1
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Bhattacharjee S, Feng X, Maji S, Dadhwal P, Zhang Z, Brown ZP, Frank J. Time resolution in cryo-EM using a PDMS-based microfluidic chip assembly and its application to the study of HflX-mediated ribosome recycling. Cell 2024; 187:782-796.e23. [PMID: 38244547 PMCID: PMC10872292 DOI: 10.1016/j.cell.2023.12.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/13/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024]
Abstract
The rapid kinetics of biological processes and associated short-lived conformational changes pose a significant challenge in attempts to structurally visualize biomolecules during a reaction in real time. Conventionally, on-pathway intermediates have been trapped using chemical modifications or reduced temperature, giving limited insights. Here, we introduce a time-resolved cryo-EM method using a reusable PDMS-based microfluidic chip assembly with high reactant mixing efficiency. Coating of PDMS walls with SiO2 virtually eliminates non-specific sample adsorption and ensures maintenance of the stoichiometry of the reaction, rendering it highly reproducible. In an operating range from 10 to 1,000 ms, the device allows us to follow in vitro reactions of biological molecules at resolution levels in the range of 3 Å. By employing this method, we show the mechanism of progressive HflX-mediated splitting of the 70S E. coli ribosome in the presence of the GTP via capture of three high-resolution reaction intermediates within 140 ms.
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Affiliation(s)
- Sayan Bhattacharjee
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Xiangsong Feng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA.
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Prikshat Dadhwal
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Zhening Zhang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Zuben P Brown
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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2
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Amann SJ, Keihsler D, Bodrug T, Brown NG, Haselbach D. Frozen in time: analyzing molecular dynamics with time-resolved cryo-EM. Structure 2023; 31:4-19. [PMID: 36584678 PMCID: PMC9825670 DOI: 10.1016/j.str.2022.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/10/2022] [Accepted: 11/25/2022] [Indexed: 12/30/2022]
Abstract
Molecular machines, such as polymerases, ribosomes, or proteasomes, fulfill complex tasks requiring the thermal energy of their environment. They achieve this by restricting random motion along a path of possible conformational changes. These changes are often directed through engagement with different cofactors, which can best be compared to a Brownian ratchet. Many molecular machines undergo three major steps throughout their functional cycles, including initialization, repetitive processing, and termination. Several of these major states have been elucidated by cryogenic electron microscopy (cryo-EM). However, the individual steps for these machines are unique and multistep processes themselves, and their coordination in time is still elusive. To measure these short-lived intermediate events by cryo-EM, the total reaction time needs to be shortened to enrich for the respective pre-equilibrium states. This approach is termed time-resolved cryo-EM (trEM). In this review, we sum up the methodological development of trEM and its application to a range of biological questions.
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Affiliation(s)
- Sascha Josef Amann
- IMP - Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Demian Keihsler
- IMP - Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Tatyana Bodrug
- IMP - Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - David Haselbach
- IMP - Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria; Institute for Physical Chemistry, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104 Freiburg, Germany.
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3
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Bhattacharjee B, Rahman MM, Hibbs RE, Stowell MHB. A simple flash and freeze system for cryogenic time-resolved electron microscopy. Front Mol Biosci 2023; 10:1129225. [PMID: 36959978 PMCID: PMC10028177 DOI: 10.3389/fmolb.2023.1129225] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/09/2023] Open
Abstract
As the resolution revolution in CryoEM expands to encompass all manner of macromolecular complexes, an important new frontier is the implementation of cryogenic time resolved EM (cryoTREM). Biological macromolecular complexes are dynamic systems that undergo conformational changes on timescales from microseconds to minutes. Understanding the dynamic nature of biological changes is critical to understanding function. To realize the full potential of CryoEM, time resolved methods will be integral in coupling static structures to dynamic functions. Here, we present an LED-based photo-flash system as a core part of the sample preparation phase in CryoTREM. The plug-and-play system has a wide range of operational parameters, is low cost and ensures uniform irradiation and minimal heating of the sample prior to plunge freezing. The complete design including electronics and optics, manufacturing, control strategies and operating procedures are discussed for the Thermo Scientific™ Vitrobot and Leica™ EM GP2 plunge freezers. Possible adverse heating effects on the biological sample are also addressed through theoretical as well as experimental studies.
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Affiliation(s)
- Biddut Bhattacharjee
- University of Colorado Boulder, Boulder, United States
- *Correspondence: Biddut Bhattacharjee, ; Michael H. B. Stowell,
| | | | - Ryan E. Hibbs
- University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael H. B. Stowell
- University of Colorado Boulder, Boulder, United States
- *Correspondence: Biddut Bhattacharjee, ; Michael H. B. Stowell,
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4
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DiIorio MC, Kulczyk AW. Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy. MICROMACHINES 2022; 14:mi14010118. [PMID: 36677177 PMCID: PMC9866264 DOI: 10.3390/mi14010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 05/15/2023]
Abstract
Biological macromolecules and assemblies precisely rearrange their atomic 3D structures to execute cellular functions. Understanding the mechanisms by which these molecular machines operate requires insight into the ensemble of structural states they occupy during the functional cycle. Single-particle cryo-electron microscopy (cryo-EM) has become the preferred method to provide near-atomic resolution, structural information about dynamic biological macromolecules elusive to other structure determination methods. Recent advances in cryo-EM methodology have allowed structural biologists not only to probe the structural intermediates of biochemical reactions, but also to resolve different compositional and conformational states present within the same dataset. This article reviews newly developed sample preparation and single-particle analysis (SPA) techniques for high-resolution structure determination of intrinsically dynamic and heterogeneous samples, shedding light upon the intricate mechanisms employed by molecular machines and helping to guide drug discovery efforts.
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Affiliation(s)
- Megan C. DiIorio
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Biochemistry and Microbiology, Rutgers University, 75 Lipman Drive, New Brunswick, NJ 08901, USA
- Correspondence:
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5
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Hands-Portman I, Bakker SE. Customising the plunge-freezing workflow for challenging conditions. Faraday Discuss 2022; 240:44-54. [PMID: 35913403 PMCID: PMC9641998 DOI: 10.1039/d2fd00060a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Grid freezing is a critical step for successful cryo-transmission electron microscopy, and optimising freezing conditions is a considerable bottleneck in many projects. To improve reproducibility in grid preparation, temperature- and humidity-controlled chambers were built into the second generation of plunge-freezers, including the ThermoFisherScientific Vitrobot and Leica GP. Since then, for most published structures, the proteins were plunge-frozen from a cold, humid environment. This provides two benefits: many proteins are more stable at 4 °C than room temperature, and both the low temperature and the humidity help control evaporation of the tiny drop of liquid. However, for optimal stability, certain samples may have different requirements. Here, we describe various (reversible) adaptations made to a Leica GP2 system to accommodate several samples with special handling requirements: a protein that is sensitive to both light and oxygen, a sample that needs to be kept at 37 °C throughout the plunge-freezing process, and a method to freeze a polymer that gels at 37 °C in its gelled state. While some of these methods are specific to these specimens, we hope sharing the ideas behind them will help people who are dealing with tricky protein samples.
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Affiliation(s)
- Ian Hands-Portman
- Advanced Bioimaging Research Technology Platform, University of WarwickGibbet Hill RoadCoventryCV4 7ALUK
| | - Saskia E. Bakker
- Advanced Bioimaging Research Technology Platform, University of WarwickGibbet Hill RoadCoventryCV4 7ALUK
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6
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Mäeots ME, Enchev RI. Structural dynamics: review of time-resolved cryo-EM. Acta Crystallogr D Struct Biol 2022; 78:927-935. [PMID: 35916218 PMCID: PMC9344476 DOI: 10.1107/s2059798322006155] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022] Open
Abstract
Time-resolved cryo-EM is an emerging technique in structural biology that allows the user to capture structural states which would otherwise be too transient for standard methods. There has been a resurgence in technical advancements in this field in the last five years and this review provides a summary of the technical highlights. The structural determination of biological macromolecules has been transformative for understanding biochemical mechanisms and developing therapeutics. However, the ultimate goal of characterizing how structural dynamics underpin biochemical processes has been difficult. This is largely due to significant technical challenges that hinder data collection and analysis on the native timescales of macromolecular dynamics. Single-particle cryo-EM provides a powerful platform to approach this challenge, since samples can be frozen faster than the single-turnover timescales of most biochemical reactions. In order to enable time-resolved analysis, significant innovations in the handling and preparation of cryo-EM samples have been implemented, bringing us closer to the goal of the direct observation of protein dynamics in the milliseconds to seconds range. Here, the current state of time-resolved cryo-EM is reviewed and the most promising future research directions are discussed.
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7
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Yoder N, Jalali-Yazdi F, Noreng S, Houser A, Baconguis I, Gouaux E. Light-coupled cryo-plunger for time-resolved cryo-EM. J Struct Biol 2020; 212:107624. [PMID: 32950604 DOI: 10.1016/j.jsb.2020.107624] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/26/2022]
Abstract
Proteins are dynamic molecules that can undergo rapid conformational rearrangements in response to stimuli. These structural changes are often critical to protein function, and thus elucidating time-dependent conformational landscapes has been a long-standing goal of structural biology. To harness the power of single particle cryo-EM methods to enable 'time-resolved' structure determination, we have developed a light-coupled cryo-plunger that pairs flash-photolysis of caged ligands with rapid sample vitrification. The 'flash-plunger' consists of a high-power ultraviolet LED coupled with focusing optics and a motorized linear actuator, enabling the user to immobilize protein targets in vitreous ice within a programmable time window - as short as tens of milliseconds - after stimulus delivery. The flash-plunger is a simple, inexpensive and flexible tool to explore short-lived conformational states previously unobtainable by conventional sample preparation methods.
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Affiliation(s)
- Nate Yoder
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Farzad Jalali-Yazdi
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sigrid Noreng
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexandra Houser
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Isabelle Baconguis
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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8
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Abstract
We present an approach for preparing cryo-electron microscopy (cryo-EM) grids to study short-lived molecular states. Using piezoelectric dispensing, two independent streams of ~50-pl droplets of sample are deposited within 10 ms of each other onto the surface of a nanowire EM grid, and the mixing reaction stops when the grid is vitrified in liquid ethane ~100 ms later. We demonstrate this approach for four biological systems where short-lived states are of high interest.
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9
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Mäeots ME, Lee B, Nans A, Jeong SG, Esfahani MMN, Ding S, Smith DJ, Lee CS, Lee SS, Peter M, Enchev RI. Modular microfluidics enables kinetic insight from time-resolved cryo-EM. Nat Commun 2020; 11:3465. [PMID: 32651368 PMCID: PMC7351747 DOI: 10.1038/s41467-020-17230-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/18/2020] [Indexed: 11/09/2022] Open
Abstract
Mechanistic understanding of biochemical reactions requires structural and kinetic characterization of the underlying chemical processes. However, no single experimental technique can provide this information in a broadly applicable manner and thus structural studies of static macromolecules are often complemented by biophysical analysis. Moreover, the common strategy of utilizing mutants or crosslinking probes to stabilize intermediates is prone to trapping off-pathway artefacts and precludes determining the order of molecular events. Here we report a time-resolved sample preparation method for cryo-electron microscopy (trEM) using a modular microfluidic device, featuring a 3D-mixing unit and variable delay lines that enables automated, fast, and blot-free sample vitrification. This approach not only preserves high-resolution structural detail but also substantially improves sample integrity and protein distribution across the vitreous ice. We validate the method by visualising reaction intermediates of early RecA filament growth across three orders of magnitude on sub-second timescales. The trEM method reported here is versatile, reproducible, and readily adaptable to a broad spectrum of fundamental questions in biology.
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Affiliation(s)
- Märt-Erik Mäeots
- Institute of Biochemistry, Department of Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Byungjin Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Yuseong-Gu, Daejeon, 305-764, Republic of Korea
| | - Andrea Nans
- Structural Biology Scientific Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Seung-Geun Jeong
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Yuseong-Gu, Daejeon, 305-764, Republic of Korea
| | - Mohammad M N Esfahani
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Shan Ding
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK
| | - Daniel J Smith
- Institute of Biochemistry, Department of Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Yuseong-Gu, Daejeon, 305-764, Republic of Korea.
| | - Sung Sik Lee
- Institute of Biochemistry, Department of Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland.
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland.
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland.
| | - Radoslav I Enchev
- Institute of Biochemistry, Department of Biology, ETH Zurich, Otto-Stern-Weg 3, 8093, Zurich, Switzerland.
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT, London, UK.
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10
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Kaledhonkar S, Fu Z, White H, Frank J. Time-Resolved Cryo-electron Microscopy Using a Microfluidic Chip. Methods Mol Biol 2018; 1764:59-71. [PMID: 29605908 DOI: 10.1007/978-1-4939-7759-8_4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the advent of direct electron detectors, cryo-EM has become a popular choice for molecular structure determination. Among its advantages over X-ray crystallography are (1) no need for crystals, (2) much smaller sample volumes, and (3) the ability to determine multiple structures or conformations coexisting in one sample. In principle, kinetic experiments can be done using standard cryo-EM, but mixing and freezing grids require several seconds. However, many biological processes are much faster than that time scale, and the ensuing short-lived states of the molecules cannot be captured. Here, we lay out a detailed protocol for how to capture such intermediate states on the millisecond time scale with time-resolved cryo-EM.
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Affiliation(s)
- Sandip Kaledhonkar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, NY, USA
| | - Ziao Fu
- Integrated Program in Cellular, Molecular and Biomolecular Studies, Columbia University College of Physicians and Surgeons, New York, 10032, NY, USA
| | - Howard White
- Physiological Sciences, Eastern Virginia Medical School, Norfolk, 23507, VA, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, 10032, NY, USA. .,Department of Biological Sciences, Columbia University, New York, 10027, NY, USA.
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11
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Feng X, Fu Z, Kaledhonkar S, Jia Y, Shah B, Jin A, Liu Z, Sun M, Chen B, Grassucci RA, Ren Y, Jiang H, Frank J, Lin Q. A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM. Structure 2017; 25:663-670.e3. [PMID: 28286002 DOI: 10.1016/j.str.2017.02.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/10/2017] [Accepted: 02/10/2017] [Indexed: 11/17/2022]
Abstract
We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new polydimethylsiloxane (PDMS)-based sprayer was tested with apoferritin. We demonstrate that the structure can be solved to high resolution with this method of sample preparation. Besides replacing the conventional pipetting-blotting-plunging method, one of many potential applications of the new sprayer is in time-resolved cryo-EM, as part of a PDMS-based microfluidic reaction channel to study short-lived intermediates on the timescale of 10-1,000 ms.
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Affiliation(s)
- Xiangsong Feng
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA; School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Ziao Fu
- Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Sandip Kaledhonkar
- Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10027, USA
| | - Yuan Jia
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA
| | - Binita Shah
- Department of Biological Sciences, Barnard College, New York, NY 10027, USA
| | - Amy Jin
- Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10027, USA
| | - Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10027, USA
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Bo Chen
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Robert A Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Hongyuan Jiang
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA.
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY 10027, USA.
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12
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Lu Z, Barnard D, Shaikh TR, Meng X, Mannella CA, Yassin A, Agrawal R, Wagenknecht T, Lu TM. Gas-Assisted Annular Microsprayer for Sample Preparation for Time-Resolved Cryo-Electron Microscopy. JOURNAL OF MICROMECHANICS AND MICROENGINEERING : STRUCTURES, DEVICES, AND SYSTEMS 2014; 24:115001. [PMID: 25530679 PMCID: PMC4266110 DOI: 10.1088/0960-1317/24/11/115001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Time-resolved cryo electron microscopy (TRCEM) has emerged as a powerful technique for transient structural characterization of isolated biomacromolecular complexes in their native state within the time scale of seconds to milliseconds. For TRCEM sample preparation, microfluidic device [9] has been demonstrated to be a promising approach to facilitate TRCEM biological sample preparation. It is capable of achieving rapidly aqueous sample mixing, controlled reaction incubation, and sample deposition on electron microscopy (EM) grids for rapid freezing. One of the critical challenges is to transfer samples to cryo-EM grids from the microfluidic device. By using microspraying method, the generated droplet size needs to be controlled to facilitate the thin ice film formation on the grid surface for efficient data collection, while not too thin to be dried out before freezing, i.e., optimized mean droplet size needs to be achieved. In this work, we developed a novel monolithic three dimensional (3D) annular gas-assisted microfluidic sprayer using 3D MEMS (MicroElectroMechanical System) fabrication techniques. The microsprayer demonstrated dense and consistent microsprays with average droplet size between 6-9 μm, which fulfilled the above droplet size requirement for TRCEM sample preparation. With droplet density of around 12-18 per grid window (window size is 58×58 μm), and the data collectible thin ice region of >50% total wetted area, we collected ~800-1000 high quality CCD micrographs in a 6-8 hour period of continuous effort. This level of output is comparable to what were routinely achieved using cryo-grids prepared by conventional blotting and manual data collection. In this case, weeks of data collection process with the previous device [9] has shortened to a day or two. And hundreds of microliter of valuable sample consumption can be reduced to only a small fraction.
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Affiliation(s)
- Zonghuan Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - David Barnard
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Tanvir R. Shaikh
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Xing Meng
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Carmen A. Mannella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Aymen Yassin
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
- Department of Microbiology and Immunology, Cairo University, Cairo, Egypt
| | - Rajendra Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Terence Wagenknecht
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201
| | - Toh-Ming Lu
- Center for Integrated Electronics, Rensselaer Polytechnic Institute, Troy, NY 12180
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13
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Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis A virus particle. J Virol 2014; 88:6093-9. [PMID: 24648455 PMCID: PMC4093863 DOI: 10.1128/jvi.01979-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The Picornaviridae family of small, nonenveloped viruses includes major pathogens of humans and animals. They have positive-sense, single-stranded RNA genomes, and the mechanism(s) by which these genomes are introduced into cells to initiate infection remains poorly understood. The structures of presumed uncoating intermediate particles of several picornaviruses show limited expansion and some increased porosity compared to the mature virions. Here, we present the cryo-electron microscopy structure of native equine rhinitis A virus (ERAV), together with the structure of a massively expanded ERAV particle, each at ∼17–Å resolution. The expanded structure has large pores on the particle 3-fold axes and has lost the RNA genome and the capsid protein VP4. The expanded structure thus illustrates both the limits of structural plasticity in such capsids and a plausible route by which genomic RNA might exit. IMPORTANCE Picornaviruses are important animal and human pathogens that protect their genomic RNAs within a protective protein capsid. Upon infection, this genomic RNA must be able to leave the capsid to initiate a new round of infection. We describe here the structure of a unique, massively expanded state of equine rhinitis A virus that provides insight into how this exit might occur.
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14
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Mu Q, Hondow NS, Krzemiński L, Brown AP, Jeuken LJC, Routledge MN. Mechanism of cellular uptake of genotoxic silica nanoparticles. Part Fibre Toxicol 2012; 9:29. [PMID: 22823932 PMCID: PMC3479067 DOI: 10.1186/1743-8977-9-29] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 07/12/2012] [Indexed: 12/30/2022] Open
Abstract
Mechanisms for cellular uptake of nanoparticles have important implications for nanoparticulate drug delivery and toxicity. We have explored the mechanism of uptake of amorphous silica nanoparticles of 14 nm diameter, which agglomerate in culture medium to hydrodynamic diameters around 500 nm. In HT29, HaCat and A549 cells, cytotoxicity was observed at nanoparticle concentrations ≥ 1 μg/ml, but DNA damage was evident at 0.1 μg/ml and above. Transmission electron microscopy (TEM) combined with energy-dispersive X-ray spectroscopy confirmed entry of the silica particles into A549 cells exposed to 10 μg/ml of nanoparticles. The particles were observed in the cytoplasm but not within membrane bound vesicles or in the nucleus. TEM of cells exposed to nanoparticles at 4°C for 30 minutes showed particles enter cells when activity is low, suggesting a passive mode of entry. Plasma lipid membrane models identified physical interactions between the membrane and the silica NPs. Quartz crystal microbalance experiments on tethered bilayer lipid membrane systems show that the nanoparticles strongly bind to lipid membranes, forming an adherent monolayer on the membrane. Leakage assays on large unilamellar vesicles (400 nm diameter) indicate that binding of the silica NPs transiently disrupts the vesicles which rapidly self-seal. We suggest that an adhesive interaction between silica nanoparticles and lipid membranes could cause passive cellular uptake of the particles.
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Affiliation(s)
- Qingshan Mu
- Centre for Molecular NanoScience (CMNS), University of Leeds, Leeds LS2 9JT, UK
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15
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Hondow N, Wang P, Brydson R, Holton MD, Rees P, Summers HD, Brown A. TEM analysis of nanoparticle dispersions with application towards the quantification ofin vitrocellular uptake. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/371/1/012020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Wallace R, Brown AP, Brydson R, Milne SJ, Hondow N, Wang P. Characterisation of ZnO nanoparticle suspensions for toxicological applications. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/371/1/012080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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17
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Lyumkis D, Moeller A, Cheng A, Herold A, Hou E, Irving C, Jacovetty EL, Lau PW, Mulder AM, Pulokas J, Quispe JD, Voss NR, Potter CS, Carragher B. Automation in single-particle electron microscopy connecting the pieces. Methods Enzymol 2010; 483:291-338. [PMID: 20888480 DOI: 10.1016/s0076-6879(10)83015-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Throughout the history of single-particle electron microscopy (EM), automated technologies have seen varying degrees of emphasis and development, usually depending upon the contemporary demands of the field. We are currently faced with increasingly sophisticated devices for specimen preparation, vast increases in the size of collected data sets, comprehensive algorithms for image processing, sophisticated tools for quality assessment, and an influx of interested scientists from outside the field who might lack the skills of experienced microscopists. This situation places automated techniques in high demand. In this chapter, we provide a generic definition of and discuss some of the most important advances in automated approaches to specimen preparation, grid handling, robotic screening, microscope calibrations, data acquisition, image processing, and computational infrastructure. Each section describes the general problem and then provides examples of how that problem has been addressed through automation, highlighting available processing packages, and sometimes describing the particular approach at the National Resource for Automated Molecular Microscopy (NRAMM). We contrast the more familiar manual procedures with automated approaches, emphasizing breakthroughs as well as current limitations. Finally, we speculate on future directions and improvements in automated technologies. Our overall goal is to present automation as more than simply a tool to save time. Rather, we aim to illustrate that automation is a comprehensive and versatile strategy that can deliver biological information on an unprecedented scale beyond the scope available with classical manual approaches.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA
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18
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Shaikh TR, Barnard D, Meng X, Wagenknecht T. Implementation of a flash-photolysis system for time-resolved cryo-electron microscopy. J Struct Biol 2008; 165:184-9. [PMID: 19114106 DOI: 10.1016/j.jsb.2008.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 11/22/2008] [Accepted: 11/24/2008] [Indexed: 10/21/2022]
Abstract
We describe here the implementation of a flash-photolysis system for time-resolved cryo-electron microscopy. A previously designed computer-controlled cryo-plunging apparatus [White, H.D., Thirumurugan, K., Walker, M.L., Trinick, J., 2003. A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray. J. Struct. Biol. 144, 246-252] was used as a hardware platform, onto which a xenon flash lamp and liquid light pipe were mounted. The irradiation initiates a reaction through cleavage of the photolabile blocking group from a biologically active compound. The timespan between flashing and freezing in cryogen is on the order of milliseconds, and defines the fastest observable reaction. Blotting of excess fluid, which takes on the order of 1s, is done before irradiation and thus does not represent a rate-limiting step. A specimen-heating problem, identified by measurements with a thermocouple, was alleviated with the use of thick, aluminum-coated grids.
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Affiliation(s)
- Tanvir R Shaikh
- Resource for the Visualization of Biological Complexity, Wadsworth Center, New York State Department of Health, P.O. Box 509, Empire State Plaza, Albany, NY 12201-0509, USA.
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19
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Plattner H, Hentschel J. Sub-second cellular dynamics: time-resolved electron microscopy and functional correlation. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 255:133-76. [PMID: 17178466 DOI: 10.1016/s0074-7696(06)55003-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Subcellular processes, from molecular events to organellar responses and cell movement, cover a broad scale in time and space. Clearly the extremes, such as ion channel activation are accessible only by electrophysiology, whereas numerous routine methods exist for relatively slow processes. However, many other processes, from a millisecond time scale on, can be "caught" only by methods providing appropriate time resolution. Fast freezing (cryofixation) is the method of choice in that case. In combination with follow-up methodologies appropriate for electron microscopic (EM) analysis, with all its variations, such technologies can also provide high spatial resolution. Such analyses may include, for example, freeze-fracturing for analyzing restructuring of membrane components, scanning EM and other standard EM techniques, as well as analytical EM analyses. The latter encompass energy-dispersive x-ray microanalysis and electron spectroscopic imaging, all applicable, for instance, to the second messenger, calcium. Most importantly, when conducted in parallel, such analyses can provide a structural background to the functional analyses, such as cyclic nucleotide formation or protein de- or rephosphorylation during cell stimulation. In sum, we discuss many examples of how it is practically possible to achieve strict function-structure correlations in the sub-second time range. We complement this review by discussing alternative methods currently available to analyze fast cellular phenomena occurring in the sub-second time range.
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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20
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Frederik P, Sommerdijk N. Spatial and temporal resolution in cryo-electron microscopy—A scope for nano-chemistry. Curr Opin Colloid Interface Sci 2005. [DOI: 10.1016/j.cocis.2005.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Gao H, Valle M, Ehrenberg M, Frank J. Dynamics of EF-G interaction with the ribosome explored by classification of a heterogeneous cryo-EM dataset. J Struct Biol 2005; 147:283-90. [PMID: 15450297 DOI: 10.1016/j.jsb.2004.02.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2004] [Revised: 02/19/2004] [Indexed: 10/26/2022]
Abstract
A method of supervised classification using two available structure templates was applied to investigate the possible heterogeneity existing in a large cryo-EM dataset of an Escherichia coli 70S ribosome-EF-G complex. Two subpopulations showing the ribosome in distinct conformational states, related by a ratchet-like rotation of the 30S subunit with respect to the 50S subunit, were extracted from the original dataset. The possible presence of additional intermediate states is discussed.
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Affiliation(s)
- Haixiao Gao
- Howard Hughes Medical Institute, Health Research, Inc., Empire State Plaza, Albany, NY 12201-0509, USA
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22
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Danino D, Moon KH, Hinshaw JE. Rapid constriction of lipid bilayers by the mechanochemical enzyme dynamin. J Struct Biol 2004; 147:259-67. [PMID: 15450295 DOI: 10.1016/j.jsb.2004.04.005] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 03/02/2004] [Indexed: 11/27/2022]
Abstract
Dynamin, a large GTPase, is located at the necks of clathrin-coated pits where it facilitates the release of coated vesicles from the plasma membrane upon GTP binding, and hydrolysis. Previously, we have shown by negative stain electron microscopy that wild-type dynamin and a dynamin mutant lacking the C-terminal proline-rich domain, DeltaPRD, form protein-lipid tubes that constrict and vesiculate upon addition of GTP. Here, we show by time-resolved cryo-electron microscopy (cryo-EM) that DeltaPRD dynamin in the presence of GTP rapidly constricts the underlying lipid bilayer, and then gradually disassembles from the lipid. In agreement with the negative stain results, the dynamin tubes constrict from 50 to 40 nm, and their helical pitch decreases from approximately 13 to 9.4 nm. However, in contrast to the previous results, examination by cryo-EM shows that the lipid bilayer remains intact and small vesicles or fragments do not form upon GTP binding and hydrolysis. Therefore, the vesicle formation seen by negative stain may be due to the lack of mobility of the dynamin tubes on the grid during the GTP-induced conformational changes. Our results confirm that dynamin is a mechanochemical enzyme and suggest that during endocytosis dynamin is directly responsible for membrane constriction. In the cell, other proteins may enhance the activity of dynamin or the constraints induced by the surrounding coated pit and plasma membrane during constriction may cause the final membrane fission event.
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Affiliation(s)
- Dganit Danino
- Department of Biotechnology and Food Engineering, Technion, Haifa 32000, Israel
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23
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White HD, Thirumurugan K, Walker ML, Trinick J. A second generation apparatus for time-resolved electron cryo-microscopy using stepper motors and electrospray. J Struct Biol 2004; 144:246-52. [PMID: 14643227 DOI: 10.1016/j.jsb.2003.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe here a second generation apparatus for studying transient reaction conformations in macromolecules and their complexes by electron cryo-microscopy. Reactions are trapped by rapid freezing in times ranging from a few milliseconds to tens of seconds after initiation. Blotting of the electron microscope grid and freezing it in liquid ethane uses computer controlled microstepping motors. For the fastest time resolution, a blotted grid containing a thin film of one reactant is sprayed with small droplets containing a second reactant just before freezing. The spray is produced electrically (electrospray), which gives a dense cloud of droplets <1 microm in diameter from the 1-2 microl of solution required per grid. A second method in which two solutions are first mixed by turbulent flow and then blotted prior to freezing is used for reactions with time courses >1s.
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Affiliation(s)
- H D White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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24
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Burgess SA, Walker ML, Sakakibara H, Oiwa K, Knight PJ. The structure of dynein-c by negative stain electron microscopy. J Struct Biol 2004; 146:205-16. [PMID: 15037251 DOI: 10.1016/j.jsb.2003.10.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Revised: 10/01/2003] [Indexed: 12/01/2022]
Abstract
Dynein ATPases contain six concatenated AAA modules within the motor region of their heavy chains. Additional regions of sequence are required to form a functional ATPase, which a previous study suggested forms seven or eight subdomains arranged in either a ring or hollow sphere. A more recent homology model of the six AAA modules suggests that these form a ring. Therefore both the number and arrangement of subdomains remain uncertain. We show two-dimensional projection images of dynein-c in negative stain which reveal new details of its structure. Initial electron cryomicroscopy shows a similar overall morphology. The molecule consists of three domains: stem, head, and stalk. In the absence of nucleotide the head has seven lobes of density forming an asymmetric ring. An eighth lobe protrudes from one side of this heptameric ring and appears to join the elongated cargo-binding stem. The proximal stem is flexible, as is the stalk, suggesting that they act as compliant elements within the motor. A new analysis of pre- and post-power stroke conformations shows the combined effect of their flexibility on the spatial distribution of the microtubule-binding domain and therefore the potential range of power stroke sizes. We present and compare two alternative models of the structure of dynein.
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Affiliation(s)
- S A Burgess
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK.
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25
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Gao H, Spahn CMT, Grassucci RA, Frank J. An assay for local quality in cryo-electron micrographs of single particles. Ultramicroscopy 2002; 93:169-78. [PMID: 12425594 DOI: 10.1016/s0304-3991(02)00157-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High quality of the cryo-electron micrographs is of crucial importance for the success of single particle three-dimensional reconstruction methods. In analyzing some micrographs from cryo-electron microscopy specimens, we found an extraordinary variability, within the same micrograph, in the appearance of particles. We developed a method for analyzing the variability of local image quality, using correspondence analysis of local power spectra. With this technique, we discovered a strong systematic variation of the envelope modulating an otherwise unchanged contrast transfer function. The underlying causes may be uncontrollable effects, such as variations in the thickness of ice, instability of the holey carbon, and charging. The method of assaying, resulting in "local quality maps", may be useful as a general tool for screening micrographs used as input for reconstructions.
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Affiliation(s)
- Haixiao Gao
- Howard Hughes Medical Institute, Wadsworth Center, Albany, New York 12201-0509, USA
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26
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Abstract
Cryo-electron microscopy has furnished direct evidence for conformational changes of the ribosome as it proceeds, in a cyclic manner, through different functional states. Strategies to explore the ribosome dynamics include trapping of particular functionally meaningful states by chemical, genetic, or physical means. The new atomic information obtained by X-ray crystallography should make it possible to track conformational changes observed by cryo-electron microscopy to changes of the underlying structural framework of the ribosome.
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Affiliation(s)
- J Frank
- Howard Hughes Medical Institute, Albany, New York 12201-0509, USA.
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27
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Ruprecht J, Nield J. Determining the structure of biological macromolecules by transmission electron microscopy, single particle analysis and 3D reconstruction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 75:121-64. [PMID: 11376797 DOI: 10.1016/s0079-6107(01)00004-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single particle analysis and 3D reconstruction of molecules imaged by transmission electron microscopy have provided a wealth of medium to low resolution structures of biological molecules and macromolecular complexes, such as the ribosome, viruses, molecular chaperones and photosystem II. In this review, the principles of these techniques are introduced in a non-mathematical way, and single particle analysis is compared to other methods used for structural studies. In particular, the recent X-ray structures of the ribosome and of ribosomal subunits allow a critical comparison of single particle analysis and X-ray crystallography. This has emphasised the rapidity with which single particle analysis can produce medium resolution structures of complexes that are difficult to crystallise. Once crystals are available, X-ray crystallography can produce structures at a much higher resolution. The great similarities now seen between the structures obtained by the two techniques reinforce confidence in the use of single particle analysis and 3D reconstruction, and show that for electron cryo-microscopy structure distortion during sample preparation and imaging has not been a significant problem. The ability to analyse conformational flexibility and the ease with which time-resolved studies can be performed are significant advantages for single particle analysis. Future improvements in single particle analysis and electron microscopy should increase the attainable resolution. Combining single particle analysis of macromolecular complexes and electron tomography of subcellular structures with high-resolution X-ray structures may enable us to realise the ultimate dream of structural biology-a complete description of the macromolecular complexes of the cell in their different functional states.
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Affiliation(s)
- J Ruprecht
- University of Cambridge, Department of Biochemistry, Hopkins Building, CB2 1QW, Cambridge, UK.
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28
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Tao Y, Zhang W. Recent developments in cryo-electron microscopy reconstruction of single particles. Curr Opin Struct Biol 2000; 10:616-22. [PMID: 11042462 DOI: 10.1016/s0959-440x(00)00139-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cryo-electron microscopy and single-particle 3D image reconstruction techniques have been used to examine a broad spectrum of samples ranging from 500 kDa protein complexes to large subcellular organelles. The attainable resolution has improved rapidly over the past few years. Structures of both symmetric and asymmetric assemblies at approximately 7.5 A have been reported. Together with X-ray crystallography, three-dimensional cryo-electron microscopy reconstruction has provided important insights into the function of many biological systems in their native biochemical contexts.
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Affiliation(s)
- Y Tao
- Department of Molecular and Cellular Biology, 7 Divinity Avenue, Harvard University, Cambridge, MA 02138, USA.
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29
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Subramaniam S, Henderson R. Electron crystallography of bacteriorhodopsin with millisecond time resolution. J Struct Biol 1999; 128:19-25. [PMID: 10600554 DOI: 10.1006/jsbi.1999.4178] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The goal of time-resolved crystallographic experiments is to capture dynamic "snapshots" of molecules at different stages of a reaction pathway. In recent work, we have developed approaches to determine determined light-induced conformational changes in the proton pump bacteriorhodopsin by electron crystallographic analysis of two-dimensional protein crystals. For this purpose, crystals of bacteriorhodopsin were deposited on an electron microscopic grid and were plunge-frozen in liquid ethane at a variety of times after illumination. Electron diffraction patterns were recorded either from unilluminated crystals or from crystals frozen as early as 1 ms after illumination and used to construct projection difference Fourier maps at 3.5-A resolution to define light-driven changes in protein conformation. As demonstrated here, the data are of a sufficiently high quality that structure factors obtained from a single electron diffraction pattern of a plunge-frozen bacteriorhodopsin crystal are adequate to obtain an interpretable difference Fourier map. These difference maps report on the nature and extent of light-induced conformational changes in the photocycle and have provided incisive tools for understanding the molecular mechanism of proton transport by bacteriorhodopsin.
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Affiliation(s)
- S Subramaniam
- Laboratory of Biochemistry, National Cancer Institute, Bethesda, Maryland 20892, USA.
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30
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Subramaniam S, Lindahl M, Bullough P, Faruqi AR, Tittor J, Oesterhelt D, Brown L, Lanyi J, Henderson R. Protein conformational changes in the bacteriorhodopsin photocycle. J Mol Biol 1999; 287:145-61. [PMID: 10074413 DOI: 10.1006/jmbi.1999.2589] [Citation(s) in RCA: 216] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report a comprehensive electron crystallographic analysis of conformational changes in the photocycle of wild-type bacteriorhodopsin and in a variety of mutant proteins with kinetic defects in the photocycle. Specific intermediates that accumulate in the late stages of the photocycle of wild-type bacteriorhodopsin, the single mutants D38R, D96N, D96G, T46V, L93A and F219L, and the triple mutant D96G/F171C/F219L were trapped by freezing two-dimensional crystals in liquid ethane at varying times after illumination with a light flash. Electron diffraction patterns recorded from these crystals were used to construct projection difference Fourier maps at 3.5 A resolution to define light-driven changes in protein conformation. Our experiments demonstrate that in wild-type bacteriorhodopsin, a large protein conformational change occurs within approximately 1 ms after illumination. Analysis of structural changes in wild-type and mutant bacteriorhodopsins under conditions when either the M or the N intermediate is preferentially accumulated reveals that there are only small differences in structure between M and N intermediates trapped in the same protein. However, a considerably larger variation is observed when the same optical intermediate is trapped in different mutants. In some of the mutants, a partial conformational change is present even prior to illumination, with additional changes occurring upon illumination. Selected mutations, such as those in the D96G/F171C/F219L triple mutant, can sufficiently destabilize the wild-type structure to generate almost the full extent of the conformational change in the dark, with minimal additional light-induced changes. We conclude that the differences in structural changes observed in mutants that display long-lived M, N or O intermediates are best described as variations of one fundamental type of conformational change, rather than representing structural changes that are unique to the optical intermediate that is accumulated. Our observations thus support a simplified view of the photocycle of wild-type bacteriorhodopsin in which the structures of the initial state and the early intermediates (K, L and M1) are well approximated by one protein conformation, while the structures of the later intermediates (M2, N and O) are well approximated by the other protein conformation. We propose that in wild-type bacteriorhodopsin and in most mutants, this conformational change between the M1 and M2 states is likely to make an important contribution towards efficiently switching proton accessibility of the Schiff base from the extracellular side to the cytoplasmic side of the membrane.
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Affiliation(s)
- S Subramaniam
- MRC Laboratory for Molecular Biology, Cambridge, England.
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31
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Walker M, Zhang XZ, Jiang W, Trinick J, White HD. Observation of transient disorder during myosin subfragment-1 binding to actin by stopped-flow fluorescence and millisecond time resolution electron cryomicroscopy: evidence that the start of the crossbridge power stroke in muscle has variable geometry. Proc Natl Acad Sci U S A 1999; 96:465-70. [PMID: 9892656 PMCID: PMC15159 DOI: 10.1073/pnas.96.2.465] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/1998] [Accepted: 11/19/1998] [Indexed: 11/18/2022] Open
Abstract
The mechanism of binding of myosin subfragment-1 (S1) to actin in the absence of nucleotides was studied by a combination of stopped-flow fluorescence and ms time resolution electron microscopy. The fluorescence data were obtained by using pyrene-labeled actin and exhibit a lag phase. This demonstrates the presence of a transient intermediate after the collision complex and before the formation of the stable "rigor" complex. The transient intermediate predominates 2-15 ms after mixing, whereas the rigor complex predominates at time >50 ms. Electron microscopy of acto-S1 frozen 10 ms after mixing revealed disordered binding. Acto-S1 frozen at 50 ms or longer showed the "arrowhead" appearance characteristic of rigor. The most likely explanation of the disorder of the transient intermediate is that the binding is through one or more flexible loops on the surfaces of the proteins. The transition from disordered to ordered binding is likely to be part of the force-generating step in muscle.
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Affiliation(s)
- M Walker
- School of Biomedical Sciences, Leeds University, Leeds LS2 9JT, United Kingdom
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