1
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. bioRxiv 2024:2024.03.13.584744. [PMID: 38559232 PMCID: PMC10979975 DOI: 10.1101/2024.03.13.584744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, time-resolved cryo-electron microscopy (cryo-EM) was used to capture four intermediates populated 120 or 500 milliseconds (ms) after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As nt-strand "read-out" extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating yet unknown conformational changes load it in subsequent steps. Because these events likely describe DNA opening at many bacterial promoters, this study provides needed insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M. Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - William C. Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Venkata P. Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Joshua H. Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Laura Y. Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
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2
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Mendez JH, Chua EYD, Paraan M, Potter CS, Carragher B. Automated pipelines for rapid evaluation during cryoEM data acquisition. Curr Opin Struct Biol 2023; 83:102729. [PMID: 37988815 DOI: 10.1016/j.sbi.2023.102729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/23/2023]
Abstract
Cryo-electron microscopy (cryoEM) has become a popular method for determining high-resolution structures of biomolecules. However, data processing can be time-consuming, particularly for new researchers entering the field. To improve data quality and increase data collection efficiency, several software packages have been developed for on-the-fly data processing with various degrees of automation. These software packages allow researchers to perform tasks such as motion correction, CTF estimation, 2D classification, and 3D reconstruction in real-time, with minimal human input. On-the-fly data processing can not only improve data collection efficiency but also increase the productivity of instrumentation in high demand. However, the various software packages available differ in their performance, computational requirements, and levels of automation. In this review, we describe the minimal metrics used to assess data quality during data collection, outline the features of an ideal on-the-fly data processing software systems, and provide results from using three of these systems.
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Affiliation(s)
- Joshua H Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y D Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mohammadreza Paraan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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3
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Walsh MA, Nannenga BL, Gonen T, Sexton PM, Wootten D, Chiu W, Sun F, Carragher B, Potter CS, Agard D, Burley SK. The next decade in structural biology. Structure 2023; 31:1284-1288. [PMID: 37922863 DOI: 10.1016/j.str.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/07/2023]
Abstract
As we celebrate the 30th anniversary of Structure, we have asked structural biologists about their expectations on how their respective fields are likely to develop in the next ten years in this collection of Voices.
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4
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Cuevas-Juárez E, Liñan-Torres A, Hernández C, Kopylov M, Potter CS, Carragher B, Ramírez OT, Palomares LA. Mimotope discovery as a tool to design a vaccine against Zika and dengue viruses. Biotechnol Bioeng 2023; 120:2658-2671. [PMID: 37058415 DOI: 10.1002/bit.28392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 04/15/2023]
Abstract
Vaccine development against dengue virus is challenging because of the antibody-dependent enhancement of infection (ADE), which causes severe disease. Consecutive infections by Zika (ZIKV) and/or dengue viruses (DENV), or vaccination can predispose to ADE. Current vaccines and vaccine candidates contain the complete envelope viral protein, with epitopes that can raise antibodies causing ADE. We used the envelope dimer epitope (EDE), which induces neutralizing antibodies that do not elicit ADE, to design a vaccine against both flaviviruses. However, EDE is a discontinuous quaternary epitope that cannot be isolated from the E protein without other epitopes. Utilizing phage display, we selected three peptides that mimic the EDE. Free mimotopes were disordered and did not elicit an immune response. After their display on adeno-associated virus (AAV) capsids (VLP), they recovered their structure and were recognized by an EDE-specific antibody. Characterization by cryo-EM and enzyme-linked immunosorbent assay confirmed the correct display of a mimotope on the surface of the AAV VLP and its recognition by the specific antibody. Immunization with the AAV VLP displaying one of the mimotopes induced antibodies that recognized ZIKV and DENV. This work provides the basis for developing a Zika and dengue virus vaccine candidate that will not induce ADE.
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Affiliation(s)
- Esmeralda Cuevas-Juárez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Arturo Liñan-Torres
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Carolina Hernández
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Clint S Potter
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, New York, USA
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Mexico
| | - Laura A Palomares
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, Mexico
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5
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Chua EYD, Neselu K, Wang B, Rice WJ, Potter CS, Carragher B. Measuring the Effect of Ice Thickness and Microscope Configuration on Resolution in Single Particle Cryo-EM. Microsc Microanal 2023; 29:1040. [PMID: 37613233 DOI: 10.1093/micmic/ozad067.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Eugene Y D Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NYUSA
| | - William J Rice
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NYUSA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
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6
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Carragher B, Potter CS. Better, Faster, Cheaper, Smarter: Advancing Cryo-EM. Microsc Microanal 2023; 29:1018. [PMID: 37613519 DOI: 10.1093/micmic/ozad067.514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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7
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Wu CG, Balakrishnan VK, Parihar PS, Konovolov K, Chen YC, Merrill RA, Wei H, Carragher B, Sundaresan R, Cui Q, Wadzinski BE, Swingle MR, Musiyenko A, Honkanen R, Chung WK, Suzuki A, Strack S, Huang X, Xing Y. Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56δ holoenzyme. bioRxiv 2023:2023.03.09.530109. [PMID: 37066309 PMCID: PMC10103954 DOI: 10.1101/2023.03.09.530109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
An increasing number of mutations associated with devastating human diseases are diagnosed by whole-genome/exon sequencing. Recurrent de novo missense mutations have been discovered in B56δ (encoded by PPP2R5D), a regulatory subunit of protein phosphatase 2A (PP2A), that cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Single-particle cryo-EM structures show that the PP2A-B56δ holoenzyme possesses closed latent and open active forms. In the closed form, the long, disordered arms of B56δ termini fold against each other and the holoenzyme core, establishing dual autoinhibition of the phosphatase active site and the substrate-binding protein groove. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is close to an allosteric network responsive to activation phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations perturb the activation phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the wild variant.
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Affiliation(s)
- Cheng-Guo Wu
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Vijaya K. Balakrishnan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Pankaj S. Parihar
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Kirill Konovolov
- Chemistry Department, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Yu-Chia Chen
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Molecular and Cellular Pharmacology program, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Hui Wei
- New York Structural biology Center, New York, NY 10027, USA
| | | | - Ramya Sundaresan
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
| | - Qiang Cui
- Department of Chemistry, Metcalf Center for Science & Engineering, Boston University, Boston, MA 02215, USA
| | - Brian E. Wadzinski
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark R. Swingle
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alla Musiyenko
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Richard Honkanen
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA
| | - Aussie Suzuki
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA 52242, USA
| | - Xuhui Huang
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
- Chemistry Department, University of Wisconsin at Madison, Wisconsin 53706, USA
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin at Madison, School of Medicine and Public Health, Madison, Wisconsin 53705, USA
- Biophysics program, University of Wisconsin at Madison, Wisconsin 53706, USA
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8
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Neselu K, Wang B, Rice WJ, Potter CS, Carragher B, Chua EY. Measuring the effects of ice thickness on resolution in single particle cryo-EM. J Struct Biol X 2023; 7:100085. [PMID: 36742017 PMCID: PMC9894782 DOI: 10.1016/j.yjsbx.2023.100085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
Ice thickness is a critical parameter in single particle cryo-EM - too thin ice can break during imaging or exclude the sample of interest, while ice that is too thick contributes to more inelastic scattering that precludes obtaining high resolution reconstructions. Here we present the practical effects of ice thickness on resolution, and the influence of energy filters, accelerating voltage, or detector mode. We collected apoferritin data with a wide range of ice thicknesses on three microscopes with different instrumentation and settings. We show that on a 300 kV microscope, using a 20 eV energy filter slit has a greater effect on improving resolution in thicker ice; that operating at 300 kV instead of 200 kV accelerating voltage provides significant resolution improvements at an ice thickness above 150 nm; and that on a 200 kV microscope using a detector operating in super resolution mode enables good reconstructions for up to 200 nm ice thickness, while collecting in counting instead of linear mode leads to improvements in resolution for ice of 50-150 nm thickness. Our findings can serve as a guide for users seeking to optimize data collection or sample preparation routines for both single particle and in situ cryo-EM. We note that most in situ data collection is done on samples in a range of ice thickness above 150 nm so these results may be especially relevant to that community.
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Affiliation(s)
- Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NY, USA
| | - William J. Rice
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NY, USA,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding authors.
| | - Eugene Y.D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding authors.
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9
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Cheng A, Kim PT, Kuang H, Mendez JH, Chua EYD, Maruthi K, Wei H, Sawh A, Aragon MF, Serbynovskyi V, Neselu K, Eng ET, Potter CS, Carragher B, Bepler T, Noble AJ. Fully automated multi-grid cryoEM screening using Smart Leginon. IUCrJ 2023; 10:77-89. [PMID: 36598504 PMCID: PMC9812217 DOI: 10.1107/s2052252522010624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Single-particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection. Screening is a major bottleneck for new cryoEM projects because grids must be optimized for several factors, including grid type, grid hole size, sample concentration, buffer conditions, ice thickness and particle behavior. Even for mature projects, multiple grids are commonly screened to select a subset for high-resolution data collection. Here, machine learning and novel purpose-built image-processing and microscope-handling algorithms are incorporated into the automated data-collection software Leginon, to provide an open-source solution for fully automated high-throughput grid screening. This new version, broadly called Smart Leginon, emulates the actions of an operator in identifying areas on the grid to explore as potentially useful for data collection. Smart Leginon Autoscreen sequentially loads and examines grids from an automated specimen-exchange system to provide completely unattended grid screening across a set of grids. Comparisons between a multi-grid autoscreen session and conventional manual screening by 5 expert microscope operators are presented. On average, Autoscreen reduces operator time from ∼6 h to <10 min and provides a percentage of suitable images for evaluation comparable to the best operator. The ability of Smart Leginon to target holes that are particularly difficult to identify is analyzed. Finally, the utility of Smart Leginon is illustrated with three real-world multi-grid user screening/collection sessions, demonstrating the efficiency and flexibility of the software package. The fully automated functionality of Smart Leginon significantly reduces the burden on operator screening time, improves the throughput of screening and recovers idle microscope time, thereby improving availability of cryoEM services.
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Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Paul T. Kim
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y. D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kashyap Maruthi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Anjelique Sawh
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mahira F. Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | | | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
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10
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Bepler T, Borst AJ, Bouvette J, Cannone G, Chen S, Cheng A, Cheng A, Fan Q, Grollios F, Gupta H, Gupta M, Humphreys T, Kim PT, Kuang H, Li Y, Noble AJ, Punjani A, Rice WJ, Oscar S Sorzano C, Stagg SM, Strauss J, Yu L, Carragher B, Potter CS. Smart data collection for CryoEM. J Struct Biol 2022; 214:107913. [PMID: 36341954 DOI: 10.1016/j.jsb.2022.107913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/29/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6-7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
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Affiliation(s)
| | - Andrew J Borst
- University of Washington, Institute for Protein Design, Seattle, WA, USA
| | - Jonathan Bouvette
- National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | - Giuseppe Cannone
- Laboratory for Molecular Biology, Medical Research Council, Cambridge, England
| | - Songye Chen
- California Institute of Technology, Pasadena, CA, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA
| | - Ao Cheng
- Northwestern University, Evanston, IL, USA
| | - Quanfu Fan
- MIT-IBM Watson AI Lab, Cambridge, MA, USA
| | | | - Harshit Gupta
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Meghna Gupta
- University of California at San Francisco, San Francisco, CA, USA
| | | | - Paul T Kim
- New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA
| | - Yilai Li
- University of Michigan, Ann Arbor, MI, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA
| | | | - William J Rice
- New York University School of Medicine, New York, NY, USA
| | | | | | - Joshua Strauss
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lingbo Yu
- ThermoFisher Scientific, Eindhoven, The Netherlands
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11
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Klykov O, Bobe D, Paraan M, Johnston JD, Potter CS, Carragher B, Kopylov M, Noble AJ. In situ cryo-FIB/SEM Specimen Preparation Using the Waffle Method. Bio Protoc 2022; 12:4544. [PMID: 36618877 PMCID: PMC9795037 DOI: 10.21769/bioprotoc.4544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/24/2022] [Accepted: 09/09/2022] [Indexed: 11/06/2022] Open
Abstract
Cryo-focused ion beam (FIB) milling of vitrified specimens is emerging as a powerful method for in situ specimen preparation. It allows for the preservation of native and near-native conditions in cells, and can reveal the molecular structure of protein complexes when combined with cryo-electron tomography (cryo-ET) and sub-tomogram averaging. Cryo-FIB milling is often performed on plunge-frozen specimens of limited thickness. However, this approach may have several disadvantages, including low throughput for cells that are small, or at low concentration, or poorly distributed across accessible areas of the grid, as well as for samples that may adopt a preferred orientation. Here, we present a detailed description of the "Waffle Method" protocol for vitrifying thick specimens followed by a semi-automated milling procedure using the Thermo Fisher Scientific (TFS) Aquilos 2 cryo-FIB/scanning electron microscope (SEM) instrument and AutoTEM Cryo software to produce cryo-lamellae. With this protocol, cryo-lamellae may be generated from specimens, such as microsporidia spores, yeast, bacteria, and mammalian cells, as well as purified proteins and protein complexes. An experienced lab can perform the entire protocol presented here within an 8-hour working day, resulting in two to three cryo-lamellae with target thicknesses of 100-200 nm and dimensions of approximately 12 μm width and 15-20 μm length. For cryo-FIB/SEMs with particularly low-contamination chambers, the protocol can be extended to overnight milling, resulting in up to 16 cryo-lamellae in 24 h. Graphical abstract.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
,
*For correspondence:
;
| | - Daija Bobe
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
,
*For correspondence:
;
| | - Mohammadreza Paraan
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Jake D. Johnston
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
,
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S. Potter
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
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Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; *Contributed equally to this work
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
,
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; *Contributed equally to this work
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J. Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
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12
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Zimanyi C, Eng E, Chua E, Aragon M, Wei H, Kopylov E, Dubbledam C, Castello C, Potter C, Carragher B. Enabling access to cryo-EM technologies by novice practitioners through access and training at multiple scales. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322097030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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13
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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14
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Paraan M, Hewitt V, Johnston J, Hirabayashi Y, Polleux F, Carragher B, Potter CS. In situ cryo-ET of ER-mitochondria contact sites. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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15
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Eng ET, Zimanyi CM, Kopylov E, Potter CS, Carragher B. The national center for cryoEM access and training utilizing cryoEM merit badges to accelerate access to cryoEM technology. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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16
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Bobe D, Kopylov M, Noble A, Raczkowski AM, Klykov O, Carragher B, Potter CS. Waffle method: an approach for cryo-FIB/SEM thin lamellae preparation. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Zimanyi CM, Kopylov M, Potter CS, Carragher B, Eng ET. Broadening access to cryoEM through centralized facilities. Trends Biochem Sci 2022; 47:106-116. [PMID: 34823974 PMCID: PMC8760164 DOI: 10.1016/j.tibs.2021.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
Cryogenic electron microscopy (cryoEM) uses images of frozen hydrated biological specimens to produce macromolecular structures, opening up previously inaccessible levels of biological organization to high-resolution structural analysis. CryoEM has the potential for broad impact in biomedical research, including basic cell, molecular, and structural biology, and increasingly in drug discovery and vaccine development. Recent advances have led to the expansion of molecular and cellular structure determination at an exponential rate. National and regional centers have emerged to support this growth by increasing the accessibility of cryoEM throughout the biomedical research community. Through cooperation and synergy, these centers form a network of resources that accelerate the adoption of best practices for access and training and establish sustainable workflows to build future research capacity.
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Affiliation(s)
- Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Correspondence: (E.T. Eng)
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18
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Ashmore J, Carragher B, Rosenthal PB, Weis W. A resolution record for cryoEM. Fac Rev 2022; 10:64. [PMID: 35088060 DOI: 10.12703/r-01-000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Cryo electron microscopy (cryoEM) is a fast-growing technique for structure determination. Two recent papers report the first atomic resolution structure of a protein obtained by averaging images of frozen-hydrated biomolecules. They both describe maps of symmetric apoferritin assemblies, a common test specimen, in unprecedented detail. New instrument improvements, different in the two studies, have contributed better images, and image analysis can extract structural information sufficient to resolve individual atomic positions. While true atomic resolution maps will not be routine for most proteins, the studies suggest structures determined by cryoEM will continue to improve, increasing their impact on biology and medicine.
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19
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Klykov O, Kopylov M, Carragher B, Heck AJ, Noble AJ, Scheltema RA. Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. Mol Cell 2022; 82:285-303. [PMID: 35063097 PMCID: PMC8842845 DOI: 10.1016/j.molcel.2021.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 01/22/2023]
Abstract
Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.
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Affiliation(s)
- Oleg Klykov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Mykhailo Kopylov
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands
| | - Alex J Noble
- National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding author for cryo-EM/ET/FIB-SEM: Alex J. Noble, tel: (+1) 212-939-0660;
| | - Richard A. Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, 3584 CH Utrecht, The Netherlands,Netherlands Proteomics Center, 3584 CH Utrecht, The Netherlands,Corresponding author for MS: Richard A. Scheltema, tel: (+31) 30 253 6804;
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20
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Bruhn JF, Scapin G, Cheng A, Mercado BQ, Waterman DG, Ganesh T, Dallakyan S, Read BN, Nieusma T, Lucier KW, Mayer ML, Chiang NJ, Poweleit N, McGilvray PT, Wilson TS, Mashore M, Hennessy C, Thomson S, Wang B, Potter CS, Carragher B. Small Molecule Microcrystal Electron Diffraction for the Pharmaceutical Industry-Lessons Learned From Examining Over Fifty Samples. Front Mol Biosci 2021; 8:648603. [PMID: 34327213 PMCID: PMC8313502 DOI: 10.3389/fmolb.2021.648603] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 11/13/2022] Open
Abstract
The emerging field of microcrystal electron diffraction (MicroED) is of great interest to industrial researchers working in the drug discovery and drug development space. The promise of being able to routinely solve high-resolution crystal structures without the need to grow large crystals is very appealing. Despite MicroED's exciting potential, adoption across the pharmaceutical industry has been slow, primarily owing to a lack of access to specialized equipment and expertise. Here we present our experience building a small molecule MicroED service pipeline for members of the pharmaceutical industry. In the past year, we have examined more than fifty small molecule samples submitted by our clients, the majority of which have yielded data suitable for structure solution. We also detail our experience determining small molecule MicroED structures of pharmaceutical interest and offer some insights into the typical experimental outcomes. This experience has led us to conclude that small molecule MicroED adoption will continue to grow within the pharmaceutical industry where it is able to rapidly provide structures inaccessible by other methods.
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Affiliation(s)
| | | | - Anchi Cheng
- NanoImaging Services, San Diego, CA, United States
| | - Brandon Q Mercado
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - David G Waterman
- UKRI STFC Rutherford Appleton Laboratory, Didcot, United Kingdom.,CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sean Thomson
- NanoImaging Services, San Diego, CA, United States
| | - Bo Wang
- Biogen, Cambridge, MA, United States
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21
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Budell WC, Allegri L, Dandey V, Potter CS, Carragher B. Cryo-Electron Microscopic Grid Preparation for Time-Resolved Studies using a Novel Robotic System, Spotiton. J Vis Exp 2021. [PMID: 33720116 DOI: 10.3791/62271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The capture of short-lived molecular states triggered by the early encounter of two or more interacting particles continues to be an experimental challenge of great interest to the field of cryo-electron microscopy (cryo-EM). A few methodological strategies have been developed that support these "time-resolved" studies, one of which, Spotiton-a novel robotic system-combines the dispensing of picoliter-sized sample droplets with precise temporal and spatial control. The time-resolved Spotiton workflow offers a uniquely efficient approach to interrogate early structural rearrangements from minimal sample volume. Fired from independently controlled piezoelectric dispensers, two samples land and rapidly mix on a nanowire EM grid as it plunges toward the cryogen. Potentially hundreds of grids can be prepared in rapid succession from only a few microliters of a sample. Here, a detailed step-by-step protocol of the operation of the Spotiton system is presented with a focus on troubleshooting specific problems that arise during grid preparation.
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Affiliation(s)
- William C Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center
| | | | - Venkat Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center;
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22
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Cheng A, Negro C, Bruhn JF, Rice WJ, Dallakyan S, Eng ET, Waterman DG, Potter CS, Carragher B. Leginon: New features and applications. Protein Sci 2021; 30:136-150. [PMID: 33030237 PMCID: PMC7737759 DOI: 10.1002/pro.3967] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023]
Abstract
Leginon is a system for automated data acquisition from a transmission electron microscope. Here we provide an updated summary of the overall Leginon architecture and an update of the current state of the package. We also highlight a few recent developments to provide some concrete examples and use cases.
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Affiliation(s)
- Anchi Cheng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Carl Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | | | - William J. Rice
- Cryo‐Electron Microscopy CoreNew York University School of MedicineNew YorkNew YorkUSA
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Sargis Dallakyan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - David G. Waterman
- STFCRutherford Appleton LaboratoryDidcotUK
- CCP4, Research Complex at HarwellRutherford Appleton LaboratoryDidcotUK
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
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23
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Abstract
The goal of structural biology is to understand biological macromolecules in as much detail as possible. Depending on the resolution of the structure obtained, insights will range from understanding interactions at the level of proteins, domains, or atoms. The three mainstay structural biology techniques are X-ray crystallography, nuclear magnetic resonance (NMR) imaging, and cryogenic electron microscopy (cryo-EM). Cryo-EM has rapidly gained popularity in recent years due to a combination of hardware and software advances, leading to the so-called Resolution Revolution (Kühlbrandt, 2014).
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Affiliation(s)
- Yong Zi Tan
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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24
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Abstract
In this issue of Structure, Li et al. (2020) describe machine learning methods that automate decision making in the cryo-EM pre-processing pipeline, eliminating the need for user-subjective decisions. They successfully tested this pipeline for a wide range of datasets, demonstrating the proof of concept and the efficiency of this approach.
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Affiliation(s)
- Kashyap Maruthi
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Mykhailo Kopylov
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA.
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25
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Wonder EA, Ewert KK, Liu C, Steffes VM, Kwak J, Qahar V, Majzoub RN, Zhang Z, Carragher B, Potter CS, Li Y, Qiao W, Safinya CR. Assembly of Building Blocks by Double-End-Anchored Polymers in the Dilute Regime Mediated by Hydrophobic Interactions at Controlled Distances. ACS Appl Mater Interfaces 2020; 12:45728-45743. [PMID: 32960036 PMCID: PMC7671076 DOI: 10.1021/acsami.0c10972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hierarchical assembly of building blocks via competing, orthogonal interactions is a hallmark of many of nature's composite materials that do not require highly specific ligand-receptor interactions. To mimic this assembly mechanism requires the development of building blocks capable of tunable interactions. In the present work, we explored the interplay between repulsive (steric and electrostatic) and attractive hydrophobic forces. The designed building blocks allow hydrophobic forces to effectively act at controlled, large distances, to create and tune the assembly of membrane-based building blocks under dilute conditions, and to affect their interactions with cellular membranes via physical cross-bridges. Specifically, we employed double-end-anchored poly(ethylene glycol)s (DEA-PEGs)-hydrophilic PEG tethers with hydrophobic tails on both ends. Using differential-interference-contrast optical microscopy, synchrotron small-angle X-ray scattering (SAXS), and cryogenic electron microscopy, we investigated the ability of DEA-PEGs to mediate assembly in the dilute regime on multiple length scales and on practical time scales. The PEG length, anchor hydrophobicity, and molar fraction of DEA-PEG molecules within a membrane strongly affect the assembly properties. Additional tuning of the intermembrane interactions can be achieved by adding repulsive interactions via PEG-lipids (steric) or cationic lipids to the DEA-PEG-mediated attractions. While the optical and electron microscopy imaging methods provided qualitative evidence of the ability of DEA-PEGs to assemble liposomes, the SAXS measurements and quantitative line-shape analysis in dilute preparations demonstrated that the ensemble average of loosely organized liposomal assemblies maintains DEA-PEG concentration-dependent tethering on defined nanometer length scales. For cationic liposome-DNA nanoparticles (CL-DNA NPs), aggregation induced by DEA-PEGs decreased internalization of NPs by cells, but tuning the DEA-PEG-induced attractions by adding repulsive steric interactions via PEG-lipids limited aggregation and increased NP uptake. Furthermore, confocal microscopy imaging together with colocalization studies with Rab11 and LysoTracker as markers of intracellular pathways showed that modifying CL-DNA NPs with DEA-PEGs alters their interactions with the plasma and endosomal membranes.
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Affiliation(s)
- Emily A. Wonder
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Kai K. Ewert
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Chenyu Liu
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Victoria M. Steffes
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Jasmin Kwak
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Vikar Qahar
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Ramsey N. Majzoub
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Youli Li
- Materials Research Laboratory, University of California, Santa Barbara, California 93106, USA
| | - Weihong Qiao
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Cyrus R. Safinya
- Materials, Physics, and Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
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26
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Rapp M, Carragher B. Better, faster, and even cheap. Science 2020; 370:171. [PMID: 33033206 DOI: 10.1126/science.abd8035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Micah Rapp
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA, and Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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27
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Bruhn J, Cheng A, Nieusma T, Dallakyan S, Speir J, Schneemann A, Potter C, Carragher B, Scapin G. Small-molecule microcrystal electron diffraction (MicroED) for the pharmaceutical industry. Acta Crystallogr A Found Adv 2020. [DOI: 10.1107/s0108767320098906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Tan YZ, Rodrigues J, Keener JE, Zheng RB, Brunton R, Kloss B, Giacometti SI, Rosário AL, Zhang L, Niederweis M, Clarke OB, Lowary TL, Marty MT, Archer M, Potter CS, Carragher B, Mancia F. Cryo-EM structure of arabinosyltransferase EmbB from Mycobacterium smegmatis. Nat Commun 2020; 11:3396. [PMID: 32636380 PMCID: PMC7341804 DOI: 10.1038/s41467-020-17202-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/21/2023] Open
Abstract
Arabinosyltransferase B (EmbB) belongs to a family of membrane-bound glycosyltransferases that build the lipidated polysaccharides of the mycobacterial cell envelope, and are targets of anti-tuberculosis drug ethambutol. We present the 3.3 Å resolution single-particle cryo-electron microscopy structure of Mycobacterium smegmatis EmbB, providing insights on substrate binding and reaction mechanism. Mutations that confer ethambutol resistance map mostly around the putative active site, suggesting this to be the location of drug binding.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - James E Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Ruixiang Blake Zheng
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY, 10027, USA
| | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
- Department of Anesthesiology, Columbia University, New York, NY, 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
- Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128, Nangang, Taipei, 11529, Taiwan
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157, Oeiras, Portugal
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, 10027, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.
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Tan YZ, Zhang L, Rodrigues J, Zheng RB, Giacometti SI, Rosário AL, Kloss B, Dandey VP, Wei H, Brunton R, Raczkowski AM, Athayde D, Catalão MJ, Pimentel M, Clarke OB, Lowary TL, Archer M, Niederweis M, Potter CS, Carragher B, Mancia F. Cryo-EM Structures and Regulation of Arabinofuranosyltransferase AftD from Mycobacteria. Mol Cell 2020; 78:683-699.e11. [PMID: 32386575 PMCID: PMC7263364 DOI: 10.1016/j.molcel.2020.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/21/2020] [Accepted: 04/13/2020] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes tuberculosis, a disease that kills over 1 million people each year. Its cell envelope is a common antibiotic target and has a unique structure due, in part, to two lipidated polysaccharides-arabinogalactan and lipoarabinomannan. Arabinofuranosyltransferase D (AftD) is an essential enzyme involved in assembling these glycolipids. We present the 2.9-Å resolution structure of M. abscessus AftD, determined by single-particle cryo-electron microscopy. AftD has a conserved GT-C glycosyltransferase fold and three carbohydrate-binding modules. Glycan array analysis shows that AftD binds complex arabinose glycans. Additionally, AftD is non-covalently complexed with an acyl carrier protein (ACP). 3.4- and 3.5-Å structures of a mutant with impaired ACP binding reveal a conformational change, suggesting that ACP may regulate AftD function. Mutagenesis experiments using a conditional knockout constructed in M. smegmatis confirm the essentiality of the putative active site and the ACP binding for AftD function.
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Affiliation(s)
- Yong Zi Tan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lei Zhang
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - José Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | | | - Sabrina I Giacometti
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Ana L Rosário
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Brian Kloss
- Center on Membrane Protein Production and Analysis, New York Structural Biology Center, New York, NY 10027, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Richard Brunton
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Ashleigh M Raczkowski
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Diogo Athayde
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA; Department of Anesthesiology, Columbia University, New York, NY 10032, USA
| | - Todd L Lowary
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada; Institute of Biological Chemistry, Academia Sinica, Academia Road, Section 2, #128 Nangang, Taipei 11529, Taiwan
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal
| | - Michael Niederweis
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA.
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Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, Gu Y, Jafari AJ, Louder MK, O'Dell S, Rowshan AP, Viox EG, Wang Y, Choi CW, Corcoran MM, Corrigan AR, Dandey VP, Eng ET, Geng H, Foulds KE, Guo Y, Kwon YD, Lin B, Liu K, Mason RD, Nason MC, Ohr TY, Ou L, Rawi R, Sarfo EK, Schön A, Todd JP, Wang S, Wei H, Wu W, Mullikin JC, Bailer RT, Doria-Rose NA, Karlsson Hedestam GB, Scorpio DG, Overbaugh J, Bloom JD, Carragher B, Potter CS, Shapiro L, Kwong PD, Mascola JR. Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Cell 2020; 178:567-584.e19. [PMID: 31348886 DOI: 10.1016/j.cell.2019.06.030] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/03/2019] [Accepted: 06/19/2019] [Indexed: 01/09/2023]
Abstract
The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
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Affiliation(s)
- Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xuejun Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Adam S Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ying Gu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Alexander J Jafari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ariana P Rowshan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Elise G Viox
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Chang W Choi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden
| | - Angela R Corrigan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Edward T Eng
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Hui Geng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Kathryn E Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Bob Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Kevin Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Martha C Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Tiffany Y Ohr
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Edward K Sarfo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John P Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Winston Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | -
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | | | - Diana G Scorpio
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Julie Overbaugh
- Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA
| | - Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; 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
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
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Kundu N, Jimah J, Stanton A, Chan LM, Dandey VP, Potter CS, Carragher B, Hinshaw JE. Dynamincs of Dynamin by CRYO-EM. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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32
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Kim J, Zi Tan Y, Wicht KJ, Erramilli SK, Dhingra SK, Okombo J, Vendome JP, Hagenah LM, Giacometti SI, Potter CS, Carragher B, Kossiakoff AA, Quick M, Fidock DA, Mancia F. Structure and Drug Resistance of the Plasmodium Falciparum Transporter PfCRT. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Steffes VM, Zhang Z, MacDonald S, Crowe J, Ewert KK, Carragher B, Potter CS, Safinya CR. PEGylation of Paclitaxel-Loaded Cationic Liposomes Drives Steric Stabilization of Bicelles and Vesicles thereby Enhancing Delivery and Cytotoxicity to Human Cancer Cells. ACS Appl Mater Interfaces 2020; 12:151-162. [PMID: 31820904 PMCID: PMC6984750 DOI: 10.1021/acsami.9b16150] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Poly(ethylene glycol) (PEG) is a polymer used widely in drug delivery to create "stealth" nanoparticles (NPs); PEG coatings suppress NP detection and clearance by the immune system and beneficially increase NP circulation time in vivo. However, NP PEGylation typically obstructs cell attachment and uptake in vitro compared to the uncoated equivalent. Here, we report on a cationic liposome (CL) NP system loaded with the hydrophobic cancer drug paclitaxel (PTX) in which PEGylation (i.e., PEG-CLPTX NPs) unexpectedly enhances, rather than diminishes, delivery efficacy and cytotoxicity to human cancer cells. This highly unexpected enhancement occurs even when the PEG-chains coating the NP are in the transition regime between the mushroom and brush conformations. Cryogenic transmission electron microscopy (TEM) of PEG-CLPTX NPs shows that PEG causes the proliferation of a mixture of sterically stabilized nanometer-scale vesicles and anisotropic micelles (e.g., bicelles). Remarkably, the onset of bicelles at sub-monolayer concentrations of the PEG coat has to our knowledge not been previously reported; it was previously thought that PEG-lipid in this composition regime was incorporated into vesicles but did not alter their shape. Confocal microscopy and flow cytometry reveal significantly greater PTX cell uptake from stabilized PEG-CLPTX NPs (vesicles and bicelles) in contrast to bare CLPTX NPs, which can aggregate in cell medium. This underscores the ability of steric stabilization to facilitate NP entry into cells via distinct size-dependent endocytic pathways, some of which cannot transport large NP aggregates into cells. This study highlights the value of understanding how PEGylation alters NP shape and structure, and thus NP efficacy, to design next-generation stealth drug carriers that integrate active cell-targeting strategies into NPs for in vivo delivery.
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Affiliation(s)
- Victoria M. Steffes
- Materials Department, University of California, Santa Barbara, California 93106, USA
- Chemistry and Biochemistry Department, University of California, Santa Barbara, California 93106, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
- Present Address: Biochemistry and Molecular Biophysics Department, Columbia University Medical Center, New York, NY 10032, USA
| | - Scott MacDonald
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - John Crowe
- Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Kai K. Ewert
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Cyrus R. Safinya
- Materials Department, University of California, Santa Barbara, California 93106, USA
- Physics Department, University of California, Santa Barbara, California 93106, USA
- Molecular, Cellular, and Developmental Biology Department, University of California, Santa Barbara, California 93106, USA
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34
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Liu Y, Zhou K, Zhang N, Wei H, Tan YZ, Zhang Z, Carragher B, Potter CS, D'Arcy S, Luger K. FACT caught in the act of manipulating the nucleosome. Nature 2020; 577:426-431. [PMID: 31775157 PMCID: PMC7441595 DOI: 10.1038/s41586-019-1820-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/07/2019] [Indexed: 01/21/2023]
Abstract
The organization of genomic DNA into nucleosomes profoundly affects all DNA-related processes in eukaryotes. The histone chaperone known as 'facilitates chromatin transcription' (FACT1) (consisting of subunits SPT16 and SSRP1) promotes both disassembly and reassembly of nucleosomes during gene transcription, DNA replication and DNA repair2. However, the mechanism by which FACT causes these opposing outcomes is unknown. Here we report two cryo-electron-microscopic structures of human FACT in complex with partially assembled subnucleosomes, with supporting biochemical and hydrogen-deuterium exchange data. We find that FACT is engaged in extensive interactions with nucleosomal DNA and all histone variants. The large DNA-binding surface on FACT appears to be protected by the carboxy-terminal domains of both of its subunits, and this inhibition is released by interaction with H2A-H2B, allowing FACT-H2A-H2B to dock onto a complex containing DNA and histones H3 and H4 (ref. 3). SPT16 binds nucleosomal DNA and tethers H2A-H2B through its carboxy-terminal domain by acting as a placeholder for DNA. SSRP1 also contributes to DNA binding, and can assume two conformations, depending on whether a second H2A-H2B dimer is present. Our data suggest a compelling mechanism for how FACT maintains chromatin integrity during polymerase passage, by facilitating removal of the H2A-H2B dimer, stabilizing intermediate subnucleosomal states and promoting nucleosome reassembly. Our findings reconcile discrepancies regarding the many roles of FACT and underscore the dynamic interactions between histone chaperones and nucleosomes.
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Affiliation(s)
- Yang Liu
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305
| | - Keda Zhou
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305
| | - Naifu Zhang
- The University of Texas at Dallas, Department of Chemistry and Biochemistry, Dallas, TX 75080
| | - Hui Wei
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Yong Zi Tan
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032
| | - Zhening Zhang
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027,Biochemistry and Molecular Biophysics Dept., Columbia University Medical Center, New York, NY 10032
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy Simons Electron Microscopy Center, New York Structural Biology Center New York, NY 10027
| | - Sheena D'Arcy
- The University of Texas at Dallas, Department of Chemistry and Biochemistry, Dallas, TX 75080
| | - Karolin Luger
- Department of Biochemistry, University of Colorado at Boulder, Boulder, CO 80305,Howard Hughes Medical Institute
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Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019; 27:1745-1759. [PMID: 31780431 DOI: 10.1016/j.str.2019.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 12/23/2022]
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling. In this approach, a structural model is constructed by combining information from multiple sources, including varied experimental methods and prior models. In 2019, a Workshop was held as a Biophysical Society Satellite Meeting to assess progress and discuss further requirements for archiving integrative structures. The primary goal of the Workshop was to build consensus for addressing the challenges involved in creating common data standards, building methods for federated data exchange, and developing mechanisms for validating integrative structures. The summary of the Workshop and the recommendations that emerged are presented here.
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Affiliation(s)
- Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA.
| | - Paul D Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Alexandre A Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, 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; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Wah Chiu
- Department of Bioengineering, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305-5447, USA; SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | - Margaret J Gabanyi
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Thomas D Goddard
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA
| | | | - Juergen Haas
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Christian A Hanke
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT 06030, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Genji Kurisu
- Protein Data Bank Japan (PDBj), Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - John L Markley
- BioMagResBank (BMRB), Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37221, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytech Institute, Troy, NY 12180, USA
| | - George N Phillips
- BioSciences at Rice and Department of Chemistry, Rice University, Houston, TX 77251, USA
| | - Thomas Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3JR, Scotland
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Torsten Schwede
- Swiss Institute of Bioinformatics and Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Claus A M Seidel
- Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | | | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation, Notkestrasse 85, 22607 Hamburg, Germany
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Brinda Vallat
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UK
| | - Geerten W Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, 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
| | - Kate L White
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA; Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA.
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Dandey VP, Wei H, Zhang Z, Tan YZ, Acharya P, Eng ET, Rice WJ, Kahn PA, Potter CS, Carragher B. Spotiton: New features and applications. J Struct Biol 2019; 202:161-169. [PMID: 29366716 DOI: 10.1016/j.jsb.2018.01.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 10/17/2022]
Abstract
We present an update describing new features and applications of Spotiton, a novel instrument for vitrifying samples for cryoEM. We have used Spotiton to prepare several test specimens that can be reconstructed using routine single particle analysis to ∼3 Å resolution, indicating that the process has no apparent deleterious effect on the sample integrity. The system is now in routine and continuous use in our lab and has been used to successfully vitrify a wide variety of samples.
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Affiliation(s)
- Venkata P Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA
| | - Hui Wei
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA
| | - Zhening Zhang
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Priyamvada Acharya
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA
| | - William J Rice
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA
| | | | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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Carragher B, Cheng Y, Frost A, Glaeser RM, Lander GC, Nogales E, Wang HW. Current outcomes when optimizing 'standard' sample preparation for single-particle cryo-EM. J Microsc 2019; 276:39-45. [PMID: 31553060 PMCID: PMC7050573 DOI: 10.1111/jmi.12834] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/10/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022]
Abstract
Although high-resolution single-particle cryo-electron microscopy (cryo-EM) is now producing a rapid stream of breakthroughs in structural biology, it nevertheless remains the case that the preparation of suitable frozen-hydrated samples on electron microscopy grids is often quite challenging. Purified samples that are intact and structurally homogeneous - while still in the test tube - may not necessarily survive the standard methods of making extremely thin, aqueous films on grids. As a result, it is often necessary to try a variety of experimental conditions before finally finding an approach that is optimal for the specimen at hand. Here, we summarize some of our collective experiences to date in optimizing sample preparation, in the hope that doing so will be useful to others, especially those new to the field. We also hope that an open discussion of these common challenges will encourage the development of more generally applicable methodology. Our collective experiences span a diverse range of biochemical samples and most of the commonly used variations in how grids are currently prepared. Unfortunately, none of the currently used optimization methods can be said, in advance, to be the one that ultimately will work when a project first begins. Nevertheless, there are some preferred first steps to explore when facing specific problems that can be more generally recommended, based on our experience and that of many others in the cryo-EM field.
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Affiliation(s)
- B Carragher
- Simon Electron Microscopy Center, New York Structural Biology Center, New York, U.S.A
| | - Y Cheng
- HHMI and Department of Biochemistry and Biophysics, University of California, San Francisco, California, U.S.A
| | - A Frost
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, U.S.A
| | - R M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, California, U.S.A
| | - G C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, U.S.A
| | - E Nogales
- Molecular and Cell Biology Department, University of California Berkeley, Berkeley, California, U.S.A
- MBIB Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, California, U.S.A
- Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California, U.S.A
| | - H-W Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, China
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38
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Eng ET, Rice WJ, Cheng A, Carragher B, Potter CS. What to expect from cryo-EM (national service centers). Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319099707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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39
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Eng ET, Kopylov M, Negro CJ, Dallaykan S, Rice WJ, Jordan KD, Kelley K, Carragher B, Potter CS. Reducing cryoEM file storage using lossy image formats. J Struct Biol 2019; 207:49-55. [PMID: 31121317 DOI: 10.1016/j.jsb.2019.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/11/2019] [Accepted: 04/16/2019] [Indexed: 10/26/2022]
Abstract
Recent advances in instrumentation and software for cryoEM have increased the applicability and utility of this method. High levels of automation and faster data acquisition rates require hard decisions to be made regarding data retention. Here we investigate the efficacy of data compression applied to aligned summed movie files. Surprisingly, these images can be compressed using a standard lossy method that reduces file storage by 90-95% and yet can still be processed to provide sub-2 Å reconstructed maps. We do not advocate this as an archival method, but it may provide a useful means for retaining images as an historical record, especially at large facilities.
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Affiliation(s)
- Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Carl J Negro
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Sarkis Dallaykan
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - William J Rice
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Kelsey D Jordan
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Kotaro Kelley
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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Abstract
As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the genetic modification and structural characterization of the Leviviridae PP7 capsid protein as a platform for the presentation of functional polypeptides. This particle was shown to tolerate the display of sequences from 1 kDa (a cell penetrating peptide) to 14 kDa (the Fc-binding double Z-domain) on its exterior surface as C-terminal genetic fusions to the coat protein. In addition, a dimeric construct allowed the presentation of exogenous loops between capsid monomers and the simultaneous presentation of two different peptides at different positions on the icosahedral structure. The PP7 particle is thereby significantly more tolerant of these types of polypeptide additions than Qβ and MS2, the other Leviviridae-derived VLPs in common use.
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Affiliation(s)
- Liangjun Zhao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Mykhailo Kopylov
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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41
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Brasch J, Goodman KM, Noble AJ, Rapp M, Mannepalli S, Bahna F, Dandey VP, Bepler T, Berger B, Maniatis T, Potter CS, Carragher B, Honig B, Shapiro L. Visualization of clustered protocadherin neuronal self-recognition complexes. Nature 2019; 569:280-283. [PMID: 30971825 DOI: 10.1038/s41586-019-1089-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/07/2019] [Indexed: 11/09/2022]
Abstract
Neurite self-recognition and avoidance are fundamental properties of all nervous systems1. These processes facilitate dendritic arborization2,3, prevent formation of autapses4 and allow free interaction among non-self neurons1,2,4,5. Avoidance among self neurites is mediated by stochastic cell-surface expression of combinations of about 60 isoforms of α-, β- and γ-clustered protocadherin that provide mammalian neurons with single-cell identities1,2,4-13. Avoidance is observed between neurons that express identical protocadherin repertoires2,5, and single-isoform differences are sufficient to prevent self-recognition10. Protocadherins form isoform-promiscuous cis dimers and isoform-specific homophilic trans dimers10,14-20. Although these interactions have previously been characterized in isolation15,17-20, structures of full-length protocadherin ectodomains have not been determined, and how these two interfaces engage in self-recognition between neuronal surfaces remains unknown. Here we determine the molecular arrangement of full-length clustered protocadherin ectodomains in single-isoform self-recognition complexes, using X-ray crystallography and cryo-electron tomography. We determine the crystal structure of the clustered protocadherin γB4 ectodomain, which reveals a zipper-like lattice that is formed by alternating cis and trans interactions. Using cryo-electron tomography, we show that clustered protocadherin γB6 ectodomains tethered to liposomes spontaneously assemble into linear arrays at membrane contact sites, in a configuration that is consistent with the assembly observed in the crystal structure. These linear assemblies pack against each other as parallel arrays to form larger two-dimensional structures between membranes. Our results suggest that the formation of ordered linear assemblies by clustered protocadherins represents the initial self-recognition step in neuronal avoidance, and thus provide support for the isoform-mismatch chain-termination model of protocadherin-mediated self-recognition, which depends on these linear chains11.
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Affiliation(s)
- Julia Brasch
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kerry M Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Micah Rapp
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Venkata P Dandey
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Tristan Bepler
- Computational and Systems Biology, MIT, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Department of Mathematics, MIT, Cambridge, MA, USA
| | - Tom Maniatis
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA. .,Department of Medicine, Columbia University, New York, NY, USA.
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.
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Bobe D, Rice WJ, Eng ET, Kim LY, Kopylov M, Raczkowski AM, Carragher B, Potter CS. Single Particle Cryo-EM Workflow: Structures of Apoferritin and Aldolase. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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43
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Eng ET, Cheng A, Rice WJ, Kopylov M, Kim LY, Raczkowski AM, Bobe D, Jordan K, Kelley K, Potter CS, Carragher B. Leginon's Extended Image Shift Mode Increases the throughput for Single Particle Data Collection. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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44
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Steffes V, Zhang Z, Crowe J, MacDonald S, Ewert KK, Carragher B, Potter CS, Safinya CR. Lipid Nanomaterials for Paclitaxel Delivery in Cancer Therapeutics: Effect of Pegylation and Charge on the Morphology and Efficacy. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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45
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Noble AJ, Wei H, Dandey VP, Zhang Z, Tan YZ, Potter CS, Carragher B. Reducing effects of particle adsorption to the air-water interface in cryo-EM. Nat Methods 2018; 15:793-795. [PMID: 30250056 PMCID: PMC6168394 DOI: 10.1038/s41592-018-0139-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022]
Abstract
Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt preferred orientations. By using a rapid plunge-freezing robot and nanowire grids, we were able to reduce some of the deleterious effects of the air-water interface by decreasing the dwell time of particles in thin liquid films. We demonstrated this by using single-particle cryo-EM and cryo-electron tomography (cryo-ET) to examine hemagglutinin, insulin receptor complex, and apoferritin.
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Affiliation(s)
- Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Zhening Zhang
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Yong Zi Tan
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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Rice WJ, Cheng A, Noble AJ, Eng ET, Kim LY, Carragher B, Potter CS. Routine determination of ice thickness for cryo-EM grids. J Struct Biol 2018; 204:38-44. [PMID: 29981485 PMCID: PMC6119488 DOI: 10.1016/j.jsb.2018.06.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 12/12/2022]
Abstract
Recent advances in instrumentation and automation have made cryo-EM a popular method for producing near-atomic resolution structures of a variety of proteins and complexes. Sample preparation is still a limiting factor in collecting high quality data. Thickness of the vitreous ice in which the particles are embedded is one of the many variables that need to be optimized for collection of the highest quality data. Here we present two methods, using either an energy filter or scattering outside the objective aperture, to measure ice thickness for potentially every image collected. Unlike geometrical or tomographic methods, these can be implemented directly in the single particle collection workflow without interrupting or significantly slowing down data collection. We describe the methods as implemented into the Leginon/Appion data collection workflow, along with some examples from test cases. Routine monitoring of ice thickness should prove helpful for optimizing sample preparation, data collection, and data processing.
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Affiliation(s)
- William J. Rice
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Anchi Cheng
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Alex J. Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Edward T. Eng
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Laura Y. Kim
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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Scapin G, Potter CS, Carragher B. Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application. Cell Chem Biol 2018; 25:1318-1325. [PMID: 30100349 DOI: 10.1016/j.chembiol.2018.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/11/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
We present a perspective of our view of the application of cryoelectron microscopy (cryo-EM) to structure-based drug design (SBDD). We discuss the basic needs and requirements for SBDD, the current state of cryo-EM, and the challenges that need to be overcome for this technique to reach its full potential in facilitating the process of drug discovery.
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Affiliation(s)
- Giovanna Scapin
- Department of Biochemical Engineering & Structure, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, 89 Convent Avenue, New York NY 10027, USA; NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, 89 Convent Avenue, New York NY 10027, USA; NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA.
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Dionne G, Qiu X, Rapp M, Liang X, Zhao B, Peng G, Katsamba PS, Ahlsen G, Rubinstein R, Potter CS, Carragher B, Honig B, Müller U, Shapiro L. Mechanotransduction by PCDH15 Relies on a Novel cis-Dimeric Architecture. Neuron 2018; 99:480-492.e5. [PMID: 30057206 DOI: 10.1016/j.neuron.2018.07.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/06/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
The tip link, a filament formed by protocadherin 15 (PCDH15) and cadherin 23, conveys mechanical force from sound waves and head movement to open hair-cell mechanotransduction channels. Tip-link cadherins are thought to have acquired structural features critical for their role in mechanotransduction. Here, we biophysically and structurally characterize the unusual cis-homodimeric architecture of PCDH15. We show that PCDH15 molecules form double-helical assemblies through cis-dimerization interfaces in the extracellular cadherin EC2-EC3 domain region and in a unique membrane-proximal domain. Electron microscopy studies visualize the cis-dimeric PCDH15 assembly and reveal the PCDH15 extracellular domain as a parallel double helix with cis cross-bridges at the two locations we defined. The helical configuration suggests the potential for elasticity through helix winding and unwinding. Functional studies in hair cells show that mutations that perturb PCDH15 dimerization contacts affect mechanotransduction. Together, these data reveal the cis-dimeric architecture of PCDH15 and show that dimerization is critical for sensing mechanical stimuli.
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Affiliation(s)
- Gilman Dionne
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Xufeng Qiu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Micah Rapp
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Xiaoping Liang
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bo Zhao
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Guihong Peng
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Phinikoula S Katsamba
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Goran Ahlsen
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Rotem Rubinstein
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Clinton S Potter
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Bridget Carragher
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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Cheng A, Eng ET, Alink L, Rice WJ, Jordan KD, Kim LY, Potter CS, Carragher B. High resolution single particle cryo-electron microscopy using beam-image shift. J Struct Biol 2018; 204:270-275. [PMID: 30055234 DOI: 10.1016/j.jsb.2018.07.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/21/2018] [Accepted: 07/24/2018] [Indexed: 11/19/2022]
Abstract
Automated data acquisition is used widely for single-particle reconstruction of three-dimensional (3D) volumes of biological complexes preserved in vitreous ice and imaged in a transmission electron microscope. Automation has become integral to this method because of the very large number of particle images required in order to overcome the typically low signal-to-noise ratio of these images. For optimal efficiency, automated data acquisition software packages typically employ some beam-image shift targeting as this method is both fast and accurate (±0.1 µm). In contrast, using only stage movement, relocation to a targeted area under low-dose conditions can only be achieved in combination with multiple iterations or long relaxation times, both reducing efficiency. Nevertheless it is well known that applying beam-image shift induces beam-tilt and with it a potential structure phase error with a phase error π/4 the highest acceptable value. This theory has been used as an argument against beam-image shift for high resolution data collection. Nevertheless, in practice many small beam-image shift datasets have resulted in 3D reconstructions beyond the π/4 phase error limit. To address this apparent contradiction, we performed cryo-EM single-particle reconstructions on a T20S proteasome sample using applied beam-image shifts corresponding to beam tilts from 0 to 10 mrad. To evaluate the results we compared the FSC values, and examined the water density peaks in the 3D map. We conclude that the phase error does not limit the validity of the 3D reconstruction from single-particle averaging beyond the π/4 resolution limit.
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Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lambertus Alink
- Thermo Fisher Scientific, Materials & Structural Analysis, Hillsboro, OR 97124, USA
| | - William J Rice
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
| | - Kelsey D Jordan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Laura Y Kim
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
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Scapin G, Dandey V, Zhang Z, Prosise W, Hruza A, Strickland C, Kelly T, Mayhood T, Potter CS, Carragher B. Structure of the insulin receptor in complex with insulin using single-particle cryo-EM analysis. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318098999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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