high-quality samples has become a bottleneck in the cryo-EM structure-determination pipeline. Macromolecules can be damaged during the purification or preparation of vitrified samples for cryo-EM, making them prone to binding to the grid support, to aggregation or to the adoption of preferential orientations at the air–water interface. Here, it is shown that coating cryo-EM grids with a negatively charged polyelectrolyte, such as single-stranded DNA, before applying the sample reduces the aggregation of macromolecules and improves their distribution. The single-stranded DNA-coated grids enabled the determination of high-resolution structures from samples that aggregated on conventional grids. The polyelectrolyte coating reduces the diffusion of macromolecules and thus may limit the negative effects of the contact of macromolecules with the grid support and blotting paper, as well as of the shear forces on macromolecules during grid blotting. Coating grids with polyelectrolytes can readily be employed in any laboratory dealing with cryo-EM sample preparation, since it is fast, simple, inexpensive and does not require specialized equipment.
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31
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Bromberg R, Cai K, Guo Y, Plymire D, Emde T, Puzio M, Borek D, Otwinowski Z. The His-tag as a decoy modulating preferred orientation in cryoEM. Front Mol Biosci 2022; 9:912072. [PMID: 36325274 PMCID: PMC9619061 DOI: 10.3389/fmolb.2022.912072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 08/19/2022] [Indexed: 12/02/2022] Open
Abstract
The His-tag is a widely used affinity tag that facilitates purification by means of affinity chromatography of recombinant proteins for functional and structural studies. We show here that His-tag presence affects how coproheme decarboxylase interacts with the air-water interface during grid preparation for cryoEM. Depending on His-tag presence or absence, we observe significant changes in patterns of preferred orientation. Our analysis of particle orientations suggests that His-tag presence can mask the hydrophobic and hydrophilic patches on a protein’s surface that mediate the interactions with the air-water interface, while the hydrophobic linker between a His-tag and the coding sequence of the protein may enhance other interactions with the air-water interface. Our observations suggest that tagging, including rational design of the linkers between an affinity tag and a protein of interest, offer a promising approach to modulating interactions with the air-water interface.
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Affiliation(s)
- Raquel Bromberg
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Ligo Analytics, Dallas, TX, United States
| | - Kai Cai
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Yirui Guo
- Ligo Analytics, Dallas, TX, United States
| | - Daniel Plymire
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Ligo Analytics, Dallas, TX, United States
| | - Tabitha Emde
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Maciej Puzio
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Center for Structural Genomics of Infectious Diseases, Dallas, TX, United States
- *Correspondence: Dominika Borek, ; Zbyszek Otwinowski,
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, United States
- Center for Structural Genomics of Infectious Diseases, Dallas, TX, United States
- *Correspondence: Dominika Borek, ; Zbyszek Otwinowski,
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32
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Luotonen OIV, Greca LG, Nyström G, Guo J, Richardson JJ, Rojas OJ, Tardy BL. Benchmarking supramolecular adhesive behavior of nanocelluloses, cellulose derivatives and proteins. Carbohydr Polym 2022; 292:119681. [PMID: 35725211 DOI: 10.1016/j.carbpol.2022.119681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/14/2022] [Accepted: 05/28/2022] [Indexed: 11/27/2022]
Abstract
One of the key steps towards a broader implementation of renewable materials is the development of biodegradable adhesives that can be attained at scale and utilized safely. Recently, cellulose nanocrystals (CNCs) were demonstrated to have remarkable adhesive properties. Herein, we study three classes of naturally synthesized biopolymers as adhesives, namely nanocelluloses (CNFs), cellulose derivatives, and proteins by themselves and when used as additives with CNCs. Among the samples evaluated, the adhesion strength was the highest for bovine serum albumin and hydroxypropyl cellulose (beyond 10 MPa). These were followed by carboxymethylcellulose and CNCs (ca. 5 MPa) and mechanically fibrillated CNFs (ca. 2 MPa), and finally by tempo-oxidized CNFs (0.2 MPa) and lysozyme (1.5 MPa). Remarkably, we find that the anisotropy of adhesion (in plane vs out of plane) falls within a narrow range across the bio-based adhesives studied. Collectively, this study benchmarks bio-based non-covalent adhesives aiming towards their improvement and implementation.
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Affiliation(s)
- Otso I V Luotonen
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P. O. Box 16300, FI-00076 Aalto, Finland
| | - Luiz G Greca
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P. O. Box 16300, FI-00076 Aalto, Finland
| | - Gustav Nyström
- Laboratory for Cellulose & Wood Materials, Empa - Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland; Department of Health Science and Technology, ETH Zürich, 8092 Zürich, Switzerland
| | - Junling Guo
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Joseph J Richardson
- Department of Materials Engineering, School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Orlando J Rojas
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P. O. Box 16300, FI-00076 Aalto, Finland; Bioproducts Institute, Department of Chemical and Biological Engineering, Department of Chemistry and Department of Wood Science, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z4, Canada.
| | - Blaise L Tardy
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P. O. Box 16300, FI-00076 Aalto, Finland; Khalifa University, Department of Chemical Engineering, Abu Dhabi, United Arab Emirates; Research and Innovation Center on CO(2) and Hydrogen, Khalifa University, Abu Dhabi, United Arab Emirates.
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33
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Esser TK, Böhning J, Fremdling P, Agasid MT, Costin A, Fort K, Konijnenberg A, Gilbert JD, Bahm A, Makarov A, Robinson CV, Benesch JLP, Baker L, Bharat TAM, Gault J, Rauschenbach S. Mass-selective and ice-free electron cryomicroscopy protein sample preparation via native electrospray ion-beam deposition. PNAS NEXUS 2022; 1:pgac153. [PMID: 36714824 PMCID: PMC9802471 DOI: 10.1093/pnasnexus/pgac153] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/03/2022] [Indexed: 02/01/2023]
Abstract
Despite tremendous advances in sample preparation and classification algorithms for electron cryomicroscopy (cryo-EM) and single-particle analysis (SPA), sample heterogeneity remains a major challenge and can prevent access to high-resolution structures. In addition, optimization of preparation conditions for a given sample can be time-consuming. In the current work, it is demonstrated that native electrospray ion-beam deposition (native ES-IBD) is an alternative, reliable approach for the preparation of extremely high-purity samples, based on mass selection in vacuum. Folded protein ions are generated by native electrospray ionization, separated from other proteins, contaminants, aggregates, and fragments, gently deposited on cryo-EM grids, frozen in liquid nitrogen, and subsequently imaged by cryo-EM. We demonstrate homogeneous coverage of ice-free cryo-EM grids with mass-selected protein complexes. SPA reveals that the complexes remain folded and assembled, but variations in secondary and tertiary structures are currently limiting information in 2D classes and 3D EM density maps. We identify and discuss challenges that need to be addressed to obtain a resolution comparable to that of the established cryo-EM workflow. Our results show the potential of native ES-IBD to increase the scope and throughput of cryo-EM for protein structure determination and provide an essential link between gas-phase and solution-phase protein structures.
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Affiliation(s)
| | - Jan Böhning
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Fremdling
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | | | - Kyle Fort
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany
| | - Albert Konijnenberg
- Thermo Fisher Scientific, Zwaanstraat 31G/H, 5651 CA Eindhoven, The Netherlands
| | - Joshua D Gilbert
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alan Bahm
- Thermo Fisher Scientific, 5350 NE Dawson Creek Drive, Hillsboro, OR 97124, USA
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath-Straße 11, 28199 Bremen, Germany,Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK,Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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34
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Piper SJ, Johnson RM, Wootten D, Sexton PM. Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM. Chem Rev 2022; 122:13989-14017. [PMID: 35849490 DOI: 10.1021/acs.chemrev.1c00837] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.
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Affiliation(s)
- Sarah J Piper
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Rachel M Johnson
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
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35
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Fan H, Sun F. Developing Graphene Grids for Cryoelectron Microscopy. Front Mol Biosci 2022; 9:937253. [PMID: 35911962 PMCID: PMC9326159 DOI: 10.3389/fmolb.2022.937253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally. Various problems occur during a vitrification procedure, including poor/nonuniform distribution of particles, preferred orientation of particles, specimen denaturation/degradation, high background from thick ice, and beam-induced motion, which have become important bottlenecks in high-resolution structural studies using cryo-EM in many projects. In recent years, grids with support films made of graphene and its derivatives have been developed to efficiently solve these problems. Here, the various advantages of graphene grids over conventional holey carbon film grids, functionalization of graphene support films, production methods of graphene grids, and origins of pristine graphene contamination are reviewed and discussed.
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Affiliation(s)
- Hongcheng Fan
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Bioland Laboratory, Guangzhou, China
- *Correspondence: Fei Sun,
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36
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Xu Y, Dang S. Recent Technical Advances in Sample Preparation for Single-Particle Cryo-EM. Front Mol Biosci 2022; 9:892459. [PMID: 35813814 PMCID: PMC9263182 DOI: 10.3389/fmolb.2022.892459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022] Open
Abstract
Cryo-sample preparation is a vital step in the process of obtaining high-resolution structures of macromolecules by using the single-particle cryo–electron microscopy (cryo-EM) method; however, cryo-sample preparation is commonly hampered by high uncertainty and low reproducibility. Specifically, the existence of air-water interfaces during the sample vitrification process could cause protein denaturation and aggregation, complex disassembly, adoption of preferred orientations, and other serious problems affecting the protein particles, thereby making it challenging to pursue high-resolution 3D reconstruction. Therefore, sample preparation has emerged as a critical research topic, and several new methods for application at various preparation stages have been proposed to overcome the aforementioned hurdles. Here, we summarize the methods developed for enhancing the quality of cryo-samples at distinct stages of sample preparation, and we offer insights for developing future strategies based on diverse viewpoints. We anticipate that cryo-sample preparation will no longer be a limiting step in the single-particle cryo-EM field as increasing numbers of methods are developed in the near future, which will ultimately benefit the entire research community.
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Affiliation(s)
- Yixin Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
| | - Shangyu Dang
- Division of Life Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
- *Correspondence: Shangyu Dang,
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37
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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38
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Iitani K, Nakaya M, Tomono T, Toma K, Arakawa T, Tsuchido Y, Mitsubayashi K, Takeda N. Enzyme-embedded electrospun fiber sensor of hydrophilic polymer for fluorometric ethanol gas imaging in vapor phase. Biosens Bioelectron 2022; 213:114453. [PMID: 35728364 DOI: 10.1016/j.bios.2022.114453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/16/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
Non-invasive measurement of volatile organic compounds (VOCs) emitted from living organisms is a powerful technique for diagnosing health conditions or diseases in humans. Bio-based gas sensors are suitable for the sensitive and selective measurement of a target VOC from a complex mixture of VOCs. Conventional bio-based sensors are normally prepared as wet-type probes to maintain proteins such as enzymes in a stable state, resulting in limitations in the commercialization of sensors, their operating environment, and performance. In this study, we present an enzyme-based fluorometric electrospun fiber sensor (eFES) mesh as a gas-phase biosensor in dry form. The eFES mesh targeting ethanol was fabricated by simple one-step electrospinning of polyvinyl alcohol with an alcohol dehydrogenase and an oxidized form of nicotinamide adenine dinucleotide. The enzyme embedded in the eFES mesh worked actively in a dry state without pretreatment. Substrate specificity was also maintained, and the sensor responded well to ethanol with a sufficient dynamic range. Adjustment of the pH and coenzyme quantity in the eFES mesh also affected enzyme activity. The dry-form biosensor-eFES mesh-will open a new direction for gas-phase biosensors because of its remarkable performance and simple fabrication, which is advantageous for commercialization.
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Affiliation(s)
- Kenta Iitani
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan; Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Misa Nakaya
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Tsubomi Tomono
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Koji Toma
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Takahiro Arakawa
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Yuji Tsuchido
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kohji Mitsubayashi
- Department of Biomedical Devices and Instrumentation, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan; Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Naoya Takeda
- Department of Life Science and Medical Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
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39
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Peters JJ, Leitz J, Guo Q, Beck F, Baumeister W, Brunger AT. A feature-guided, focused 3D signal permutation method for subtomogram averaging. J Struct Biol 2022; 214:107851. [PMID: 35346811 PMCID: PMC9149098 DOI: 10.1016/j.jsb.2022.107851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023]
Abstract
Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing pipelines commonly extract subtomograms as a cubic subvolume with the key assumption that the selected object of interest is discrete from its surroundings. However, in instances when the object is in its native environment, surrounding densities may negatively affect the subsequent alignment and refinement processes, leading to loss of information due to misalignment. For example, the strong densities from surrounding membranes may dominate the alignment process for membrane proteins. Here, we developed methods for feature-guided subtomogram alignment and 3D signal permutation for subtomogram averaging. Our 3D signal permutation method randomizes and filters voxels outside a mask of any shape and blurs the boundary of the mask that encapsulates the object of interest. The randomization preserves global statistical properties such as mean density and standard deviation of voxel density values, effectively producing a featureless background surrounding the object of interest. This signal permutation process can be repeatedly applied with intervening alignments of the 3D signal-permuted subvolumes, recentering of the mask, and optional adjustments of the shape of the mask. We have implemented these methods in a new processing pipeline which starts from tomograms, contains feature-guided subtomogram extraction and alignment, 3D signal-permutation, and subtomogram visualization tools. As an example, feature-guided alignment and 3D signal permutation leads to improved subtomogram average maps for a dataset of synaptic protein complexes in their native environment.
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Affiliation(s)
- John Jacob Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Beck
- CryoEM Technology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States.
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40
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Olek M, Cowtan K, Webb D, Chaban Y, Zhang P. IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice. Structure 2022; 30:522-531.e4. [PMID: 35150604 PMCID: PMC9033277 DOI: 10.1016/j.str.2022.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/01/2021] [Accepted: 01/18/2022] [Indexed: 12/23/2022]
Abstract
Despite the abundance of available software tools, optimal particle selection is still a vital issue in single-particle cryoelectron microscopy (cryo-EM). Regardless of the method used, most pickers struggle when ice thickness varies on a micrograph. IceBreaker allows users to estimate the relative ice gradient and flatten it by equalizing the local contrast. It allows the differentiation of particles from the background and improves overall particle picking performance. Furthermore, we introduce an additional parameter corresponding to local ice thickness for each particle. Particles with a defined ice thickness can be grouped and filtered based on this parameter during processing. These functionalities are especially valuable for on-the-fly processing to automatically pick as many particles as possible from each micrograph and to select optimal regions for data collection. Finally, estimated ice gradient distributions can be stored separately and used to inspect the quality of prepared samples.
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Affiliation(s)
- Mateusz Olek
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Department of Chemistry, University of York, York, UK
| | - Kevin Cowtan
- Department of Chemistry, University of York, York, UK
| | - Donovan Webb
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Yuriy Chaban
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Peijun Zhang
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7BN, UK.
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41
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Chen S, Li J, Vinothkumar KR, Henderson R. Interaction of human erythrocyte catalase with air-water interface in cryoEM. Microscopy (Oxf) 2022; 71:i51-i59. [PMID: 35275189 PMCID: PMC8855524 DOI: 10.1093/jmicro/dfab037] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/13/2021] [Accepted: 09/16/2021] [Indexed: 11/14/2022] Open
Abstract
One of the key goals in single-particle cryo-microscopy is to obtain a uniform distribution of particle orientations, so that the three-dimensional structure has isotropic resolution in Fourier space. A common problem arises from the interaction of protein molecules with the air-water interface that exists on both surfaces of the thin film of liquid that is formed prior to plunge-freezing into liquid ethane. Some proteins and other macromolecular complexes are disrupted by interaction with the air-water interface. Other proteins or macromolecules either become concentrated through their interaction with the interface or are excluded because they bind strongly to some other part of the grid or the filter paper used in blotting. In this paper, the interaction of human erythrocyte catalase with the air-water interface is investigated and minimized by the addition of certain detergents. Detergents can form an amphipathic monolayer at the air-water interface that creates a barrier and leaves the molecules free to adopt a variety of orientations, thus facilitating the 3D structure determination. These results suggest that further characterization and development of detergents for cryo-microscopy plunge-freezing would be useful.
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Affiliation(s)
- Shaoxia Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jade Li
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kutti R Vinothkumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bellary Road, Bengaluru 560065, India
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42
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Meijer DH, Frias CP, Beugelink JW, Deurloo YN, Janssen BJC. Teneurin4 dimer structures reveal a calcium‐stabilized compact conformation supporting homomeric trans‐interactions. EMBO J 2022; 41:e107505. [PMID: 35099835 PMCID: PMC9058538 DOI: 10.15252/embj.2020107505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/18/2022] Open
Abstract
Establishment of correct synaptic connections is a crucial step during neural circuitry formation. The Teneurin family of neuronal transmembrane proteins promotes cell–cell adhesion via homophilic and heterophilic interactions, and is required for synaptic partner matching in the visual and hippocampal systems in vertebrates. It remains unclear how individual Teneurins form macromolecular cis‐ and trans‐synaptic protein complexes. Here, we present a 2.7 Å cryo‐EM structure of the dimeric ectodomain of human Teneurin4. The structure reveals a compact conformation of the dimer, stabilized by interactions mediated by the C‐rich, YD‐shell, and ABD domains. A 1.5 Å crystal structure of the C‐rich domain shows three conserved calcium binding sites, and thermal unfolding assays and SAXS‐based rigid‐body modeling demonstrate that the compactness and stability of Teneurin4 dimers are calcium‐dependent. Teneurin4 dimers form a more extended conformation in conditions that lack calcium. Cellular assays reveal that the compact cis‐dimer is compatible with homomeric trans‐interactions. Together, these findings support a role for teneurins as a scaffold for macromolecular complex assembly and the establishment of cis‐ and trans‐synaptic interactions to construct functional neuronal circuits.
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Affiliation(s)
- Dimphna H Meijer
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
| | - Cátia P Frias
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
| | - J Wouter Beugelink
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
| | - Yanthi N Deurloo
- Department of Bionanoscience Kavli Institute of Nanoscience Delft University of Technology Delft The Netherlands
| | - Bert J C Janssen
- Department of Chemistry Faculty of Science Structural Biochemistry Bijvoet Center for Biomolecular Research Utrecht University Utrecht The Netherlands
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43
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Huber ST, Sarajlic E, Huijink R, Weis F, Evers WH, Jakobi AJ. Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes. eLife 2022; 11:72629. [PMID: 35060902 PMCID: PMC8786315 DOI: 10.7554/elife.72629] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 01/25/2023] Open
Abstract
Cryogenic electron microscopy has become an essential tool for structure determination of biological macromolecules. In practice, the difficulty to reliably prepare samples with uniform ice thickness still represents a barrier for routine high-resolution imaging and limits the current throughput of the technique. We show that a nanofluidic sample support with well-defined geometry can be used to prepare cryo-EM specimens with reproducible ice thickness from picoliter sample volumes. The sample solution is contained in electron-transparent nanochannels that provide uniform thickness gradients without further optimisation and eliminate the potentially destructive air-water interface. We demonstrate the possibility to perform high-resolution structure determination with three standard protein specimens. Nanofabricated sample supports bear potential to automate the cryo-EM workflow, and to explore new frontiers for cryo-EM applications such as time-resolved imaging and high-throughput screening.
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Affiliation(s)
- Stefan T Huber
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
| | | | | | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)
| | - Wiel H Evers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
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44
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Wood DM, Dobson RC, Horne CR. Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation. Biochem Soc Trans 2021; 49:2711-2726. [PMID: 34854920 PMCID: PMC8786299 DOI: 10.1042/bst20210674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/10/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022]
Abstract
Transcription is the principal control point for bacterial gene expression, and it enables a global cellular response to an intracellular or environmental trigger. Transcriptional regulation is orchestrated by transcription factors, which activate or repress transcription of target genes by modulating the activity of RNA polymerase. Dissecting the nature and precise choreography of these interactions is essential for developing a molecular understanding of transcriptional regulation. While the contribution of X-ray crystallography has been invaluable, the 'resolution revolution' of cryo-electron microscopy has transformed our structural investigations, enabling large, dynamic and often transient transcription complexes to be resolved that in many cases had resisted crystallisation. In this review, we highlight the impact cryo-electron microscopy has had in gaining a deeper understanding of transcriptional regulation in bacteria. We also provide readers working within the field with an overview of the recent innovations available for cryo-electron microscopy sample preparation and image reconstruction of transcription complexes.
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Affiliation(s)
- David M. Wood
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R. Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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45
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Han BG, Glaeser RM. Simple assay for adsorption of proteins to the air-water interface. J Struct Biol 2021; 213:107798. [PMID: 34534654 DOI: 10.1016/j.jsb.2021.107798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
A rapid assay is described, based upon the Marangoni effect, which detects the formation of a denatured-protein film at the air-water interface (AWI) of aqueous samples. This assay requires no more than a 20 µL aliquot of sample, at a protein concentration of no more than1 mg/ml, and it can be performed with any buffer that is used to prepare grids for electron cryo-microscopy (cryo-EM). In addition, this assay provides an easy way to estimate the rate at which a given protein forms such a film at the AWI. Use of this assay is suggested as a way to pre-screen the effect of various additives and chemical modifications that one might use to optimize the preparation of grids, although the final proof of optimization still requires further screening of grids in the electron microscope. In those cases when the assay establishes that a given protein does form a sacrificial, denatured-protein monolayer, it is suggested that subsequent optimization strategies might focus on discovering how to improve the adsorption of native proteins onto that monolayer, rather than to prevent its formation. A second alternative might be to bind such proteins to the surface of rationally designed affinity grids, in order to prevent their diffusion to, and unwanted interaction with, the AWI.
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Affiliation(s)
- Bong-Gyoon Han
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, United States
| | - Robert M Glaeser
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, United States.
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46
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Li B, Zhu D, Shi H, Zhang X. Effect of charge on protein preferred orientation at the air-water interface in cryo-electron microscopy. J Struct Biol 2021; 213:107783. [PMID: 34454014 DOI: 10.1016/j.jsb.2021.107783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/21/2021] [Accepted: 08/21/2021] [Indexed: 01/08/2023]
Abstract
The air-water interface (AWI) tends to adsorb proteins and frequently causes preferred orientation problems in cryo-electron microscopy (cryo-EM). Here, we examined cryo-EM data from protein samples frozen with different detergents and found that both anionic and cationic detergents promoted binding of proteins to the AWI. By contrast, some of the nonionic and zwitterionic detergents tended to prevent proteins from attaching to the AWI. The protein orientation distributions with different anionic detergents were similar and resembled that obtained without detergent. By contrast, cationic detergents gave distinct orientation distributions. Our results indicate that proteins adsorb to charged interface and the negative charge of the AWI plays an important role in adsorbing proteins in the conventional cryo-EM sample preparation. According to these findings, a new method was developed by adding anionic detergent at a concentration between 0.002% and 0.005%. Using this method, the protein particles exhibited a more evenly distributed orientations and still adsorbed to the AWI enabling them embedding in a thin layer of ice with high concentration, which will benefit the cryo-EM structural determination.
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Affiliation(s)
- Bufan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Dongjie Zhu
- School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Huigang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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47
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Wu K, Wu D, Zhu L, Wu Y. Application of Monolayer Graphene and Its Derivative in Cryo-EM Sample Preparation. Int J Mol Sci 2021; 22:8940. [PMID: 34445650 PMCID: PMC8396334 DOI: 10.3390/ijms22168940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Cryo-electron microscopy (Cryo-EM) has become a routine technology for resolving the structure of biological macromolecules due to the resolution revolution in recent years. The specimens are typically prepared in a very thin layer of vitrified ice suspending in the holes of the perforated amorphous carbon film. However, the samples prepared by directly applying to the conventional support membranes may suffer from partial or complete denaturation caused by sticking to the air-water interface (AWI). With the application in materials, graphene has also been used recently to improve frozen sample preparation instead of a suspended conventional amorphous thin carbon. It has been proven that graphene or graphene oxide and various chemical modifications on its surface can effectively prevent particles from adsorbing to the AWI, which improves the dispersion, adsorbed number, and orientation preference of frozen particles in the ice layer. Their excellent properties and thinner thickness can significantly reduce the background noise, allowing high-resolution three-dimensional reconstructions using a minimum data set.
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Affiliation(s)
- Ke Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
| | - Di Wu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
| | - Li Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (K.W.); (D.W.)
- Electron Microscopy Centre of Lanzhou University, Lanzhou 730000, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi’an Jiaotong University, Xi’an 710049, China
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48
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Wang YY, Zhang J, Liu XM, Li Y, Sui J, Dong MQ, Ye K, Du LL. Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. EMBO J 2021; 40:e107497. [PMID: 34169534 DOI: 10.15252/embj.2020107497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.
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Affiliation(s)
- Ying-Ying Wang
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Jianxiu Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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Januliene D, Moeller A. Cryo-EM of ABC transporters: an ice-cold solution to everything? FEBS Lett 2021; 594:3776-3789. [PMID: 33156959 DOI: 10.1002/1873-3468.13989] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/28/2020] [Accepted: 10/27/2020] [Indexed: 01/10/2023]
Abstract
High-resolution cryo-EM has revolutionized how we look at ABC transporters and membrane proteins in general. An ever-increasing number of software tools and faster processing now allow dissecting the molecular details of nanomachines at atomic precision. Considering the further benefits of significantly reduced sample demands and increased speed, cryo-EM will dominate the structure determination of membrane proteins in the near future without compromising on data quality or detail. Moreover, improved and new algorithms make it now possible to resolve the conformational spectrum of macromolecular machines under turnover conditions and to analyze heterogeneous samples at high resolution. The future of cryo-EM is, therefore, bright, and the growing number of imaging facilities and groups active in this field will amplify this trend even further. Nevertheless, expectations have to be managed, as cryo-EM alone cannot provide an ultimate answer to all scientific questions. In this review, we discuss the capabilities and limitations of cryo-EM together with possible solutions for studies of ABC transporters.
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Affiliation(s)
- Dovile Januliene
- University of Osnabrück, Germany.,Max-Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Arne Moeller
- University of Osnabrück, Germany.,Max-Planck Institute of Biophysics, Frankfurt am Main, Germany
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Atherton J, Moores CA. Cryo-EM of kinesin-binding protein: challenges and opportunities from protein-surface interactions. Acta Crystallogr D Struct Biol 2021; 77:411-423. [PMID: 33825702 PMCID: PMC8025885 DOI: 10.1107/s2059798321001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/17/2021] [Indexed: 11/10/2022] Open
Abstract
Kinesin-binding protein (KBP) is an important selective inhibitor of specific kinesin family members and its genetic disruption causes Goldberg-Shprintzen syndrome. Cryo-electron microscopy (cryo-EM) has recently been used to reveal the structure of KBP alone (72 kDa) and in complex with the motor domain of the mitotic kinesin-12 KIF15 (110 kDa). KBP is an α-solenoid, tetratricopeptide-repeat protein that interacts with the microtubule-binding region of the kinesin motor domain and blocks microtubule attachment. Numerous challenges arose relating to the behavior of KBP and KBP-kinesin complexes during cryo-EM sample preparation. These included the partial denaturation of KBP by air-water interfaces, protein aggregation resulting from carbon interaction and preferential orientation. Sample preparation with a graphene oxide substrate enabled the eventual structure determination. Here, experiences with preparing these samples are detailed, bringing attention to some of the challenges and opportunities that are likely to arise from protein-surface interactions.
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Affiliation(s)
- Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, United Kingdom
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Carolyn A. Moores
- Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
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