101
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Markert JW, Vos SM, Farnung L. Structure of the complete S. cerevisiae Rpd3S-nucleosome complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551877. [PMID: 37577459 PMCID: PMC10418238 DOI: 10.1101/2023.08.03.551877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Acetylation of histones is a key post-translational modification that guides gene expression regulation. In yeast, the class I histone deacetylase containing Rpd3S complex plays a critical role in the suppression of spurious transcription by removing histone acetylation from actively transcribed genes. The Saccharomyces cerevisiae Rpd3S complex has five subunits (Rpd3, Sin3, Rco1, Eaf3, and Ume1) but its subunit stoichiometry and how the complex engages nucleosomes to achieve substrate specificity remains elusive. Here we report the cryo-EM structure of the complete Rpd3S complex bound to a nucleosome. Sin3 and two copies of subunits Rco1 and Eaf3 encircle the deacetylase subunit Rpd3 and coordinate the binding of Ume1. The Rpd3S complex binds both trimethylated H3 tails at position lysine 36 and makes multiple additional contacts with the nucleo-somal DNA, the H2A-H2B acidic patch, and histone H3. Direct regulation via the Sin3 subunit coordinates binding of the acetylated histone substrate to achieve substrate specificity.
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102
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Lucas BA. Visualizing everything, everywhere, all at once: Cryo-EM and the new field of structureomics. Curr Opin Struct Biol 2023; 81:102620. [PMID: 37279614 DOI: 10.1016/j.sbi.2023.102620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/03/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023]
Abstract
Twenty years ago, the release of the first draft of the human genome sequence instigated a paradigm shift in genomics and molecular biology. Arguably, structural biology is entering an analogous era, with availability of an experimentally determined or predicted molecular model for almost every protein-coding gene from many genomes-producing a reference "structureome". Structural predictions require experimental validation and not all proteins conform to a single structure, making any reference structureome necessarily incomplete. Despite these limitations, a reference structureome can be used to characterize cell state in more detail than by quantifying sequence or expression levels alone. Cryogenic electron microscopy (cryo-EM) is a method that can generate atomic resolution views of molecules and cells frozen in place. In this perspective I consider how emerging cryo-EM methods are contributing to the new field of structureomics.
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Affiliation(s)
- Bronwyn A Lucas
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Center for Computational Biology, University of California Berkeley, Berkeley, CA, USA.
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103
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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104
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Obr M, Percipalle M, Chernikova D, Yang H, Thader A, Pinke G, Porley D, Mansky LM, Dick RA, Schur FKM. Unconventional stabilization of the human T-cell leukemia virus type 1 immature Gag lattice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.24.548988. [PMID: 37546793 PMCID: PMC10402013 DOI: 10.1101/2023.07.24.548988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Human T-cell leukemia virus type 1 (HTLV-1) has an atypical immature particle morphology compared to other retroviruses. This indicates that these particles are formed in a way that is unique. Here we report the results of cryo-electron tomography (cryo-ET) studies of HTLV-1 virus-like particles (VLPs) assembled in vitro, as well as derived from cells. This work shows that HTLV-1 employs an unconventional mechanism of Gag-Gag interactions to form the immature viral lattice. Analysis of high-resolution structural information from immature CA tubular arrays reveals that the primary stabilizing component in HTLV-1 is CA-NTD. Mutagenesis and biophysical analysis support this observation. This distinguishes HTLV-1 from other retroviruses, in which the stabilization is provided primarily by the CA-CTD. These results are the first to provide structural details of the quaternary arrangement of Gag for an immature deltaretrovirus, and this helps explain why HTLV-1 particles are morphologically distinct.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Mathias Percipalle
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Darya Chernikova
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Gergely Pinke
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Dario Porley
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, Minneapolis, MN, USA
| | - Robert A Dick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Florian KM Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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105
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Khavnekar S, Kelley R, Waltz F, Wietrzynski W, Zhang X, Obr M, Tagiltsev G, Beck F, Wan W, Briggs J, Engel B, Plitzko J, Kotecha A. Towards the Visual Proteomics of C. reinhardtii using High-throughput Collaborative in situ Cryo-ET. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:961-963. [PMID: 37613825 DOI: 10.1093/micmic/ozad067.480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Sagar Khavnekar
- Cryo-EM Technology group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ron Kelley
- Thermo Fisher Scientific, Eindhoven, The Netherlands
| | | | | | - Xianjun Zhang
- Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Martin Obr
- Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Grigory Tagiltsev
- Department of Virus and Cell structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Beck
- Cryo-EM Technology group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - John Briggs
- Department of Virus and Cell structure, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ben Engel
- Biozentrum, University of Basel, Basel, Switzerland
| | - Juergen Plitzko
- Cryo-EM Technology group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Abhay Kotecha
- Thermo Fisher Scientific, Eindhoven, The Netherlands
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106
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Sibert BS, Kim JY, Yang JE, Hannon-Hatfield A, Ke Z, Garfinkel DJ, Wright ER. Workflow for High-resolution Sub-volume Averaging from Heterogenous Viral and Virus-like Assemblies. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:943-944. [PMID: 37613807 DOI: 10.1093/micmic/ozad067.470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Bryan S Sibert
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Joseph Y Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Department of Chemistry, University of Wisconsin, Madison, WI, United States
| | - Jae E Yang
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Adam Hannon-Hatfield
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Zunlong Ke
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David J Garfinkel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Elizabeth R Wright
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Cryo-Electron Microscopy Research Center, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Midwest Center for Cryo-Electron Tomography, Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- Morgridge Institute for Research, Madison, WI, United States
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107
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Chang ML, Erwin AL, Mosalaganti S. Image Processing Pipeline for In Situ Structural Characterization of Filaments. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:952-953. [PMID: 37613656 DOI: 10.1093/micmic/ozad067.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Matthew L Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States
| | - Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Departments of Cell and Developmental Biology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States
- Departments of Cell and Developmental Biology and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, United States
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan, United States
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108
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Xing H, Taniguchi R, Khusainov I, Kreysing JP, Welsch S, Turoňová B, Beck M. Translation dynamics in human cells visualized at high resolution reveal cancer drug action. Science 2023; 381:70-75. [PMID: 37410833 DOI: 10.1126/science.adh1411] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/05/2023] [Indexed: 07/08/2023]
Abstract
Ribosomes catalyze protein synthesis by cycling through various functional states. These states have been extensively characterized in vitro, but their distribution in actively translating human cells remains elusive. We used a cryo-electron tomography-based approach and resolved ribosome structures inside human cells with high resolution. These structures revealed the distribution of functional states of the elongation cycle, a Z transfer RNA binding site, and the dynamics of ribosome expansion segments. Ribosome structures from cells treated with Homoharringtonine, a drug used against chronic myeloid leukemia, revealed how translation dynamics were altered in situ and resolve the small molecules within the active site of the ribosome. Thus, structural dynamics and drug effects can be assessed at high resolution within human cells.
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Affiliation(s)
- Huaipeng Xing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry and Pharmacy, Goethe University Frankfurt am Main, 60438 Frankfurt am Main, Germany
| | - Reiya Taniguchi
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Iskander Khusainov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- IMPRS on Cellular Biophysics, 60438 Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute of Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
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109
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Powell BM, Davis JH. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542975. [PMID: 37398315 PMCID: PMC10312494 DOI: 10.1101/2023.05.31.542975] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via iterative alignment and averaging are well-developed but rely on assumptions of structural homogeneity among the complexes under consideration. Recently developed downstream analysis tools allow for some assessment of macromolecular diversity but have limited capacity to represent highly heterogeneous macromolecules, including those undergoing continuous conformational changes. Here, we extend the highly expressive cryoDRGN deep learning architecture, originally created for cryo-electron microscopy single particle analysis, to sub-tomograms. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct a large, heterogeneous ensemble of structures supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET data. We additionally illustrate tomoDRGN's efficacy in analyzing an exemplar dataset, using it to reveal extensive structural heterogeneity among ribosomes imaged in situ.
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Affiliation(s)
- Barrett M. Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joseph H. Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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110
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Rice G, Wagner T, Stabrin M, Sitsel O, Prumbaum D, Raunser S. TomoTwin: generalized 3D localization of macromolecules in cryo-electron tomograms with structural data mining. Nat Methods 2023; 20:871-880. [PMID: 37188953 PMCID: PMC10250198 DOI: 10.1038/s41592-023-01878-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Cryogenic-electron tomography enables the visualization of cellular environments in extreme detail, however, tools to analyze the full amount of information contained within these densely packed volumes are still needed. Detailed analysis of macromolecules through subtomogram averaging requires particles to first be localized within the tomogram volume, a task complicated by several factors including a low signal to noise ratio and crowding of the cellular space. Available methods for this task suffer either from being error prone or requiring manual annotation of training data. To assist in this crucial particle picking step, we present TomoTwin: an open source general picking model for cryogenic-electron tomograms based on deep metric learning. By embedding tomograms in an information-rich, high-dimensional space that separates macromolecules according to their three-dimensional structure, TomoTwin allows users to identify proteins in tomograms de novo without manually creating training data or retraining the network to locate new proteins.
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Affiliation(s)
- Gavin Rice
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Markus Stabrin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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111
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Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J. Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. Cell Rep 2023; 42:112432. [PMID: 37120812 PMCID: PMC10299810 DOI: 10.1016/j.celrep.2023.112432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/28/2023] [Accepted: 04/08/2023] [Indexed: 05/01/2023] Open
Abstract
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Thomas G Laughlin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Amber Lee
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kyle P Thomas
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika E Sy
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tara Spencer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aileen Asavavimol
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Allison Cafferata
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Mia Cameron
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Nicholas Chiu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Demyan Davydov
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Isha Desai
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gabriel Diaz
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Melissa Guereca
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kiley Hearst
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leyi Huang
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily Jacobs
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Annika Johnson
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Samuel Kahn
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ryan Koch
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Adamari Martinez
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Meliné Norquist
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tyler Pau
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gino Prasad
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Saam
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Milan Sandhu
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Angel Jose Sarabia
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Siena Schumaker
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Aaron Sonin
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Ariya Uyeno
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alison Zhao
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Justin Meyer
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Julianne H Grose
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Elizabeth Villa
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Rachel Dutton
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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112
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Zhang H, Li Y, Liu Y, Li D, Wang L, Song K, Bao K, Zhu P. A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST. Nat Commun 2023; 14:2937. [PMID: 37217501 DOI: 10.1038/s41467-023-38539-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Cryo-electron tomography (cryo-ET) is widely used to explore the 3D density of biomacromolecules. However, the heavy noise and missing wedge effect prevent directly visualizing and analyzing the 3D reconstructions. Here, we introduced REST, a deep learning strategy-based method to establish the relationship between low-quality and high-quality density and transfer the knowledge to restore signals in cryo-ET. Test results on the simulated and real cryo-ET datasets show that REST performs well in denoising and compensating the missing wedge information. The application in dynamic nucleosomes, presenting either in the form of individual particles or in the context of cryo-FIB nuclei section, indicates that REST has the capability to reveal different conformations of target macromolecules without subtomogram averaging. Moreover, REST noticeably improves the reliability of particle picking. These advantages enable REST to be a powerful tool for the straightforward interpretation of target macromolecules by visual inspection of the density and of a broad range of other applications in cryo-ET, such as segmentation, particle picking, and subtomogram averaging.
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Affiliation(s)
- Haonan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanan Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongyu Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kai Song
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Keyan Bao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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113
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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114
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Li Z, Du W, Yang J, Lai DH, Lun ZR, Guo Q. Cryo-Electron Tomography of Toxoplasma gondii Indicates That the Conoid Fiber May Be Derived from Microtubules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206595. [PMID: 36840635 DOI: 10.1002/advs.202206595] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/04/2023] [Indexed: 05/18/2023]
Abstract
Toxoplasma gondii (T. gondii) is the causative agent of toxoplasmosis and can infect numerous warm-blooded animals. An improved understanding of the fine structure of this parasite can help elucidate its replication mechanism. Previous studies have resolved the ultrastructure of the cytoskeleton using purified samples, which eliminates their cellular context. Here the application of cryo-electron tomography to visualize T. gondii tachyzoites in their native state is reported. The fine structure and cellular distribution of the cytoskeleton are resolved and analyzed at nanometer resolution. Additionally, the tachyzoite structural characteristics are annotated during its endodyogeny for the first time. By comparing the structural features in mature tachyzoites and their daughter buds, it is proposed that the conoid fiber of the Apicomplexa originates from microtubules. This work represents the detailed molecular anatomy of T. gondii, particularly during the budding replication stage of tachyzoite, and provides a reference for further studies of this fascinating organism.
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Affiliation(s)
- Zhixun Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Wenjing Du
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Jiong Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - De-Hua Lai
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zhao-Rong Lun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, School of Life Sciences, Peking University, Beijing, 100871, P. R. China
- Changping Laboratory, Yard 28, Science Park Road, Beijing, 102206, P. R. China
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115
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Zhang X, Sridharan S, Zagoriy I, Eugster Oegema C, Ching C, Pflaesterer T, Fung HKH, Becher I, Poser I, Müller CW, Hyman AA, Savitski MM, Mahamid J. Molecular mechanisms of stress-induced reactivation in mumps virus condensates. Cell 2023; 186:1877-1894.e27. [PMID: 37116470 PMCID: PMC10156176 DOI: 10.1016/j.cell.2023.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 09/21/2022] [Accepted: 03/14/2023] [Indexed: 04/30/2023]
Abstract
Negative-stranded RNA viruses can establish long-term persistent infection in the form of large intracellular inclusions in the human host and cause chronic diseases. Here, we uncover how cellular stress disrupts the metastable host-virus equilibrium in persistent infection and induces viral replication in a culture model of mumps virus. Using a combination of cell biology, whole-cell proteomics, and cryo-electron tomography, we show that persistent viral replication factories are dynamic condensates and identify the largely disordered viral phosphoprotein as a driver of their assembly. Upon stress, increased phosphorylation of the phosphoprotein at its interaction interface with the viral polymerase coincides with the formation of a stable replication complex. By obtaining atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events constitute a stress-mediated switch within viral condensates that provide an environment to support upregulation of viral replication.
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Affiliation(s)
- Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christina Eugster Oegema
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Cyan Ching
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tim Pflaesterer
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Herman K H Fung
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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116
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Shah PNM, Gilchrist JB, Forsberg BO, Burt A, Howe A, Mosalaganti S, Wan W, Radecke J, Chaban Y, Sutton G, Stuart DI, Boyce M. Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography. Cell Host Microbe 2023; 31:604-615.e4. [PMID: 36996819 PMCID: PMC7615348 DOI: 10.1016/j.chom.2023.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/27/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023]
Abstract
Rotavirus assembly is a complex process that involves the stepwise acquisition of protein layers in distinct intracellular locations to form the fully assembled particle. Understanding and visualization of the assembly process has been hampered by the inaccessibility of unstable intermediates. We characterize the assembly pathway of group A rotaviruses observed in situ within cryo-preserved infected cells through the use of cryoelectron tomography of cellular lamellae. Our findings demonstrate that the viral polymerase VP1 recruits viral genomes during particle assembly, as revealed by infecting with a conditionally lethal mutant. Additionally, pharmacological inhibition to arrest the transiently enveloped stage uncovered a unique conformation of the VP4 spike. Subtomogram averaging provided atomic models of four intermediate states, including a pre-packaging single-layered intermediate, the double-layered particle, the transiently enveloped double-layered particle, and the fully assembled triple-layered virus particle. In summary, these complementary approaches enable us to elucidate the discrete steps involved in forming an intracellular rotavirus particle.
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Affiliation(s)
- Pranav N M Shah
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford, UK.
| | - James B Gilchrist
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Björn O Forsberg
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Alister Burt
- Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Andrew Howe
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Shyamal Mosalaganti
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - William Wan
- Vanderbilt University Center for Structural Biology, PMB 407917, 465 21st Ave S, 5140 MRB3, Nashville, TN, USA
| | - Julika Radecke
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Yuriy Chaban
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Geoff Sutton
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK; CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford, UK; Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Mark Boyce
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK.
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117
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Zeng X, Kahng A, Xue L, Mahamid J, Chang YW, Xu M. High-throughput cryo-ET structural pattern mining by unsupervised deep iterative subtomogram clustering. Proc Natl Acad Sci U S A 2023; 120:e2213149120. [PMID: 37027429 PMCID: PMC10104553 DOI: 10.1073/pnas.2213149120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023] Open
Abstract
Cryoelectron tomography directly visualizes heterogeneous macromolecular structures in their native and complex cellular environments. However, existing computer-assisted structure sorting approaches are low throughput or inherently limited due to their dependency on available templates and manual labels. Here, we introduce a high-throughput template-and-label-free deep learning approach, Deep Iterative Subtomogram Clustering Approach (DISCA), that automatically detects subsets of homogeneous structures by learning and modeling 3D structural features and their distributions. Evaluation on five experimental cryo-ET datasets shows that an unsupervised deep learning based method can detect diverse structures with a wide range of molecular sizes. This unsupervised detection paves the way for systematic unbiased recognition of macromolecular complexes in situ.
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Affiliation(s)
- Xiangrui Zeng
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA15213
| | - Anson Kahng
- Computer Science Department, University of Rochester, Rochester, NY14620
| | - Liang Xue
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between European Molecular Biology Laboratory and Heidelberg University, Heidelberg69117, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg69117, Germany
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Min Xu
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA15213
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118
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Barad BA, Medina M, Fuentes D, Wiseman RL, Grotjahn DA. Quantifying organellar ultrastructure in cryo-electron tomography using a surface morphometrics pipeline. J Cell Biol 2023; 222:e202204093. [PMID: 36786771 PMCID: PMC9960335 DOI: 10.1083/jcb.202204093] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/22/2022] [Accepted: 01/17/2023] [Indexed: 02/15/2023] Open
Abstract
Cellular cryo-electron tomography (cryo-ET) enables three-dimensional reconstructions of organelles in their native cellular environment at subnanometer resolution. However, quantifying ultrastructural features of pleomorphic organelles in three dimensions is challenging, as is defining the significance of observed changes induced by specific cellular perturbations. To address this challenge, we established a semiautomated workflow to segment organellar membranes and reconstruct their underlying surface geometry in cryo-ET. To complement this workflow, we developed an open-source suite of ultrastructural quantifications, integrated into a single pipeline called the surface morphometrics pipeline. This pipeline enables rapid modeling of complex membrane structures and allows detailed mapping of inter- and intramembrane spacing, curvedness, and orientation onto reconstructed membrane meshes, highlighting subtle organellar features that are challenging to detect in three dimensions and allowing for statistical comparison across many organelles. To demonstrate the advantages of this approach, we combine cryo-ET with cryo-fluorescence microscopy to correlate bulk mitochondrial network morphology (i.e., elongated versus fragmented) with membrane ultrastructure of individual mitochondria in the presence and absence of endoplasmic reticulum (ER) stress. Using our pipeline, we demonstrate ER stress promotes adaptive remodeling of ultrastructural features of mitochondria including spacing between the inner and outer membranes, local curvedness of the inner membrane, and spacing between mitochondrial cristae. We show that differences in membrane ultrastructure correlate to mitochondrial network morphologies, suggesting that these two remodeling events are coupled. Our pipeline offers opportunities for quantifying changes in membrane ultrastructure on a single-cell level using cryo-ET, opening new opportunities to define changes in ultrastructural features induced by diverse types of cellular perturbations.
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Affiliation(s)
- Benjamin A. Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michaela Medina
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel Fuentes
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - R. Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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119
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Riechmann C, Zhang P. Recent structural advances in bacterial chemotaxis signalling. Curr Opin Struct Biol 2023; 79:102565. [PMID: 36868078 PMCID: PMC10460253 DOI: 10.1016/j.sbi.2023.102565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/25/2023] [Accepted: 01/28/2023] [Indexed: 03/05/2023]
Abstract
Bacterial chemosensory arrays have served as a model system for in-situ structure determination, clearly cataloguing the improvement of cryo-electron tomography (cryoET) over the past decade. In recent years, this has culminated in an accurately fitted atomistic model for the full-length core signalling unit (CSU) and numerous insights into the function of the transmembrane receptors responsible for signal transduction. Here, we review the achievements of the latest structural advances in bacterial chemosensory arrays and the developments which have made such advances possible.
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Affiliation(s)
- Carlos Riechmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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120
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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121
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Dutka P, Metskas LA, Hurt RC, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TF, Shapiro MG, Jensen GJ. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 2023; 31:518-528.e6. [PMID: 37040766 PMCID: PMC10185304 DOI: 10.1016/j.str.2023.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
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Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hossein Salahshoor
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
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122
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Tai L, Yin G, Sun F, Zhu Y. Cryo-electron microscopy reveals the structure of the nuclear pore complex. J Mol Biol 2023; 435:168051. [PMID: 36933820 DOI: 10.1016/j.jmb.2023.168051] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
The nuclear pore complex (NPC) is a giant protein assembly that penetrates the double layers of the nuclear membrane. The overall structure of the NPC has approximately eightfold symmetry and is formed by approximately 30 nucleoporins. The great size and complexity of the NPC have hindered the study of its structure for many years until recent breakthroughs were achieved by integrating the latest high-resolution cryo-electron microscopy (cryo-EM), the emerging artificial intelligence-based modeling and all other available structural information from crystallography and mass spectrometry. Here, we review our latest knowledge of the NPC architecture and the history of its structural study from in vitro to in situ with progressively improved resolutions by cryo-EM, with a particular focus on the latest subnanometer-resolution structural studies. The future directions for structural studies of NPCs are also discussed.
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Affiliation(s)
- Linhua Tai
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoliang Yin
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, Guangdong 510005, China.
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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123
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Cheng J, Liu T, You X, Zhang F, Sui SF, Wan X, Zhang X. Determining protein structures in cellular lamella at pseudo-atomic resolution by GisSPA. Nat Commun 2023; 14:1282. [PMID: 36922493 PMCID: PMC10017804 DOI: 10.1038/s41467-023-36175-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/18/2023] [Indexed: 03/17/2023] Open
Abstract
Cryo-electron tomography is a major tool used to study the structure of protein complexes in situ. However, the throughput of tilt-series image data collection is still quite low. Here, we show that GisSPA, a GPU accelerated program, can translationally and rotationally localize the target protein complex in cellular lamellae, as prepared with a focused ion beam, using single cryo-electron microscopy images without tilt-series, and reconstruct the protein complex at near-atomic resolution. GisSPA allows high-throughput data collection without the acquisition of tilt-series images and reconstruction of the tomogram, which is essential for high-resolution reconstruction of asymmetric or low-symmetry protein complexes. We demonstrate the power of GisSPA with 3.4-Å and 3.9-Å resolutions of resolving phycobilisome and tetrameric photosystem II complex structures in cellular lamellae, respectively. In this work, we present GisSPA as a practical tool that facilitates high-resolution in situ protein structure determination.
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Affiliation(s)
- Jing Cheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tong Liu
- High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xin You
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fa Zhang
- Beijing Institute of Technology, Beijing, 100081, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaohua Wan
- Beijing Institute of Technology, Beijing, 100081, China.
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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124
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Are extraordinary nucleosome structures more ordinary than we thought? Chromosoma 2023:10.1007/s00412-023-00791-w. [PMID: 36917245 DOI: 10.1007/s00412-023-00791-w] [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: 01/23/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023]
Abstract
The nucleosome is a DNA-protein assembly that is the basic unit of chromatin. A nucleosome can adopt various structures. In the canonical nucleosome structure, 145-147 bp of DNA is wrapped around a histone heterooctamer. The strong histone-DNA interactions cause the DNA to be inaccessible for nuclear processes such as transcription. Therefore, the canonical nucleosome structure has to be altered into different, non-canonical structures to increase DNA accessibility. While it is recognised that non-canonical structures do exist, these structures are not well understood. In this review, we discuss both the evidence for various non-canonical nucleosome structures in the nucleus and the factors that are believed to induce these structures. The wide range of non-canonical structures is likely to regulate the amount of accessible DNA, and thus have important nuclear functions.
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125
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Bromberg R, Guo Y, Borek D, Otwinowski Z. CryoEM single particle reconstruction with a complex-valued particle stack. J Struct Biol 2023; 215:107945. [PMID: 36889560 DOI: 10.1016/j.jsb.2023.107945] [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: 08/08/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resolution data. The field now performs analyses of smaller particles and to higher resolution, and these conditions result in a broader PSF that requires larger padding and slower calculations to integrate information for each particle. Consequently, the approach to handling structures such as the particle stack should be reexamined to optimize data processing. Here we propose to use as a source image for the particle stack a complex-valued image, in which CTF correction is implicitly applied as a real component of the image. We can achieve it by applying an initial CTF correction to the entire micrograph first and perform box cutouts as a subsequent step. The final CTF correction that we refine and apply later has a very narrow PSF, and so cutting out particles from micrographs that were approximately corrected for CTF does not require extended buffering, i.e. the boxes during the analysis only have to be large enough to encompass the particle. The Fourier Transform of an exit-wave reconstruction creates an image that has complex values. This is a complex value image considered in real space, opposed to standard SPR data processing where complex numbers appear only in Fourier space. This extension of the micrograph concept provides multiple advantages because the particle box size can be small and calculations crucial for high resolution reconstruction such as Ewald sphere correction, aberration refinement, and particle-specific defocus refinement can be performed on the small box data.
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Affiliation(s)
- Raquel Bromberg
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Ligo Analytics, Dallas, TX, USA
| | | | - Dominika Borek
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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126
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Khavnekar S, Wan W, Majumder P, Wietrzynski W, Erdmann PS, Plitzko JM. Multishot tomography for high-resolution in situ subtomogram averaging. J Struct Biol 2023; 215:107911. [PMID: 36343843 DOI: 10.1016/j.jsb.2022.107911] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) can resolve protein complexes at near atomic resolution, and when combined with focused ion beam (FIB) milling, macromolecules can be observed within their native context. Unlike single particle acquisition (SPA), cryo-ET can be slow, which may reduce overall project throughput. We here propose a fast, multi-position tomographic acquisition scheme based on beam-tilt corrected beam-shift imaging along the tilt axis, which yields sub-nanometer in situ STA averages.
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Affiliation(s)
| | - W Wan
- Vanderbilt University, United States
| | | | | | - P S Erdmann
- MPI for Biochemistry, Germany; Human Technopole, Italy.
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127
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Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochem Soc Trans 2023; 51:87-99. [PMID: 36695514 PMCID: PMC9987995 DOI: 10.1042/bst20220221] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/26/2023]
Abstract
The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.
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128
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Marcink TC, Zipursky G, Cheng W, Stearns K, Stenglein S, Golub K, Cohen F, Bovier F, Pfalmer D, Greninger AL, Porotto M, des Georges A, Moscona A. Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms. SCIENCE ADVANCES 2023; 9:eade2727. [PMID: 36763666 PMCID: PMC9917000 DOI: 10.1126/sciadv.ade2727] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Paramyxoviruses-including important pathogens like parainfluenza, measles, and Nipah viruses-use a receptor binding protein [hemagglutinin-neuraminidase (HN) for parainfluenza] and a fusion protein (F), acting in a complex, to enter cells. We use cryo-electron tomography to visualize the fusion complex of human parainfluenza virus 3 (HN/F) on the surface of authentic clinical viruses at a subnanometer resolution sufficient to answer mechanistic questions. An HN loop inserts in a pocket on F, showing how the fusion complex remains in a ready but quiescent state until activation. The globular HN heads are rotated with respect to each other: one downward to contact F, and the other upward to grapple cellular receptors, demonstrating how HN/F performs distinct steps before F activation. This depiction of viral fusion illuminates potentially druggable targets for paramyxoviruses and sheds light on fusion processes that underpin wide-ranging biological processes but have not been visualized in situ or at the present resolution.
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Affiliation(s)
- Tara C. Marcink
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Gillian Zipursky
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wenjing Cheng
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kyle Stearns
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Shari Stenglein
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Kate Golub
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Frances Cohen
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Francesca Bovier
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Daniel Pfalmer
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli,” 81100 Caserta, Italy
| | - Amedee des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, City University of New York, New York, NY, USA
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, USA
- PhD Programs in Chemistry and Biochemistry, The Graduate Center, City University of New York, New York, NY, USA
| | - Anne Moscona
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Center for Host-Pathogen Interaction, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
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129
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Huang Q, Zhou Y, Liu HF, Bartesaghi A. Multiple-image super-resolution of cryo-electron micrographs based on deep internal learning. BIOLOGICAL IMAGING 2023; 3:e3. [PMID: 38510165 PMCID: PMC10951919 DOI: 10.1017/s2633903x2300003x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 03/22/2024]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) is a powerful imaging modality capable of visualizing proteins and macromolecular complexes at near-atomic resolution. The low electron-doses used to prevent radiation damage to the biological samples, however, result in images where the power of the noise is 100 times greater than the power of the signal. To overcome these low signal-to-noise ratios (SNRs), hundreds of thousands of particle projections are averaged to determine the three-dimensional structure of the molecule of interest. The sampling requirements of high-resolution imaging impose limitations on the pixel sizes that can be used for acquisition, limiting the size of the field of view and requiring data collection sessions of several days to accumulate sufficient numbers of particles. Meanwhile, recent image super-resolution (SR) techniques based on neural networks have shown state-of-the-art performance on natural images. Building on these advances, here, we present a multiple-image SR algorithm based on deep internal learning designed specifically to work under low-SNR conditions. Our approach leverages the internal image statistics of cryo-EM movies and does not require training on ground-truth data. When applied to single-particle datasets of apoferritin and T20S proteasome, we show that the resolution of the 3D structure obtained from SR micrographs can surpass the limits imposed by the imaging system. Our results indicate that the combination of low magnification imaging with in silico image SR has the potential to accelerate cryo-EM data collection by virtue of including more particles in each exposure and doing so without sacrificing resolution.
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Affiliation(s)
- Qinwen Huang
- Department of Computer Science, Duke University, Durham, North Carolina, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, North Carolina, USA
| | - Hsuan-Fu Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, North Carolina, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, USA
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130
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Berger C, Dumoux M, Glen T, Yee NBY, Mitchels JM, Patáková Z, Darrow MC, Naismith JH, Grange M. Plasma FIB milling for the determination of structures in situ. Nat Commun 2023; 14:629. [PMID: 36746945 PMCID: PMC9902539 DOI: 10.1038/s41467-023-36372-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Structural biology studies inside cells and tissues require methods to thin vitrified specimens to electron transparency. Until now, focused ion beams based on gallium have been used. However, ion implantation, changes to surface chemistry and an inability to access high currents limit gallium application. Here, we show that plasma-coupled ion sources can produce cryogenic lamellae of vitrified human cells in a robust and automated manner, with quality sufficient for pseudo-atomic structure determination. Lamellae were produced in a prototype microscope equipped for long cryogenic run times (> 1 week) and with multi-specimen support fully compatible with modern-day transmission electron microscopes. We demonstrate that plasma ion sources can be used for structural biology within cells, determining a structure in situ to 4.9 Å, and characterise the resolution dependence on particle distance from the lamella edge. We describe a workflow upon which different plasmas can be examined to further streamline lamella fabrication.
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Affiliation(s)
- Casper Berger
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Maud Dumoux
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Thomas Glen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - Neville B-Y Yee
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - John M Mitchels
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Zuzana Patáková
- Thermo Fisher Scientific Brno s.r.o, Brno, 627 00, Czech Republic
| | - Michele C Darrow
- Artificial Intelligence & Informatics, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom
| | - Michael Grange
- Structural Biology, The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, OX11 0QS, United Kingdom. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, OX3 7BN, Oxford, United Kingdom.
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131
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Song J, Gooding AR, Hemphill WO, Kasinath V, Cech TR. Structural basis for inactivation of PRC2 by G-quadruplex RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.06.527314. [PMID: 36798278 PMCID: PMC9934548 DOI: 10.1101/2023.02.06.527314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The histone methyltransferase PRC2 (Polycomb Repressive Complex 2) silences genes via successively attaching three methyl groups to lysine 27 of histone H3. PRC2 associates with numerous pre-mRNA and lncRNA transcripts with a binding preference for G-quadruplex RNA. Here, we present a 3.3Ã…-resolution cryo-EM structure of PRC2 bound to a G-quadruplex RNA. Notably, RNA mediates the dimerization of PRC2 by binding both protomers and inducing a protein interface comprised of two copies of the catalytic subunit EZH2, which limits nucleosome DNA interaction and occludes H3 tail accessibility to the active site. Our results reveal an unexpected mechanism for RNA-mediated inactivation of a chromatin-modifying enzyme. Furthermore, the flexible loop of EZH2 that helps stabilize RNA binding also facilitates the handoff between RNA and DNA, an activity implicated in PRC2 regulation by RNA. One-Sentence Summary Cryo-EM structure of RNA-bound PRC2 dimer elucidates an unexpected mechanism of PRC2 inhibition by RNA.
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132
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Bourke AM, Schwarz A, Schuman EM. De-centralizing the Central Dogma: mRNA translation in space and time. Mol Cell 2023; 83:452-468. [PMID: 36669490 DOI: 10.1016/j.molcel.2022.12.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023]
Abstract
As our understanding of the cell interior has grown, we have come to appreciate that most cellular operations are localized, that is, they occur at discrete and identifiable locations or domains. These cellular domains contain enzymes, machines, and other components necessary to carry out and regulate these localized operations. Here, we review these features of one such operation: the localization and translation of mRNAs within subcellular compartments observed across cell types and organisms. We describe the conceptual advantages and the "ingredients" and mechanisms of local translation. We focus on the nature and features of localized mRNAs, how they travel and get localized, and how this process is regulated. We also evaluate our current understanding of protein synthesis machines (ribosomes) and their cadre of regulatory elements, that is, the translation factors.
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Affiliation(s)
- Ashley M Bourke
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Andre Schwarz
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany
| | - Erin M Schuman
- Max Planck Institute for Brain Research, Max von Laue Strasse 4, 60438 Frankfurt, Germany.
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133
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Du DX, Fitzpatrick AW. Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography. CELL REPORTS METHODS 2023; 3:100387. [PMID: 36814846 PMCID: PMC9939428 DOI: 10.1016/j.crmeth.2022.100387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/09/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Ponderomotive phase plates have shown that temporally consistent phase contrast is possible within electron microscopes via high-fluence static laser modes resonating in Fabry-Perot cavities. Here, we explore using pulsed laser beams as an alternative method of generating high fluences. We find through forward-stepping finite element models that picosecond or shorter interactions are required for meaningful fluences and phase shifts, with higher pulse energies and smaller beam waists leading to predicted higher fluences. An additional model based on quasi-classical assumptions is used to discover the shape of the phase plate by incorporating the oscillatory nature of the electric field. From these results, we find the transient nature of the laser pulses removes the influence of Kapitza-Dirac diffraction patterns that appear in the static resonator cases. We conclude by predicting that a total laser pulse energy of 8.7 μJ is enough to induce the required π/2 phase shift for Zernike-like phase microscopy.
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Affiliation(s)
- Daniel X. Du
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Anthony W.P. Fitzpatrick
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
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134
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Fäßler F, Javoor MG, Datler J, Döring H, Hofer FW, Dimchev G, Hodirnau VV, Faix J, Rottner K, Schur FK. ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning. SCIENCE ADVANCES 2023; 9:eadd6495. [PMID: 36662867 PMCID: PMC9858492 DOI: 10.1126/sciadv.add6495] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 12/20/2022] [Indexed: 05/10/2023]
Abstract
Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform-specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.
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Affiliation(s)
- Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Hermann Döring
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Florian W. Hofer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Georgi Dimchev
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Jan Faix
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Klemens Rottner
- Zoological Institute, Technische Universität Braunschweig, Braunschweig, Germany
- Department of Cell Biology, Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Florian K.M. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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135
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Lacey SE, Foster HE, Pigino G. The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Nat Struct Mol Biol 2023; 30:584-593. [PMID: 36593313 DOI: 10.1038/s41594-022-00905-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here we use in situ cryo-electron tomography of Chlamydomonas reinhardtii cilia and AlphaFold2 protein structure predictions to generate a molecular model of the entire anterograde train. We show how the conformations of both IFT-A and IFT-B are dependent on lateral interactions with neighboring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. Following three-dimensional classification, we reveal how IFT-B extends two flexible tethers to maintain a connection with IFT-A that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that govern cilia assembly.
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136
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Fast cryo-electron tomography data acquisition to determine molecular structures in situ. Nat Methods 2023; 20:42-43. [PMID: 36456789 DOI: 10.1038/s41592-022-01691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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137
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Lai L, Cheung YW, Martinez M, Kixmoeller K, Palao L, Steimle S, Ho MC, Black BE, Lai EM, Chang YW. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol 2023; 2646:211-248. [PMID: 36842118 DOI: 10.1007/978-1-0716-3060-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.
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Affiliation(s)
- Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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138
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Eisenstein F, Yanagisawa H, Kashihara H, Kikkawa M, Tsukita S, Danev R. Parallel cryo electron tomography on in situ lamellae. Nat Methods 2023; 20:131-138. [PMID: 36456783 DOI: 10.1038/s41592-022-01690-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
In situ cryo electron tomography of cryo focused ion beam milled samples has emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. However, the possibilities for recording tomographic tilt series in a high-throughput manner are limited, in part by the lamella-shaped samples. Here we utilize a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining access to sample areas conventionally used for tracking specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows for the collection of sample areas that were previously unreachable, thus maximizing the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high throughput and quality of PACE-tomo.
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Affiliation(s)
| | | | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | | | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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139
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Tollervey F, Zhang X, Bose M, Sachweh J, Woodruff JB, Franzmann TM, Mahamid J. Cryo-Electron Tomography of Reconstituted Biomolecular Condensates. Methods Mol Biol 2023; 2563:297-324. [PMID: 36227480 DOI: 10.1007/978-1-0716-2663-4_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The assembly of membraneless compartments by phase separation has recently been recognized as a mechanism for spatial and temporal organization of biomolecules within the cell. The functions of such mesoscale assemblies, termed biomolecular condensates, depend on networks of multivalent interactions between proteins, their structured and disordered domains, and commonly also include nucleic acids. Cryo-electron tomography is an ideal tool to investigate the three-dimensional architecture of such pleomorphic interaction networks at nanometer resolution and thus form inferences about function. However, preparation of suitable cryo-electron microscopy samples of condensates may be prone to protein denaturation, low retention of material on the sample carrier, and contamination associated with cryo-sample preparation and transfers. Here, we describe a series of protocols designed to obtain high-quality cryo-electron tomography data of biomolecular condensates reconstituted in vitro. These include critical screening by light microscopy, cryo-fixation by plunge freezing, sample loading into an electron microscope operated at liquid nitrogen temperature, data collection, processing of the data into three-dimensional tomograms, and their interpretation.
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Affiliation(s)
- Fergus Tollervey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Between EMBL and Heidelberg University Faculty of Biosciences, Heidelberg, Germany
| | - Xiaojie Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mainak Bose
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jenny Sachweh
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Jeffrey B Woodruff
- Department of Cell Biology, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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140
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Burton-Smith RN, Murata K. Cryo-electron Microscopy of Protein Cages. Methods Mol Biol 2023; 2671:173-210. [PMID: 37308646 DOI: 10.1007/978-1-0716-3222-2_11] [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] [Indexed: 06/14/2023]
Abstract
Protein cages are one of the most widely studied objects in the field of cryogenic electron microscopy-encompassing natural and synthetic constructs, from enzymes assisting protein folding such as chaperonin to virus capsids. Tremendous diversity of morphology and function is demonstrated by the structure and role of proteins, some of which are nearly ubiquitous, while others are present in few organisms. Protein cages are often highly symmetrical, which helps improve the resolution obtained by cryo-electron microscopy (cryo-EM). Cryo-EM is the study of vitrified samples using an electron probe to image the subject. A sample is rapidly frozen in a thin layer on a porous grid, attempting to keep the sample as close to a native state as possible. This grid is kept at cryogenic temperatures throughout imaging in an electron microscope. Once image acquisition is complete, a variety of software packages may be employed to carry out analysis and reconstruction of three-dimensional structures from the two-dimensional micrograph images. Cryo-EM can be used on samples that are too large or too heterogeneous to be amenable to other structural biology techniques like NMR or X-ray crystallography. In recent years, advances in both hardware and software have provided significant improvements to the results obtained using cryo-EM, recently demonstrating true atomic resolution from vitrified aqueous samples. Here, we review these advances in cryo-EM, especially in that of protein cages, and introduce several tips for situations we have experienced.
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Affiliation(s)
- Raymond N Burton-Smith
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- National Institute for Physiological Sciences (NIPS), National Institute for Natural Sciences, Okazaki, Aichi, Japan.
- Department of Physiological Sciences, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan.
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141
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Vijayakrishnan S. In Situ Imaging of Virus-Infected Cells by Cryo-Electron Tomography: An Overview. Subcell Biochem 2023; 106:3-36. [PMID: 38159222 DOI: 10.1007/978-3-031-40086-5_1] [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] [Indexed: 01/03/2024]
Abstract
Cryo-electron tomography (cryo-ET) has emerged as a powerful tool in structural biology to study viruses and is undergoing a resolution revolution. Enveloped viruses comprise several RNA and DNA pleomorphic viruses that are pathogens of clinical importance to humans and animals. Considerable efforts in cryogenic correlative light and electron microscopy (cryo-CLEM), cryogenic focused ion beam milling (cryo-FIB), and integrative structural techniques are helping to identify virus structures within cells leading to a rise of in situ discoveries shedding light on how viruses interact with their hosts during different stages of infection. This chapter reviews recent advances in the application of cryo-ET in imaging enveloped viruses and the structural and mechanistic insights revealed studying the viral infection cycle within their eukaryotic cellular hosts, with particular attention to viral entry, replication, assembly, and egress during infection.
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Affiliation(s)
- Swetha Vijayakrishnan
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, Glasgow, Scotland, UK.
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142
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Visualization of translation and protein biogenesis at the ER membrane. Nature 2023; 614:160-167. [PMID: 36697828 PMCID: PMC9892003 DOI: 10.1038/s41586-022-05638-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/07/2022] [Indexed: 01/26/2023]
Abstract
The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome1,2. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation3-7, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery.
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143
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Wang C, Wojtynek M, Medalia O. Structural investigation of eukaryotic cells: From the periphery to the interior by cryo-electron tomography. Adv Biol Regul 2023; 87:100923. [PMID: 36280452 DOI: 10.1016/j.jbior.2022.100923] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Abstract
Cryo-electron tomography (cryo-ET) combines a close-to-life preservation of the cell with high-resolution three-dimensional (3D) imaging. This allows to study the molecular architecture of the cellular landscape and provides unprecedented views on biological processes and structures. In this review we mainly focus on the application of cryo-ET to visualize and structurally characterize eukaryotic cells - from the periphery to the cellular interior. We discuss strategies that can be employed to investigate the structure of challenging targets in their cellular environment as well as the application of complimentary approaches in conjunction with cryo-ET.
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Affiliation(s)
- Chunyang Wang
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Matthias Wojtynek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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144
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de Teresa-Trueba I, Goetz SK, Mattausch A, Stojanovska F, Zimmerli CE, Toro-Nahuelpan M, Cheng DWC, Tollervey F, Pape C, Beck M, Diz-Muñoz A, Kreshuk A, Mahamid J, Zaugg JB. Convolutional networks for supervised mining of molecular patterns within cellular context. Nat Methods 2023; 20:284-294. [PMID: 36690741 PMCID: PMC9911354 DOI: 10.1038/s41592-022-01746-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/02/2022] [Indexed: 01/24/2023]
Abstract
Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
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Affiliation(s)
- Irene de Teresa-Trueba
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Computer Science and Artificial Intelligence Lab, ENGIE Lab Crigen, Stains, France
| | - Sara K. Goetz
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Alexander Mattausch
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Frosina Stojanovska
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Christian E. Zimmerli
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mauricio Toro-Nahuelpan
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,Present Address: Santiago GmbH & Co. KG, Willich, Germany
| | - Dorothy W. C. Cheng
- grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fergus Tollervey
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Constantin Pape
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.7450.60000 0001 2364 4210Present Address: Institute for Computer Science, Universität Göttingen, Göttingen, Germany
| | - Martin Beck
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.419494.50000 0001 1018 9466Present Address: Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Alba Diz-Muñoz
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna Kreshuk
- grid.4709.a0000 0004 0495 846XCell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Judith B. Zaugg
- grid.4709.a0000 0004 0495 846XStructural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany ,grid.4709.a0000 0004 0495 846XGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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145
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DiIorio MC, Kulczyk AW. Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy. MICROMACHINES 2022; 14:118. [PMID: 36677177 PMCID: PMC9866264 DOI: 10.3390/mi14010118] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 05/15/2023]
Abstract
Biological macromolecules and assemblies precisely rearrange their atomic 3D structures to execute cellular functions. Understanding the mechanisms by which these molecular machines operate requires insight into the ensemble of structural states they occupy during the functional cycle. Single-particle cryo-electron microscopy (cryo-EM) has become the preferred method to provide near-atomic resolution, structural information about dynamic biological macromolecules elusive to other structure determination methods. Recent advances in cryo-EM methodology have allowed structural biologists not only to probe the structural intermediates of biochemical reactions, but also to resolve different compositional and conformational states present within the same dataset. This article reviews newly developed sample preparation and single-particle analysis (SPA) techniques for high-resolution structure determination of intrinsically dynamic and heterogeneous samples, shedding light upon the intricate mechanisms employed by molecular machines and helping to guide drug discovery efforts.
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Affiliation(s)
- Megan C. DiIorio
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Biochemistry and Microbiology, Rutgers University, 75 Lipman Drive, New Brunswick, NJ 08901, USA
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146
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Heymann JB. The Ewald sphere/focus gradient does not limit the resolution of cryoEM reconstructions. J Struct Biol X 2022; 7:100083. [PMID: 36632443 PMCID: PMC9826812 DOI: 10.1016/j.yjsbx.2022.100083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022] Open
Abstract
In our quest to solve biomolecular structures to higher resolutions in cryoEM, care must be taken to deal with all aspects of image formation in the electron microscope. One of these is the Ewald sphere/focus gradient that derives from the scattering geometry in the microscope and its implications for recovering high resolution and handedness information. While several methods to deal with it has been proposed and implemented, there are still questions as to the correct approach. At the high acceleration voltages used for cryoEM, the traditional projection approximation that ignores the Ewald sphere breaks down around 2-3 Å and with large particles. This is likely not crucial for most biologically interesting molecules, but is required to understand detail about catalytic events, molecular orbitals, orientation of bound water molecules, etc. Through simulation I show that integration along the Ewald spheres in frequency space during reconstruction, the "simple insertion method" is adequate to reach resolutions to the Nyquist frequency. Both theory and simulations indicate that the handedness information encoded in such phases is irretrievably lost in the formation of real space images. The conclusion is that correct reconstruction along the Ewald spheres avoids the limitations of the projection approximation.
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Affiliation(s)
- J. Bernard Heymann
- National Cryo-EM Program, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
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147
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Hoffmann PC, Kreysing JP, Khusainov I, Tuijtel MW, Welsch S, Beck M. Structures of the eukaryotic ribosome and its translational states in situ. Nat Commun 2022; 13:7435. [PMID: 36460643 PMCID: PMC9718845 DOI: 10.1038/s41467-022-34997-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
Ribosomes translate genetic information into primary structure. During translation, various cofactors transiently bind to the ribosome that undergoes prominent conformational and structural changes. Different translational states of ribosomes have been well characterized in vitro. However, to which extent the known translational states are representative of the native situation inside cells has thus far only been addressed in prokaryotes. Here, we apply cryo-electron tomography to cryo-FIB milled Dictyostelium discoideum cells combined with subtomogram averaging and classification. We obtain an in situ structure that is locally resolved up to 3 Angstrom, the distribution of eukaryotic ribosome translational states, and unique arrangement of rRNA expansion segments. Our work demonstrates the use of in situ structural biology techniques for identifying distinct ribosome states within the cellular environment.
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Affiliation(s)
- Patrick C Hoffmann
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Jan Philipp Kreysing
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
- Department of Molecular Sociology, IMPRS on Cellular Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Iskander Khusainov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Maarten W Tuijtel
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany.
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148
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Ermel UH, Arghittu SM, Frangakis AS. ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX. Protein Sci 2022; 31:e4472. [PMID: 36251681 PMCID: PMC9667824 DOI: 10.1002/pro.4472] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Cryo-electron tomography analysis involves the selection of macromolecular complexes to be used for subsequent sub-tomogram averaging and structure determination. Here, we describe a plugin developed for UCSF ChimeraX that allows for the display, selection, and editing of particles within tomograms. Positions and orientations of selected particles can be manually set, modified and inspected in real time, both on screen and in virtual reality, and exported to various file formats. The plugin allows for the parallel visualization of particles stored in several meta data lists, in the context of any three-dimensional image that can be opened with UCSF ChimeraX. The particles are rendered in user-defined colors or using colormaps, such that individual classes or groups of particles, cross-correlation coefficients, or other types of information can be highlighted to the user. The implemented functions are fast, reliable, and intuitive, exploring the broad range of features in UCSF ChimeraX. They allow for a fluent human-machine interaction, which enables an effective understanding of the sub-tomogram processing pipeline, even for non-specialist users.
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Affiliation(s)
- Utz H. Ermel
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
| | - Serena M. Arghittu
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
- Buchmann Institute for Molecular Life SciencesFrankfurt Institute for Advanced StudiesFrankfurtGermany
| | - Achilleas S. Frangakis
- Buchmann Institute for Molecular Life Sciences and Institute for BiophysicsGoethe University FrankfurtFrankfurtGermany
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149
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Cryo-electron tomography: The power of seeing the whole picture. Biochem Biophys Res Commun 2022; 633:26-28. [DOI: 10.1016/j.bbrc.2022.08.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 08/25/2022] [Indexed: 11/06/2022]
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150
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Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 2022; 14:1281-1301. [PMID: 36474933 PMCID: PMC9715422 DOI: 10.1007/s12551-022-01013-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/06/2022] [Indexed: 12/04/2022] Open
Abstract
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| | - Wei Dai
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901 USA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | | | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158 USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
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