1
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Catalano C, Lucier KW, To D, Senko S, Tran NL, Farwell AC, Silva SM, Dip PV, Poweleit N, Scapin G. The CryoEM structure of human serum albumin in complex with ligands. J Struct Biol 2024; 216:108105. [PMID: 38852682 DOI: 10.1016/j.jsb.2024.108105] [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: 03/29/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024]
Abstract
Human serum albumin (HSA) is the most prevalent plasma protein in the human body, accounting for 60 % of the total plasma protein. HSA plays a major pharmacokinetic function, serving as a facilitator in the distribution of endobiotics and xenobiotics within the organism. In this paper we report the cryoEM structures of HSA in the apo form and in complex with two ligands (salicylic acid and teniposide) at a resolution of 3.5, 3.7 and 3.4 Å, respectively. We expand upon previously published work and further demonstrate that sub-4 Å maps of ∼60 kDa proteins can be routinely obtained using a 200 kV microscope, employing standard workflows. Most importantly, these maps allowed for the identification of small molecule ligands, emphasizing the practical applicability of this methodology and providing a starting point for subsequent computational modeling and in silico optimization.
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Affiliation(s)
- Claudio Catalano
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA.
| | - Kyle W Lucier
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Dennis To
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Skerdi Senko
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Nhi L Tran
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Ashlyn C Farwell
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Sabrina M Silva
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Phat V Dip
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Nicole Poweleit
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Giovanna Scapin
- NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
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2
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Zhou T, Chen L, Gorman J, Wang S, Kwon YD, Lin BC, Louder MK, Rawi R, Stancofski ESD, Yang Y, Zhang B, Quigley AF, McCoy LE, Rutten L, Verrips T, Weiss RA, Doria-Rose NA, Shapiro L, Kwong PD. Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure 2022; 30:862-875.e4. [PMID: 35413243 PMCID: PMC9177634 DOI: 10.1016/j.str.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/15/2021] [Accepted: 03/17/2022] [Indexed: 11/30/2022]
Abstract
Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lei Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D Stancofski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Forsman Quigley
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy Rutten
- University of Utrecht, Utrecht, the Netherlands
| | | | - Robin A Weiss
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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3
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Cheung CSF, Gorman J, Andrews SF, Rawi R, Reveiz M, Shen CH, Wang Y, Harris DR, Nazzari AF, Olia AS, Raab J, Teng IT, Verardi R, Wang S, Yang Y, Chuang GY, McDermott AB, Zhou T, Kwong PD. Structure of an influenza group 2-neutralizing antibody targeting the hemagglutinin stem supersite. Structure 2022; 30:993-1003.e6. [PMID: 35489332 DOI: 10.1016/j.str.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 01/18/2022] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
Several influenza antibodies with broad group 2 neutralization have recently been isolated. Here, we analyze the structure, class, and binding of one of these antibodies from an H7N9 vaccine trial, 315-19-1D12. The cryo-EM structure of 315-19-1D12 Fab in complex with the hemagglutinin (HA) trimer revealed the antibody to recognize the helix A region of the HA stem, at the supersite of vulnerability recognized by group 1-specific and by cross-group-neutralizing antibodies. 315-19-1D12 was derived from HV1-2 and KV2-28 genes and appeared to form a new antibody class. Bioinformatic analysis indicated its group 2 neutralization specificity to be a consequence of four key residue positions. We specifically tested the impact of the group 1-specific N33 glycan, which decreased but did not abolish group 2 binding of 315-19-1D12. Overall, this study highlights the recognition of a broad group 2-neutralizing antibody, revealing unexpected diversity in neutralization specificity for antibodies that recognize the HA stem supersite.
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Affiliation(s)
- Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah F Andrews
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mateo Reveiz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R Harris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra F Nazzari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julie Raab
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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4
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Swanson KA, Rainho-Tomko JN, Williams ZP, Lanza L, Peredelchuk M, Kishko M, Pavot V, Alamares-Sapuay J, Adhikarla H, Gupta S, Chivukula S, Gallichan S, Zhang L, Jackson N, Yoon H, Edwards D, Wei CJ, Nabel GJ. A respiratory syncytial virus (RSV) F protein nanoparticle vaccine focuses antibody responses to a conserved neutralization domain. Sci Immunol 2020; 5:5/47/eaba6466. [PMID: 32358170 DOI: 10.1126/sciimmunol.aba6466] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022]
Abstract
A stabilized form of the respiratory syncytial virus (RSV) fusion (F) protein has been explored as a vaccine to prevent viral infection because it presents several potent neutralizing epitopes. Here, we used a structure-based rational design to optimize antigen presentation and focus antibody (Ab) responses to key epitopes on the pre-fusion (pre-F) protein. This protein was fused to ferritin nanoparticles (pre-F-NP) and modified with glycans to mask nonneutralizing or poorly neutralizing epitopes to further focus the Ab response. The multimeric pre-F-NP elicited durable pre-F-specific Abs in nonhuman primates (NHPs) after >150 days and elicited potent neutralizing Ab (NAb) responses in mice and NHPs in vivo, as well as in human cells evaluated in the in vitro MIMIC system. This optimized pre-F-NP stimulated a more potent Ab response than a representative pre-F trimer, DS-Cav1. Collectively, this pre-F vaccine increased the generation of NAbs targeting the desired pre-F conformation, an attribute that facilitates the development of an effective RSV vaccine.
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Affiliation(s)
| | | | - Zachary P Williams
- Sanofi Pasteur VaxDesign, 2501 Discovery Drive, Suite 300, Orlando, FL 32826, USA
| | - Lilibeth Lanza
- Sanofi Pasteur VaxDesign, 2501 Discovery Drive, Suite 300, Orlando, FL 32826, USA
| | - Michael Peredelchuk
- Sanofi Pasteur VaxDesign, 2501 Discovery Drive, Suite 300, Orlando, FL 32826, USA
| | - Michael Kishko
- Sanofi Pasteur, 38 Sidney Street, Cambridge, MA 02139, USA
| | - Vincent Pavot
- Sanofi Pasteur, 1541 Avenue Marcel Mérieux, Marcy l'Etoile, France
| | | | | | - Sankalp Gupta
- Sanofi Pasteur, 38 Sidney Street, Cambridge, MA 02139, USA
| | | | - Scott Gallichan
- Sanofi Pasteur, 95 Willowdale Blvd, Toronto, Ontario, Canada
| | - Linong Zhang
- Sanofi Pasteur, 38 Sidney Street, Cambridge, MA 02139, USA
| | | | - Heesik Yoon
- Sanofi Pasteur VaxDesign, 2501 Discovery Drive, Suite 300, Orlando, FL 32826, USA
| | - Darin Edwards
- Sanofi Pasteur VaxDesign, 2501 Discovery Drive, Suite 300, Orlando, FL 32826, USA
| | | | - Gary J Nabel
- Sanofi, 640 Memorial Drive, Cambridge, MA 02139, USA.
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5
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Jiménez A, Jonic S, Majtner T, Otón J, Vilas JL, Maluenda D, Mota J, Ramírez-Aportela E, Martínez M, Rancel Y, Segura J, Sánchez-García R, Melero R, Del Cano L, Conesa P, Skjaerven L, Marabini R, Carazo JM, Sorzano COS. Validation of electron microscopy initial models via small angle X-ray scattering curves. Bioinformatics 2020; 35:2427-2433. [PMID: 30500892 DOI: 10.1093/bioinformatics/bty985] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/29/2018] [Accepted: 11/29/2018] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Cryo electron microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The re-construction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes and structures of the analyzed particles. RESULTS In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. AVAILABILITY AND IMPLEMENTATION The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.
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Affiliation(s)
- Amaya Jiménez
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Slavica Jonic
- UMR CNRS 7590, Muséum National d ´Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Tomas Majtner
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Joaquín Otón
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Jose Luis Vilas
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - David Maluenda
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Javier Mota
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | | | - Marta Martínez
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Yaiza Rancel
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Joan Segura
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | | | - Roberto Melero
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Laura Del Cano
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Pablo Conesa
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Lars Skjaerven
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Roberto Marabini
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain.,Department of Computer Science, University Autónoma de Madrid, Cantoblanco, Madrid, Spain
| | - Jose M Carazo
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nac. Biotecnología (CSIC), Cantoblanco, Madrid, Spain.,Department of Engineering of Electronic and Telecommunication System, University San Pablo-CEU, Campus Urb. Montepríncipe, Boadilla del Monte, Madrid, Spain
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6
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Non-uniformity of projection distributions attenuates resolution in Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:160-183. [PMID: 31525386 DOI: 10.1016/j.pbiomolbio.2019.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/02/2019] [Accepted: 09/07/2019] [Indexed: 11/23/2022]
Abstract
Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of non-uniform sampling have been described qualitatively, we know little about how sampling quantitatively affects resolution in cryo-EM. Here, we show how inhomogeneity in any projection distribution scheme attenuates the global Fourier Shell Correlation (FSC) in relation to the number of particles and a single geometrical parameter, which we term the sampling compensation factor (SCF). The reciprocal of the SCF is defined as the average over Fourier shells of the reciprocal of the per-particle sampling and normalized to unity for uniform distributions. The SCF therefore ranges from one to zero, with values close to the latter implying large regions of poorly sampled or completely missing data in Fourier space. Using two synthetic test cases, influenza hemagglutinin and human apoferritin, we demonstrate how any amount of sampling inhomogeneity always attenuates the FSC compared to a uniform distribution. We advocate quantitative evaluation of the SCF criterion to approximate the effect of non-uniform sampling on resolution within experimental single-particle cryo-EM reconstructions.
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7
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Zhang C, Cantara W, Jeon Y, Musier-Forsyth K, Grigorieff N, Lyumkis D. Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification. Ultramicroscopy 2019; 203:170-180. [PMID: 30528101 PMCID: PMC6476647 DOI: 10.1016/j.ultramic.2018.11.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 11/07/2018] [Accepted: 11/26/2018] [Indexed: 01/30/2023]
Abstract
Single-particle electron cryo-microscopy and computational image classification can be used to analyze structural variability in macromolecules and their assemblies. In some cases, a particle may contain different regions that each display a range of distinct conformations. We have developed strategies, implemented within the Frealign and cisTEM image processing packages, to focus-classify on specific regions of a particle and detect potential covariance. The strategies are based on masking the region of interest using either a 2-D mask applied to reference projections and particle images, or a 3-D mask applied to the 3-D volume. We show that focused classification approaches can be used to study structural covariance, a concept that is likely to gain more importance as datasets grow in size, allowing the distinction of more structural states and smaller differences between states. Finally, we apply the approaches to an experimental dataset containing the HIV-1 Transactivation Response (TAR) element RNA fused into the large bacterial ribosomal subunit to deconvolve structural mobility within localized regions of interest, and to a dataset containing assembly intermediates of the large subunit to measure structural covariance.
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Affiliation(s)
- Cheng Zhang
- Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - William Cantara
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Youngmin Jeon
- Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Nikolaus Grigorieff
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, USA.
| | - Dmitry Lyumkis
- Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA.
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8
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Chase J, Catalano A, Noble AJ, Eng ET, Olinares PD, Molloy K, Pakotiprapha D, Samuels M, Chait B, des Georges A, Jeruzalmi D. Mechanisms of opening and closing of the bacterial replicative helicase. eLife 2018; 7:41140. [PMID: 30582519 PMCID: PMC6391071 DOI: 10.7554/elife.41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Assembly of bacterial ring-shaped hexameric replicative helicases on single-stranded (ss) DNA requires specialized loading factors. However, mechanisms implemented by these factors during opening and closing of the helicase, which enable and restrict access to an internal chamber, are not known. Here, we investigate these mechanisms in the Escherichia coli DnaB helicase•bacteriophage λ helicase loader (λP) complex. We show that five copies of λP bind at DnaB subunit interfaces and reconfigure the helicase into an open spiral conformation that is intermediate to previously observed closed ring and closed spiral forms; reconfiguration also produces openings large enough to admit ssDNA into the inner chamber. The helicase is also observed in a restrained inactive configuration that poises it to close on activating signal, and transition to the translocation state. Our findings provide insights into helicase opening, delivery to the origin and ssDNA entry, and closing in preparation for translocation.
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Affiliation(s)
- Jillian Chase
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States
| | - Andrew Catalano
- Department of Chemistry and Biochemistry, City College of New York, New York, United States
| | - Alex J Noble
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Edward T Eng
- Simons Electron Microscopy Center, The New York Structural Biology Center, New York, United States
| | - Paul Db Olinares
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Kelly Molloy
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Danaya Pakotiprapha
- Department of Biochemistry, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Martin Samuels
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Brian Chait
- Laboratory for Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Amedee des Georges
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,Structural Biology Initiative, CUNY Advanced Science Research Center, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States
| | - David Jeruzalmi
- Department of Chemistry and Biochemistry, City College of New York, New York, United States.,PhD Program in Biochemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, United States.,PhD Program in Biology, The Graduate Center of the City University of New York, New York, United States
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9
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Rheinberger J, Gao X, Schmidpeter PA, Nimigean CM. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. eLife 2018; 7:39775. [PMID: 30028291 PMCID: PMC6093708 DOI: 10.7554/elife.39775] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 12/11/2022] Open
Abstract
Cyclic nucleotide-modulated channels have important roles in visual signal transduction and pacemaking. Binding of cyclic nucleotides (cAMP/cGMP) elicits diverse functional responses in different channels within the family despite their high sequence and structure homology. The molecular mechanisms responsible for ligand discrimination and gating are unknown due to lack of correspondence between structural information and functional states. Using single particle cryo-electron microscopy and single-channel recording, we assigned functional states to high-resolution structures of SthK, a prokaryotic cyclic nucleotide-gated channel. The structures for apo, cAMP-bound, and cGMP-bound SthK in lipid nanodiscs, correspond to no, moderate, and low single-channel activity, respectively, consistent with the observation that all structures are in resting, closed states. The similarity between apo and ligand-bound structures indicates that ligand-binding domains are strongly coupled to pore and SthK gates in an allosteric, concerted fashion. The different orientations of cAMP and cGMP in the ‘resting’ and ‘activated’ structures suggest a mechanism for ligand discrimination. Ion channels are essential for transmitting signals in the nervous system and brain. One large group of ion channels includes members that are activated by cyclic nucleotides, small molecules used to transmit signals within cells. These cyclic nucleotide-gated channels play an important role in regulating our ability to see and smell. The activity of these ion channels has been studied for years, but scientists have only recently been able to look into their structure. Since structural biology methods require purified, well-behaved proteins, the members of this ion channel family selected for structural studies do not necessarily match those whose activity has been well established. There is a need for a good model that would allow both the structure and activity of a cyclic nucleotide-gated ion channel to be characterized. The cyclic nucleotide-gated ion channel, SthK, from bacteria called Spirochaeta thermophila, was identified as such model because both its activity and its structure are accessible. Rheinberger et al. have used cryo electron microscopy to solve several high-resolution structures of SthK channels. In two of the structures, SthK was bound to either one of two types of activating cyclic nucleotides – cAMP or cGMP – and in another structure, no cyclic nucleotides were bound. Separately recording the activity of individual channels allowed the activity states likely to be represented by these structures to be identified. Combining the results of the experiments revealed no activity from channels in an unbound state, low levels of activity for channels bound to cGMP, and moderate activity for channels bound to cAMP. Rheinberger et al. show that the channel, under the conditions experienced in cryo electron microscopy, is closed in all of the states studied. Unexpectedly, the binding of cyclic nucleotides produced no structural change even in the cyclic nucleotide-binding pocket of the channel, a region that was previously observed to undergo such changes when this region alone was crystallized. Rheinberger et al. deduce from this that the four subunits that make up the channel likely undergo the conformational change towards an open state all at once, rather than one by one. The structures and the basic functional characterization of SthK channels provide a strong starting point for future research into determining the entire opening and closing cycle for a cyclic nucleotide-gated channel. Human equivalents of the channel are likely to work in similar ways. The results presented by Rheinberger et al. could therefore be built upon to help address diseases that result from deficiencies in cyclic nucleotide-gated channels, such as loss of vision due to retinal degradation (retinitis pigmentosa or progressive cone dystrophy) and achromatopsia.
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Affiliation(s)
- Jan Rheinberger
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Xiaolong Gao
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States
| | | | - Crina M Nimigean
- Departments of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
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10
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Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer. Nat Commun 2018; 9:1956. [PMID: 29769533 PMCID: PMC5955915 DOI: 10.1038/s41467-018-04272-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/13/2018] [Indexed: 11/25/2022] Open
Abstract
Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a “closed-form”, native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates. Native-like soluble HIV envelope (Env) trimers are potential vaccine immunogens, and elimination of furin-dependence could provide a DNA-based alternative. Here, Sarkar et al. show that a cleavage-independent Env construct recapitulates the architecture and glycosylation of the native cleaved trimer.
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11
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Schmidpeter PAM, Gao X, Uphadyay V, Rheinberger J, Nimigean CM. Ligand binding and activation properties of the purified bacterial cyclic nucleotide-gated channel SthK. J Gen Physiol 2018; 150:821-834. [PMID: 29752414 PMCID: PMC5987880 DOI: 10.1085/jgp.201812023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
SthK is a bacterial cyclic nucleotide–gated ion channel from Spirochaeta thermophila. By optimizing the expression and purification of SthK, Schmidpeter et al. show that cAMP and cGMP bind to the channel with similar affinity but activate it with different efficacy. Cyclic nucleotide–modulated ion channels play several essential physiological roles. They are involved in signal transduction in photoreceptors and olfactory sensory neurons as well as pacemaking activity in the heart and brain. Investigations of the molecular mechanism of their actions, including structural and electrophysiological characterization, are restricted by the availability of stable, purified protein obtained from accessible systems. Here, we establish that SthK, a cyclic nucleotide–gated (CNG) channel from Spirochaeta thermophila, is an excellent model for investigating the gating of eukaryotic CNG channels at the molecular level. The channel has high sequence similarity with its eukaryotic counterparts and was previously reported to be activated by cyclic nucleotides in patch-clamp experiments with Xenopus laevis oocytes. We optimized protein expression and purification to obtain large quantities of pure, homogeneous, and active recombinant SthK protein from Escherichia coli. A negative-stain electron microscopy (EM) single-particle analysis indicated that this channel is a promising candidate for structural studies with cryo-EM. Using radioactivity and fluorescence flux assays, as well as single-channel recordings in lipid bilayers, we show that the protein is partially activated by micromolar concentrations of cyclic adenosine monophosphate (cAMP) and that channel activity is increased by depolarization. Unlike previous studies, we find that cyclic guanosine monophosphate (cGMP) is also able to activate SthK, but with much lower efficiency than cAMP. The distinct sensitivities to different ligands resemble eukaryotic CNG and hyperpolarization-activated and cyclic nucleotide–modulated channels. Using a fluorescence binding assay, we show that cGMP and cAMP bind to SthK with similar apparent affinities, suggesting that the large difference in channel activation by cAMP or cGMP is caused by the efficacy with which each ligand promotes the conformational changes toward the open state. We conclude that the functional characteristics of SthK reported here will permit future studies to analyze ligand gating and discrimination in CNG channels.
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Affiliation(s)
| | - Xiaolong Gao
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Vikrant Uphadyay
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Jan Rheinberger
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY .,Department of Biochemistry, Weill Cornell Medicine, New York, NY.,Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY
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12
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Geary C, Chworos A, Verzemnieks E, Voss NR, Jaeger L. Composing RNA Nanostructures from a Syntax of RNA Structural Modules. NANO LETTERS 2017; 17:7095-7101. [PMID: 29039189 PMCID: PMC6363482 DOI: 10.1021/acs.nanolett.7b03842] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Natural stable RNAs fold and assemble into complex three-dimensional architectures by relying on the hierarchical formation of intricate, recurrent networks of noncovalent tertiary interactions. These sequence-dependent networks specify RNA structural modules enabling orientational and topological control of helical struts to form larger self-folding domains. Borrowing concepts from linguistics, we defined an extended structural syntax of RNA modules for programming RNA strands to assemble into complex, responsive nanostructures under both thermodynamic and kinetic control. Based on this syntax, various RNA building blocks promote the multimolecular assembly of objects with well-defined three-dimensional shapes as well as the isothermal folding of long RNAs into complex single-stranded nanostructures during transcription. This work offers a glimpse of the limitless potential of RNA as an informational medium for designing programmable and functional nanomaterials useful for synthetic biology, nanomedicine, and nanotechnology.
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Affiliation(s)
- Cody Geary
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Arkadiusz Chworos
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Erik Verzemnieks
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
| | - Neil R. Voss
- Biological, Chemical, and Physical Sciences Department, Roosevelt University, 1400 North Roosevelt Blvd., Schaumburg, Illinois 60173, United States
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106-9510, United States
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13
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Best practices for managing large CryoEM facilities. J Struct Biol 2017; 199:225-236. [PMID: 28827185 DOI: 10.1016/j.jsb.2017.07.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 01/26/2023]
Abstract
This paper provides an overview of the discussion and presentations from the Workshop on the Management of Large CryoEM Facilities held at the New York Structural Biology Center, New York, NY on February 6-7, 2017. A major objective of the workshop was to discuss best practices for managing cryoEM facilities. The discussions were largely focused on supporting single-particle methods for cryoEM and topics included: user access, assessing projects, workflow, sample handling, microscopy, data management and processing, and user training.
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14
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Bharat TAM, Russo CJ, Löwe J, Passmore LA, Scheres SHW. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging. Structure 2015; 23:1743-1753. [PMID: 26256537 PMCID: PMC4559595 DOI: 10.1016/j.str.2015.06.026] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 06/11/2015] [Accepted: 06/21/2015] [Indexed: 01/03/2023]
Abstract
Recent innovations in specimen preparation, data collection, and image processing have led to improved structure determination using single-particle electron cryomicroscopy (cryo-EM). Here we explore some of these advances to improve structures determined using electron cryotomography (cryo-ET) and sub-tomogram averaging. We implement a new three-dimensional model for the contrast transfer function, and use this in a regularized likelihood optimization algorithm as implemented in the RELION program. Using direct electron detector data, we apply both single-particle analysis and sub-tomogram averaging to analyze radiation-induced movements of the specimen. As in single-particle cryo-EM, we find that significant sample movements occur during tomographic data acquisition, and that these movements are substantially reduced through the use of ultrastable gold substrates. We obtain a sub-nanometer resolution structure of the hepatitis B capsid, and show that reducing radiation-induced specimen movement may be central to attempts at further improving tomogram quality and resolution. The Bayesian approach in RELION is extended to sub-tomogram averaging A new 3D CTF and missing-wedge model for sub-tomogram averaging is proposed Ultrastable gold supports reduce radiation-induced motion in tomography tilt series Using the above, an 8 Å structure of hepatitis B capsid from cryo-ET is presented
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Affiliation(s)
- Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Christopher J Russo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lori A Passmore
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sjors H W Scheres
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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15
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Moriya T, Acar E, Cheng RH, Ruotsalainen U. A Bayesian approach for suppression of limited angular sampling artifacts in single particle 3D reconstruction. J Struct Biol 2015; 191:318-31. [PMID: 26193484 DOI: 10.1016/j.jsb.2015.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/10/2015] [Accepted: 07/16/2015] [Indexed: 10/23/2022]
Abstract
In the single particle reconstruction, the initial 3D structure often suffers from the limited angular sampling artifact. Selecting 2D class averages of particle images generally improves the accuracy and efficiency of the reference-free 3D angle estimation, but causes an insufficient angular sampling to fill the information of the target object in the 3D frequency space. Similarly, the initial 3D structure by the random-conical tilt reconstruction has the well-known "missing cone" artifact. Here, we attempted to solve the limited angular sampling problem by sequentially applying maximum a posteriori estimate with expectation maximization algorithm (sMAP-EM). Using both simulated and experimental cryo-electron microscope images, the sMAP-EM was compared to the direct Fourier method on the basis of reconstruction error and resolution. To establish selection criteria of the final regularization weight for the sMAP-EM, the effects of noise level and sampling sparseness on the reconstructions were examined with evenly distributed sampling simulations. The frequency information filled in the missing cone of the conical tilt sampling simulations was assessed by developing new quantitative measurements. All the results of visual and numerical evaluations showed the sMAP-EM performed better than the direct Fourier method, regardless of the sampling method, noise level, and sampling sparseness. Furthermore, the frequency domain analysis demonstrated that the sMAP-EM can fill the meaningful information in the unmeasured angular space without detailed a priori knowledge of the objects. The current research demonstrated that the sMAP-EM has a high potential to facilitate the determination of 3D protein structures at near atomic-resolution.
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Affiliation(s)
- Toshio Moriya
- Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland; BioMediTech, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland.
| | - Erman Acar
- Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland; BioMediTech, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland.
| | - R Holland Cheng
- Department of Molecular and Cellular Biology, University of California, Briggs7 (MailCode#0390), Davis, CA 95616, USA.
| | - Ulla Ruotsalainen
- Department of Signal Processing, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland; BioMediTech, Tampere University of Technology, P.O. Box 553, FI-33101 Tampere, Finland.
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16
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Dvornek NC, Sigworth FJ, Tagare HD. SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction. J Struct Biol 2015; 190:200-14. [PMID: 25839831 DOI: 10.1016/j.jsb.2015.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 12/01/2022]
Abstract
Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E-M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300.
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Affiliation(s)
- Nicha C Dvornek
- Department of Diagnostic Radiology, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Fred J Sigworth
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Hemant D Tagare
- Department of Diagnostic Radiology, Yale School of Medicine, New Haven, CT 06510, USA; Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA; Department of Electrical Engineering, Yale University, New Haven, CT 06520, USA
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17
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Chen P, Liu Z, Wang X, Peng J, Sun Q, Li J, Wang M, Niu L, Zhang Z, Cai G, Teng M, Li X. Crystal and EM structures of human phosphoribosyl pyrophosphate synthase I (PRS1) provide novel insights into the disease-associated mutations. PLoS One 2015; 10:e0120304. [PMID: 25781187 PMCID: PMC4363470 DOI: 10.1371/journal.pone.0120304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 02/05/2015] [Indexed: 11/30/2022] Open
Abstract
Human PRS1, which is indispensable for the biosynthesis of nucleotides, deoxynucleotides and their derivatives, is associated directly with multiple human diseases because of single base mutation. However, a molecular understanding of the effect of these mutations is hampered by the lack of understanding of its catalytic mechanism. Here, we reconstruct the 3D EM structure of the PRS1 apo state. Together with the native stain EM structures of AMPNPP, AMPNPP and R5P, ADP and the apo states with distinct conformations, we suggest the hexamer is the enzymatically active form. Based on crystal structures, sequence analysis, mutagenesis, enzyme kinetics assays, and MD simulations, we reveal the conserved substrates binding motifs and make further analysis of all pathogenic mutants.
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Affiliation(s)
- Peng Chen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Zheng Liu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Xuejuan Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Junhui Peng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Qianqian Sun
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Jianzhong Li
- Department of Otolaryngology Head and Neck Surgery, Fuzhou general hospital of Nanjing Command, PLA, Fuzhou 350025, China
| | - Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
| | - Gang Cai
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China
- Key Laboratory of Structural Biology, Chinese Academy of Sciences, Hefei, Anhui 230026, People’s Republic of China
- * E-mail: (XL); (MT); (GC)
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18
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Huang C, Tagare HD. Robust estimation for class averaging in cryo-EM Single Particle Reconstruction. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2015; 2014:3329-32. [PMID: 25570703 DOI: 10.1109/embc.2014.6944335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Single Particle Reconstruction (SPR) for Cryogenic Electron Microscopy (cryo-EM) aligns and averages the images extracted from micrographs to improve the Signal-to-Noise ratio (SNR). Outliers compromise the fidelity of the averaging. We propose a robust cross-correlation-like w-estimator for combating the effect of outliers on the average images in cryo-EM. The estimator accounts for the natural variation of signal contrast among the images and eliminates the need for a threshold for outlier rejection. We show that the influence function of our estimator is asymptotically bounded. Evaluations of the estimator on simulated and real cryo-EM images show good performance in the presence of outliers.
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19
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Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. eLife 2014; 3. [PMID: 25313868 PMCID: PMC4371863 DOI: 10.7554/elife.04491] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 10/13/2014] [Indexed: 12/13/2022] Open
Abstract
Ribosome assembly is a complex process involving the folding and processing of ribosomal RNAs (rRNAs), concomitant binding of ribosomal proteins (r-proteins), and participation of numerous accessory cofactors. Here, we use a quantitative mass spectrometry/electron microscopy hybrid approach to determine the r-protein composition and conformation of 30S ribosome assembly intermediates in Escherichia coli. The relative timing of assembly of the 3' domain and the formation of the central pseudoknot (PK) structure depends on the presence of the assembly factor RimP. The central PK is unstable in the absence of RimP, resulting in the accumulation of intermediates in which the 3'-domain is unanchored and the 5'-domain is depleted for r-proteins S5 and S12 that contact the central PK. Our results reveal the importance of the cofactor RimP in central PK formation, and introduce a broadly applicable method for characterizing macromolecular assembly in cells.
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Affiliation(s)
- Dipali G Sashital
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Candacia A Greeman
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Dmitry Lyumkis
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Clinton S Potter
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - Bridget Carragher
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, United States
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20
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Abstract
NOSs are homodimeric multidomain enzymes responsible for producing NO. In mammals, NO acts as an intercellular messenger in a variety of signaling reactions, as well as a cytotoxin in the innate immune response. Mammals possess three NOS isoforms--inducible, endothelial, and neuronal NOS--that are composed of an N-terminal oxidase domain and a C-terminal reductase domain. Calmodulin (CaM) activates NO synthesis by binding to the helical region connecting these two domains. Although crystal structures of isolated domains have been reported, no structure is available for full-length NOS. We used high-throughput single-particle EM to obtain the structures and higher-order domain organization of all three NOS holoenzymes. The structures of inducible, endothelial, and neuronal NOS with and without CaM bound are similar, consisting of a dimerized oxidase domain flanked by two separated reductase domains. NOS isoforms adopt many conformations enabled by three flexible linkers. These conformations represent snapshots of the continuous electron transfer pathway from the reductase domain to the oxidase domain, which reveal that only a single reductase domain participates in electron transfer at a time, and that CaM activates NOS by constraining rotational motions and by directly binding to the oxidase domain. Direct visualization of these large conformational changes induced during electron transfer provides significant insight into the molecular underpinnings governing NO formation.
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21
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Vargas J, Álvarez-Cabrera AL, Marabini R, Carazo JM, Sorzano COS. Efficient initial volume determination from electron microscopy images of single particles. ACTA ACUST UNITED AC 2014; 30:2891-8. [PMID: 24974203 DOI: 10.1093/bioinformatics/btu404] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to the final 3D map requires an approximate initial model. Generation of an initial model is still an open and challenging problem in single-particle analysis. RESULTS We present a fast and efficient approach to obtain a reliable, low-resolution estimation of the 3D structure of a macromolecule, without any a priori knowledge, addressing the well-known issue of initial volume estimation in the field of single-particle analysis. The input of the algorithm is a set of class average images obtained from individual projections of a biological object at random and unknown orientations by transmission electron microscopy micrographs. The proposed method is based on an initial non-lineal dimensionality reduction approach, which allows to automatically selecting representative small sets of class average images capturing the most of the structural information of the particle under study. These reduced sets are then used to generate volumes from random orientation assignments. The best volume is determined from these guesses using a random sample consensus (RANSAC) approach. We have tested our proposed algorithm, which we will term 3D-RANSAC, with simulated and experimental data, obtaining satisfactory results under the low signal-to-noise conditions typical of cryo-electron microscopy. AVAILABILITY The algorithm is freely available as part of the Xmipp 3.1 package [http://xmipp.cnb.csic.es]. CONTACT jvargas@cnb.csic.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Javier Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3 and Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, 28049, Cantoblanco (Madrid), Spain
| | - Ana-Lucia Álvarez-Cabrera
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3 and Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, 28049, Cantoblanco (Madrid), Spain
| | - Roberto Marabini
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3 and Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, 28049, Cantoblanco (Madrid), Spain
| | - Jose M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3 and Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, 28049, Cantoblanco (Madrid), Spain
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/Darwin 3 and Escuela Politécnica Superior, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, 28049, Cantoblanco (Madrid), Spain
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Single-particle EM reveals the higher-order domain architecture of soluble guanylate cyclase. Proc Natl Acad Sci U S A 2014; 111:2960-5. [PMID: 24516165 DOI: 10.1073/pnas.1400711111] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is the primary nitric oxide (NO) receptor in mammals and a central component of the NO-signaling pathway. The NO-signaling pathways mediate diverse physiological processes, including vasodilation, neurotransmission, and myocardial functions. sGC is a heterodimer assembled from two homologous subunits, each comprised of four domains. Although crystal structures of isolated domains have been reported, no structure is available for full-length sGC. We used single-particle electron microscopy to obtain the structure of the complete sGC heterodimer and determine its higher-order domain architecture. Overall, the protein is formed of two rigid modules: the catalytic dimer and the clustered Per/Art/Sim and heme-NO/O2-binding domains, connected by a parallel coiled coil at two hinge points. The quaternary assembly demonstrates a very high degree of flexibility. We captured hundreds of individual conformational snapshots of free sGC, NO-bound sGC, and guanosine-5'-[(α,β)-methylene]triphosphate-bound sGC. The molecular architecture and pronounced flexibility observed provides a significant step forward in understanding the mechanism of NO signaling.
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23
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Jinek M, Jiang F, Taylor DW, Sternberg SH, Kaya E, Ma E, Anders C, Hauer M, Zhou K, Lin S, Kaplan M, Iavarone AT, Charpentier E, Nogales E, Doudna JA. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 2014; 343:1247997. [PMID: 24505130 PMCID: PMC4184034 DOI: 10.1126/science.1247997] [Citation(s) in RCA: 762] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.
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Affiliation(s)
- Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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24
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The ArrayGrid: A methodology for applying multiple samples to a single TEM specimen grid. Ultramicroscopy 2013; 135:105-12. [DOI: 10.1016/j.ultramic.2013.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/16/2013] [Accepted: 07/19/2013] [Indexed: 11/20/2022]
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25
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Lyumkis D, Vinterbo S, Potter CS, Carragher B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J Struct Biol 2013; 184:417-26. [PMID: 24161732 DOI: 10.1016/j.jsb.2013.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/04/2013] [Accepted: 10/08/2013] [Indexed: 12/13/2022]
Abstract
Single-particle cryo-electron microscopy is now well established as a technique for the structural characterization of large macromolecules and macromolecular complexes. The raw data is very noisy and consists of two-dimensional projections, from which the 3D biological object must be reconstructed. The 3D object depends upon knowledge of proper angular orientations assigned to the 2D projection images. Numerous algorithms have been developed for determining relative angular orientations between 2D images, but the transition from 2D to 3D remains challenging and can result in erroneous and conflicting results. Here we describe a general, automated procedure, called OptiMod, for reconstructing and optimizing 3D models using common-lines methodologies. OptiMod approximates orientation angles and reconstructs independent maps from 2D class averages. It then iterates the procedure, while considering each map as a raw solution that needs to be compared with other possible outcomes. We incorporate procedures for 3D alignment, clustering, and refinement to optimize each map, as well as standard scoring metrics to facilitate the selection of the optimal model. We also show that small angle tilt-pair data can be included as one of the scoring metrics to improve the selection of the optimal initial model, and also to provide a validation check. The overall approach is demonstrated using two experimental cryo-EM data sets--the 80S ribosome that represents a relatively straightforward case for ab initio reconstruction, and the Tf-TfR complex that represents a challenging case in that it has previously been shown to provide multiple equally plausible solutions to the initial model problem.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Institute, La Jolla, CA 92037, United States
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26
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Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure 2013; 21:1848-58. [PMID: 24055317 PMCID: PMC3898938 DOI: 10.1016/j.str.2013.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic mechanism that is allosterically activated 200- to 500-fold by effector DNA, with a concomitant expansion of its DNA sequence specificity. Using single-particle transmission electron microscopy to reconstruct distinct populations of SgrAI oligomers, we show that in the presence of allosteric, activating DNA, the enzyme forms regular, repeating helical structures characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on manner. We also present the structure of oligomeric SgrAI at 8.6 Å resolution, demonstrating the conformational state of SgrAI in its activated form. Activated and oligomeric SgrAI displays key protein-protein interactions near the helix axis between its N termini, as well as allosteric protein-DNA interactions that are required for enzymatic activation. The hybrid approach reveals an unusual mechanism of enzyme activation that explains SgrAI's oligomerization and allosteric behavior.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Heather Talley
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
- Genetics Interdisciplinary Graduate Program, University of Arizona, Tucson, AZ, 85721
| | - Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Florence Tama
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
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27
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Wang X, Wang J, Ding Z, Ji J, Sun Q, Cai G. Structural flexibility and functional interaction of Mediator Cdk8 module. Protein Cell 2013; 4:911-20. [PMID: 24043446 DOI: 10.1007/s13238-013-3069-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 08/26/2013] [Indexed: 11/25/2022] Open
Abstract
Mediator is a highly conserved large protein complex (25 proteins, >1000 kDa) and preeminently responsible for eukaryotic transcription, which contains a dissociable 'Cdk8 module'. Although increasing evidence demonstrates that Cdk8 module plays both positive and negative roles in transcription regulation, the detailed structure, and subunit organization, molecular mechanism how it regulates transcription remain elusive. Here we used single-particle electron microscopy to characterize the structure and subunit organization of the Cdk8 module and illuminated the substantial mobility of the Med13 subunit results in the structural flexibility. The Cdk8 module interaction with core Mediator is concurrent with active transcription in vivo. An interaction with the Cdk8 module induces core Mediator into very extended conformation in vitro, which is presumed to be an active functional state of Mediator. Taken together, our results illuminated the detailed architecture of Cdk8 module, and suggested the Cdk8 module could positively regulate transcription by modulating Mediator conformation.
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Affiliation(s)
- Xuejuan Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
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28
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Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol 2013; 183:377-388. [PMID: 23872434 DOI: 10.1016/j.jsb.2013.07.005] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/03/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
We describe an implementation of maximum likelihood classification for single particle electron cryo-microscopy that is based on the FREALIGN software. Particle alignment parameters are determined by maximizing a joint likelihood that can include hierarchical priors, while classification is performed by expectation maximization of a marginal likelihood. We test the FREALIGN implementation using a simulated dataset containing computer-generated projection images of three different 70S ribosome structures, as well as a publicly available dataset of 70S ribosomes. The results show that the mixed strategy of the new FREALIGN algorithm yields performance on par with other maximum likelihood implementations, while remaining computationally efficient.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Axel F Brilot
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Douglas L Theobald
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA; Howard Hughes Medical Institute, Brandeis University, MS029, 415 South Street, Waltham, MA 02454, USA.
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29
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Chen X, Taylor DW, Fowler CC, Galan JE, Wang HW, Wolin SL. An RNA degradation machine sculpted by Ro autoantigen and noncoding RNA. Cell 2013; 153:166-77. [PMID: 23540697 DOI: 10.1016/j.cell.2013.02.037] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 01/10/2013] [Accepted: 02/19/2013] [Indexed: 11/18/2022]
Abstract
Many bacteria contain an ortholog of the Ro autoantigen, a ring-shaped protein that binds noncoding RNAs (ncRNAs) called Y RNAs. In the only studied bacterium, Deinococcus radiodurans, the Ro ortholog Rsr functions in heat-stress-induced ribosomal RNA (rRNA) maturation and starvation-induced rRNA decay. However, the mechanism by which this conserved protein and its associated ncRNAs act has been obscure. We report that Rsr and the exoribonuclease polynucleotide phosphorylase (PNPase) form an RNA degradation machine that is scaffolded by Y RNA. Single-particle electron microscopy, followed by docking of atomic models into the reconstruction, suggests that Rsr channels single-stranded RNA into the PNPase cavity. Biochemical assays reveal that Rsr and Y RNA adapt PNPase for effective degradation of structured RNAs. A Ro ortholog and ncRNA also associate with PNPase in Salmonella Typhimurium. Our studies identify another ribonucleoprotein machine and demonstrate that ncRNA, by tethering a protein cofactor, can alter the substrate specificity of an enzyme.
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Affiliation(s)
- Xinguo Chen
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06510, USA
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30
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DOLORS: versatile strategy for internal labeling and domain localization in electron microscopy. Structure 2013; 20:1995-2002. [PMID: 23217681 DOI: 10.1016/j.str.2012.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/11/2012] [Accepted: 10/31/2012] [Indexed: 11/22/2022]
Abstract
Single-particle electron microscopy (EM) is a powerful tool for studying the structures of large biological molecules. However, the achievable resolution does not always allow for direct recognition of individual protein domains. Labels that can be visualized by EM have been developed for protein termini, but tagging internal domains remains a challenge. We describe a robust strategy for determining the position of internal sites within EM maps, termed domain localization by RCT sampling (DOLORS). DOLORS uses monovalent streptavidin added posttranslationally to tagged sites in the target protein. Internal labels generally display less conformational flexibility than terminal labels, providing more precise positional information. Automated methods are used to rapidly generate assemblies of unique 3D models allowing the attachment sites of labeled domains to be accurately identified and thus provide an overall architectural map of the molecule.
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31
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Substrate-specific structural rearrangements of human Dicer. Nat Struct Mol Biol 2013; 20:662-70. [PMID: 23624860 PMCID: PMC3676429 DOI: 10.1038/nsmb.2564] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/15/2013] [Indexed: 12/25/2022]
Abstract
Dicer plays a central role in RNA interference pathways by cleaving double-stranded RNAs (dsRNAs) to produce small regulatory RNAs. Human Dicer can process long double-stranded and hairpin precursor RNAs to yield short interfering RNAs (siRNAs) or microRNAs (miRNAs), respectively. Previous studies have shown that pre-miRNAs are cleaved more rapidly than pre-siRNAs in vitro and are the predominant natural Dicer substrates. We have used electron microscopy and single particle analysis of Dicer–RNA complexes to gain insight into the structural basis for human Dicer’s substrate preference. Our studies show that Dicer traps pre-siRNAs in a non-productive conformation, while interactions of Dicer with pre-miRNAs and dsRNA binding proteins induce structural changes in the enzyme that enable productive substrate recognition in the central catalytic channel. These findings implicate RNA structure and cofactors in determining substrate recognition and processing efficiency by human Dicer.
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32
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Correia I, Sung J, Burton R, Jakob CG, Carragher B, Ghayur T, Radziejewski C. The structure of dual-variable-domain immunoglobulin molecules alone and bound to antigen. MAbs 2013; 5:364-72. [PMID: 23572180 DOI: 10.4161/mabs.24258] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A dual-specific, tetravalent immunoglobulin G-like molecule, termed dual variable domain immunoglobulin (DVD-Ig™), is engineered to block two targets. Flexibility modulates Fc receptor and complement binding, but could result in undesirable cross-linking of surface antigens and downstream signaling. Understanding the flexibility of parental mAbs is important for designing and retaining functionality of DVD-Ig™ molecules. The architecture and dynamics of a DVD-Ig™ molecule and its parental mAbs was examined using single particle electron microscopy. Hinge angles measured for the DVD-Ig™ molecule were similar to the inner antigen parental mAb. The outer binding domain of the DVD-Ig™ molecule was highly mobile and three-dimensional (3D) analysis showed binding of inner antigen caused the outer domain to fold out of the plane with a major morphological change. Docking high-resolution X-ray structures into the 3D electron microscopy map supports the extraordinary domain flexibility observed in the DVD-Ig™ molecule allowing antigen binding with minimal steric hindrance.
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Affiliation(s)
- Ivan Correia
- Protein Analytics; AbbVie Bioresearch Center; Worcester, MA USA
| | - Joyce Sung
- NanoImaging Services, Inc.; La Jolla, CA USA
| | - Randall Burton
- Protein Analytics; AbbVie Bioresearch Center; Worcester, MA USA
| | - Clarissa G Jakob
- Department of Structural Biology; AbbVie Laboratories; Abbott Park, IL USA
| | | | - Tariq Ghayur
- Biologics; AbbVie Bioresearch Center; Worcester, MA USA
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33
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Lerch TF, O’Donnell JK, Meyer NL, Xie Q, Taylor KA, Stagg SM, Chapman MS. Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 Å resolution. Structure 2012; 20:1310-20. [PMID: 22727812 PMCID: PMC3418430 DOI: 10.1016/j.str.2012.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/10/2012] [Accepted: 05/11/2012] [Indexed: 12/19/2022]
Abstract
AAV-DJ, a leading candidate vector for liver gene therapy, was created through random homologous recombination followed by directed evolution, selecting for in vivo liver tropism and resistance to in vitro immune neutralization. Here, the 4.5 Å resolution cryo-EM structure is determined for the engineered AAV vector, revealing structural features that illuminate its phenotype. The heparan sulfate receptor-binding site is little changed from AAV-2, and heparin-binding affinity is similar. A loop that is antigenic in other serotypes has a unique conformation in AAV-DJ that would conflict with the binding of an AAV-2 neutralizing monoclonal antibody. This is consistent with increased resistance to neutralization by human polyclonal sera, raising the possibility that changed tropism may be a secondary effect of altered immune interactions. The reconstruction exemplifies analysis of fine structural changes and the potential of cryo-EM, in favorable cases, to characterize mutant or ligand-bound complexes.
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Affiliation(s)
- Thomas F. Lerch
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jason K. O’Donnell
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Nancy L. Meyer
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Qing Xie
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kenneth A. Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Scott M. Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Department of Chemistry & Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Michael S. Chapman
- Department of Biochemistry & Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA
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34
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Kucukelbir A, Sigworth FJ, Tagare HD. A Bayesian adaptive basis algorithm for single particle reconstruction. J Struct Biol 2012; 179:56-67. [PMID: 22564910 DOI: 10.1016/j.jsb.2012.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 04/16/2012] [Accepted: 04/20/2012] [Indexed: 01/08/2023]
Abstract
Traditional single particle reconstruction methods use either the Fourier or the delta function basis to represent the particle density map. This paper proposes a more flexible algorithm that adaptively chooses the basis based on the data. Because the basis adapts to the data, the reconstruction resolution and signal-to-noise ratio (SNR) is improved compared to a reconstruction with a fixed basis. Moreover, the algorithm automatically masks the particle, thereby separating it from the background. This eliminates the need for ad hoc filtering or masking in the refinement loop. The algorithm is formulated in a Bayesian maximum-a-posteriori framework and uses an efficient optimization algorithm for the maximization. Evaluations using simulated and actual cryogenic electron microscopy data show resolution and SNR improvements as well as the effective masking of particle from background.
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Affiliation(s)
- Alp Kucukelbir
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.
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35
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Kim LY, Johnson MC, Schmidt‐Krey I. Cryo‐EM in the Study of Membrane Transport Proteins. Compr Physiol 2012; 2:283-93. [DOI: 10.1002/cphy.c110028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Fisher LS, Ward A, Milligan RA, Unwin N, Potter CS, Carragher B. A helical processing pipeline for EM structure determination of membrane proteins. Methods 2011; 55:350-62. [PMID: 21964395 PMCID: PMC3262078 DOI: 10.1016/j.ymeth.2011.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/07/2011] [Accepted: 09/13/2011] [Indexed: 01/27/2023] Open
Abstract
Electron crystallography plays a key role in the structural biology of integral membrane proteins (IMPs) by offering one of the most direct means of providing insight into the functional state of these molecular machines in their lipid-associated forms, and also has the potential to facilitate examination of physiologically relevant transitional states and complexes. Helical or tubular crystals, which are the natural product of proteins crystallizing on the surface of a cylindrical vesicle, offer some unique advantages, such as three-dimensional (3D) information from a single view, compared to other crystalline forms. While a number of software packages are available for processing images of helical crystals to produce 3D electron density maps, widespread exploitation of helical image reconstruction is limited by a lack of standardized approaches and the initial effort and specialized expertise required. Our goal is to develop an integrated pipeline to enable structure determination by transmission electron microscopy (TEM) of IMPs in the form of tubular crystals. We describe here the integration of standard Fourier-Bessel helical analysis techniques into Appion, an integrated, database-driven pipeline.
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Affiliation(s)
- Lauren S. Fisher
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Andrew Ward
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Ronald A. Milligan
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Nigel Unwin
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- MRC Laboratory of Molecular Biology Hills Road, Cambridge CB2 2QH, UK
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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37
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Banerjee D, Liu AP, Voss N, Schmid SL, Finn M. Multivalent display and receptor-mediated endocytosis of transferrin on virus-like particles. Chembiochem 2010; 11:1273-9. [PMID: 20455239 PMCID: PMC4180096 DOI: 10.1002/cbic.201000125] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Indexed: 11/06/2022]
Abstract
The structurally regular and stable self-assembled capsids derived from viruses can be used as scaffolds for the display of multiple copies of cell- and tissue-targeting molecules and therapeutic agents in a convenient and well-defined manner. The human iron-transfer protein transferrin, a high affinity ligand for receptors upregulated in a variety of cancers, has been arrayed on the exterior surface of the protein capsid of bacteriophage Qbeta. Selective oxidation of the sialic acid residues on the glycan chains of transferrin was followed by introduction of a terminal alkyne functionality through an oxime linkage. Attachment of the protein to azide-functionalized Qbeta capsid particles in an orientation allowing access to the receptor binding site was accomplished by the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click reaction. Transferrin conjugation to Qbeta particles allowed specific recognition by transferrin receptors and cellular internalization through clathrin-mediated endocytosis, as determined by fluorescence microscopy on cells expressing GFP-labeled clathrin light chains. By testing Qbeta particles bearing different numbers of transferrin molecules, it was demonstrated that cellular uptake was proportional to ligand density, but that internalization was inhibited by equivalent concentrations of free transferrin. These results suggest that cell targeting with transferrin can be improved by local concentration (avidity) effects.
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Affiliation(s)
- Deboshri Banerjee
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Rd., La Jolla, CA, USA
| | - Allen P. Liu
- Department of Cell Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., La Jolla, CA, USA
| | - Neil Voss
- Department of Cell Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., La Jolla, CA, USA
| | - Sandra L. Schmid
- Department of Cell Biology The Scripps Research Institute 10550 N. Torrey Pines Rd., La Jolla, CA, USA
| | - M.G. Finn
- Department of Chemistry The Scripps Research Institute 10550 N. Torrey Pines Rd., La Jolla, CA, USA
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38
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Abstract
With the advent of computationally feasible approaches to maximum-likelihood (ML) image processing for cryo-electron microscopy, these methods have proven particularly useful in the classification of structurally heterogeneous single-particle data. A growing number of experimental studies have applied these algorithms to study macromolecular complexes with a wide range of structural variability, including nonstoichiometric complex formation, large conformational changes, and combinations of both. This chapter aims to share the practical experience that has been gained from the application of these novel approaches. Current insights on how to prepare the data and how to perform two- or three-dimensional classifications are discussed together with the aspects related to high-performance computing. Thereby, this chapter will hopefully be of practical use for those microscopists wishing to apply ML methods in their own investigations.
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Affiliation(s)
- Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
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39
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Böttcher B, Hipp K. Single-particle applications at intermediate resolution. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2010; 81:61-88. [PMID: 21115173 DOI: 10.1016/b978-0-12-381357-2.00003-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Electron microscopy together with single-particle image processing is an excellent method for structure determination of biological assemblies that exist in multiple identical copies. Typical assemblies contain several proteins and/or nucleic acids in a defined and reproducible arrangement. Coherent averaging of electron microscopic images of 5000-100,000 copies of these assemblies allows the determination of three-dimensional structures at ca. 1-3-nm resolution. At this intermediate resolution, it is possible to map individual subunits and thus to understand the architecture and quaternary structure of the assemblies. The intermediate resolution structural information gives a solid basis on which pseudo-atomic models of the assemblies can be modeled provided that high-resolution structures of smaller entities are known. The architecture of the assemblies, their pseudo-atomic models, and knowledge on their plasticity during function give a comprehensive understanding of large-scale structural dynamics of multicopy biological complexes. In this review, we will introduce the experimental pipeline and discuss selected examples.
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40
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Lyumkis D, Moeller A, Cheng A, Herold A, Hou E, Irving C, Jacovetty EL, Lau PW, Mulder AM, Pulokas J, Quispe JD, Voss NR, Potter CS, Carragher B. Automation in single-particle electron microscopy connecting the pieces. Methods Enzymol 2010; 483:291-338. [PMID: 20888480 DOI: 10.1016/s0076-6879(10)83015-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Throughout the history of single-particle electron microscopy (EM), automated technologies have seen varying degrees of emphasis and development, usually depending upon the contemporary demands of the field. We are currently faced with increasingly sophisticated devices for specimen preparation, vast increases in the size of collected data sets, comprehensive algorithms for image processing, sophisticated tools for quality assessment, and an influx of interested scientists from outside the field who might lack the skills of experienced microscopists. This situation places automated techniques in high demand. In this chapter, we provide a generic definition of and discuss some of the most important advances in automated approaches to specimen preparation, grid handling, robotic screening, microscope calibrations, data acquisition, image processing, and computational infrastructure. Each section describes the general problem and then provides examples of how that problem has been addressed through automation, highlighting available processing packages, and sometimes describing the particular approach at the National Resource for Automated Molecular Microscopy (NRAMM). We contrast the more familiar manual procedures with automated approaches, emphasizing breakthroughs as well as current limitations. Finally, we speculate on future directions and improvements in automated technologies. Our overall goal is to present automation as more than simply a tool to save time. Rather, we aim to illustrate that automation is a comprehensive and versatile strategy that can deliver biological information on an unprecedented scale beyond the scope available with classical manual approaches.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA
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