1
|
Egelman EH. Helical reconstruction, again. Curr Opin Struct Biol 2024; 85:102788. [PMID: 38401399 PMCID: PMC10923117 DOI: 10.1016/j.sbi.2024.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/26/2024]
Abstract
Many protein and nucleoprotein complexes exist as helical polymers. As a result, much effort has been invested in developing methods for using electron microscopy to determine the structure of these assemblies. With the revolution in cryo-electron microscopy (cryo-EM), it has now become routine to reach a near-atomic level of resolution for these structures, and it is the exception when this is not possible. However, the greatest challenge is frequently determining the correct symmetry. This review focuses on why this can be so difficult and the current absence of a better approach than trial-and-error.
Collapse
Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22903, USA.
| |
Collapse
|
2
|
Dutka P, Metskas LA, Hurt RC, Salahshoor H, Wang TY, Malounda D, Lu GJ, Chou TF, Shapiro MG, Jensen GJ. Structure of Anabaena flos-aquae gas vesicles revealed by cryo-ET. Structure 2023; 31:518-528.e6. [PMID: 37040766 PMCID: PMC10185304 DOI: 10.1016/j.str.2023.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 03/01/2023] [Accepted: 03/16/2023] [Indexed: 04/13/2023]
Abstract
Gas vesicles (GVs) are gas-filled protein nanostructures employed by several species of bacteria and archaea as flotation devices to enable access to optimal light and nutrients. The unique physical properties of GVs have led to their use as genetically encodable contrast agents for ultrasound and MRI. Currently, however, the structure and assembly mechanism of GVs remain unknown. Here we employ cryoelectron tomography to reveal how the GV shell is formed by a helical filament of highly conserved GvpA subunits. This filament changes polarity at the center of the GV cylinder, a site that may act as an elongation center. Subtomogram averaging reveals a corrugated pattern of the shell arising from polymerization of GvpA into a β sheet. The accessory protein GvpC forms a helical cage around the GvpA shell, providing structural reinforcement. Together, our results help explain the remarkable mechanical properties of GVs and their ability to adopt different diameters and shapes.
Collapse
Affiliation(s)
- Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Robert C Hurt
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hossein Salahshoor
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ting-Yu Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - George J Lu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; College of Physical and Mathematical Sciences, Brigham Young University, Provo, UT 84602, USA.
| |
Collapse
|
3
|
Cryo-electron tomography reveals structural insights into the membrane remodeling mode of dynamin-like EHD filaments. Nat Commun 2022; 13:7641. [PMID: 36496453 PMCID: PMC9741607 DOI: 10.1038/s41467-022-35164-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Eps15-homology domain containing proteins (EHDs) are eukaryotic, dynamin-related ATPases involved in cellular membrane trafficking. They oligomerize on membranes into filaments that induce membrane tubulation. While EHD crystal structures in open and closed conformations were previously reported, little structural information is available for the membrane-bound oligomeric form. Consequently, mechanistic insights into the membrane remodeling mechanism have remained sparse. Here, by using cryo-electron tomography and subtomogram averaging, we determined structures of nucleotide-bound EHD4 filaments on membrane tubes of various diameters at an average resolution of 7.6 Å. Assembly of EHD4 is mediated via interfaces in the G-domain and the helical domain. The oligomerized EHD4 structure resembles the closed conformation, where the tips of the helical domains protrude into the membrane. The variation in filament geometry and tube radius suggests a spontaneous filament curvature of approximately 1/70 nm-1. Combining the available structural and functional data, we suggest a model for EHD-mediated membrane remodeling.
Collapse
|
4
|
Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
Collapse
Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| |
Collapse
|
5
|
Zhang X. Python-based Helix Indexer: A graphical user interface program for finding symmetry of helical assembly through Fourier-Bessel indexing of electron microscopic data. Protein Sci 2022; 31:107-117. [PMID: 34529294 PMCID: PMC8740834 DOI: 10.1002/pro.4186] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 01/03/2023]
Abstract
Many macromolecules form helical assemblies to carry out their functions. Helical reconstruction from electron microscopic images is a powerful approach for solving high-resolution structures of such assemblies. Determination of the symmetry parameters of the helical assemblies is a prerequisite step in helical reconstruction. The most widely used method for deducing the symmetry is through Fourier-Bessel indexing the diffraction pattern of the helical assemblies. This method, however, often leads to incorrect solutions, due to intrinsic ambiguities in indexing helical diffraction patterns. Here, we present Python-based Helix Indexer (PyHI), which provides a graphical user interface (GUI) to guide the users through the process of symmetry determination. Diffraction patterns can be read into the program directly or calculated on the fly from two-dimensional class averages of helical assemblies. PyHI allows deducing the Bessel orders of diffraction peaks by using both the amplitudes and phases of the diffraction data. Based on the Bessel orders of two unit vectors, the Fourier space lattice is constructed with minimal user inputs. The program then uses a refinement algorithm to optimize the Fourier space lattice, and subsequently generate the helical assembly in real space. The program provides both a publication-quality graphic representation of the helical assembly and the symmetry parameters required for subsequent helical reconstruction steps.
Collapse
Affiliation(s)
- Xuewu Zhang
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTexas,Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexas
| |
Collapse
|
6
|
Egelman EH, Wang F. Cryo-EM is a powerful tool, but helical applications can have pitfalls. SOFT MATTER 2021; 17:3291-3293. [PMID: 33729271 PMCID: PMC8086904 DOI: 10.1039/d1sm00282a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In structural biology, cryo-electron microscopy (cryo-EM) has emerged as the main technique for determining the atomic structures of macromolecular complexes. This has largely been due to the introduction of direct electron detectors, which have allowed for routinely reaching a near-atomic resolution when imaging such complexes. In chemistry and materials science, the applications of cryo-EM have been much more limited. A recent paper (Z. Li et al., Chemically Controlled Helical Polymorphism In Protein Tubes By Selective Modulation Of Supramolecular Interactions, J. Am. Chem. Soc. 2019, 141, 19448-19457) has used low resolution cryo-EM to analyze polymorphic helical tubes formed by a tetrameric protein, and has made detailed models for the interfaces between the tetramers in these assemblies. Due to intrinsic ambiguities in determining the correct helical symmetry, we show that many of the models are likely to be wrong. This note highlights both the enormous potential for using cryo-EM, and also the pitfalls possible for helical assemblies when a near-atomic level of resolution is not reached.
Collapse
Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | | |
Collapse
|
7
|
Penczek PA. Reliable cryo-EM resolution estimation with modified Fourier shell correlation. IUCRJ 2020; 7:995-1008. [PMID: 33209314 PMCID: PMC7642792 DOI: 10.1107/s2052252520011574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
A modified Fourier shell correlation (mFSC) methodology is introduced that is aimed at addressing two fundamental problems that mar the use of the FSC: the strong influence of mask-induced artifacts on resolution estimation and the lack of assessment of FSC uncertainties stemming from the inability to determine the associated number of degrees of freedom. It is shown that by simply changing the order of the steps in which the FSC is computed, the correlations induced by masking of the input data can be eliminated. In addition, to further reduce artifacts, a smooth Gaussian window function is used to outline the regions of reciprocal space within which the mFSC is computed. Next, it is shown that the number of degrees of freedom (ndf) of the system is approximated well by combining the ndf associated with the Gaussian window in reciprocal space with further reduction of the ndf owing to the use of the mask in real space. It is demonstrated through the application of the mFSC to both single-particle and helical structures that the mFSC yields reliable, mask-induced artifact-free results as a result of the introduced modifications. Since the adverse effect of the mask is eliminated, it also becomes possible to compute robust local resolutions both per voxel of a 3D map as well as, in a newly developed approach, per functional subunit, segment or even larger secondary element of the studied complex.
Collapse
Affiliation(s)
- Pawel A. Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas – Houston Medical Center, 6431 Fannin Street, Houston, TX 77030, USA
| |
Collapse
|
8
|
Craig L, Forest KT, Maier B. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol 2020; 17:429-440. [PMID: 30988511 DOI: 10.1038/s41579-019-0195-4] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The surfaces of many bacteria are decorated with long, exquisitely thin appendages called type IV pili (T4P), dynamic filaments that are rapidly polymerized and depolymerized from a pool of pilin subunits. Cycles of pilus extension, binding and retraction enable T4P to perform a phenomenally diverse array of functions, including twitching motility, DNA uptake and microcolony formation. On the basis of recent developments, a comprehensive understanding is emerging of the molecular architecture of the T4P machinery and the filament it builds, providing mechanistic insights into the assembly and retraction processes. Combined microbiological and biophysical approaches have revealed how T4P dynamics influence self-organization of bacteria, how bacteria respond to external stimuli to regulate T4P activity for directed movement, and the role of T4P retraction in surface sensing. In this Review, we discuss the T4P machine architecture and filament structure and present current molecular models for T4P dynamics, with a particular focus on recent insights into T4P retraction. We also discuss the functional consequences of T4P dynamics, which have important implications for bacterial lifestyle and pathogenesis.
Collapse
Affiliation(s)
- Lisa Craig
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Berenike Maier
- Institute for Biological Physics, University of Cologne, Köln, Germany.
| |
Collapse
|
9
|
Hughes SA, Wang F, Wang S, Kreutzberger MAB, Osinski T, Orlova A, Wall JS, Zuo X, Egelman EH, Conticello VP. Ambidextrous helical nanotubes from self-assembly of designed helical hairpin motifs. Proc Natl Acad Sci U S A 2019; 116:14456-14464. [PMID: 31262809 PMCID: PMC6642399 DOI: 10.1073/pnas.1903910116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tandem repeat proteins exhibit native designability and represent potentially useful scaffolds for the construction of synthetic biomimetic assemblies. We have designed 2 synthetic peptides, HEAT_R1 and LRV_M3Δ1, based on the consensus sequences of single repeats of thermophilic HEAT (PBS_HEAT) and Leucine-Rich Variant (LRV) structural motifs, respectively. Self-assembly of the peptides afforded high-aspect ratio helical nanotubes. Cryo-electron microscopy with direct electron detection was employed to analyze the structures of the solvated filaments. The 3D reconstructions from the cryo-EM maps led to atomic models for the HEAT_R1 and LRV_M3Δ1 filaments at resolutions of 6.0 and 4.4 Å, respectively. Surprisingly, despite sequence similarity at the lateral packing interface, HEAT_R1 and LRV_M3Δ1 filaments adopt the opposite helical hand and differ significantly in helical geometry, while retaining a local conformation similar to previously characterized repeat proteins of the same class. The differences in the 2 filaments could be rationalized on the basis of differences in cohesive interactions at the lateral and axial interfaces. These structural data reinforce previous observations regarding the structural plasticity of helical protein assemblies and the need for high-resolution structural analysis. Despite these observations, the native designability of tandem repeat proteins offers the opportunity to engineer novel helical nanotubes. Moreover, the resultant nanotubes have independently addressable and chemically distinguishable interior and exterior surfaces that would facilitate applications in selective recognition, transport, and release.
Collapse
Affiliation(s)
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Shengyuan Wang
- Department of Chemistry, Emory University, Atlanta, GA 30322
| | - Mark A B Kreutzberger
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Tomasz Osinski
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Albina Orlova
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY 11973
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Argonne, IL 60439
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908
| | | |
Collapse
|
10
|
TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 2017; 550:265-269. [PMID: 28976958 PMCID: PMC5640987 DOI: 10.1038/nature24021] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/21/2017] [Indexed: 12/17/2022]
Abstract
The Target of Rapamycin (TOR) is a eukaryotic serine/threonine protein kinase that functions in two distinct complexes, TORC1 and TORC2, to regulate growth and metabolism1,2. GTPases, responding to signals generated by abiotic stressors, nutrients, and, in metazoans, growth factors, play an important3, but poorly understood role in TORC1 regulation. Here, we report that, in budding yeast, glucose withdrawal, which leads to an acute loss of TORC1 kinase activity4, triggers a similarly rapid Rag GTPase-dependent redistribution of TORC1 from being semi-uniform around the vacuolar membrane to a single, vacuole-associated cylindrical structure visible by super-resolution optical microscopy. 3D reconstructions of cryo-electron micrograph images of these purified cylinders demonstrate that TORC1 oligomerizes into a higher-level hollow helical assembly which we name a TOROID (TORC1 Organised in Inhibited Domain). Fitting of the recently described mammalian TORC1 structure into our helical map revealed that oligomerisation leads to steric occlusion of the active site. Guided by the implications from our reconstruction, we present a TOR1 allele that prevents both TOROID formation and TORC1 inactivation in response to glucose withdrawal demonstrating that oligomerisation is necessary for TORC1 inactivation. Our results reveal a novel mechanism by which Rag-GTPases regulate TORC1 activity and suggest that the reversible assembly/disassembly of higher-level structure may be a new paradigm for the regulation of protein kinases.
Collapse
|
11
|
Fibre diffraction studies of biological macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:43-87. [DOI: 10.1016/j.pbiomolbio.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
|
12
|
Bacterial Filamentous Appendages Investigated by Solid-State NMR Spectroscopy. Methods Mol Biol 2017. [PMID: 28667627 DOI: 10.1007/978-1-4939-7033-9_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The assembly of filamentous appendages at the surface of bacteria is essential in many infection mechanisms. The extent of mechanical, dynamical, and functional properties of such appendages is very diverse, ranging from a structural scaffold of the pathogen-host cell interaction to cell motility, surface adhesion, or the export of virulence effectors. In particular, the architectures of several bacterial secretion systems have revealed the presence of filamentous architectures, known as pili, fimbriae, andneedles. At the macroscopic level, filamentous bacterial appendages appear as thin extracellular filaments of several nanometers in diameter and up to several microns in length. The structural characterization of these appendages at atomic-scale resolution represents an extremely challenging task because of their inherent noncrystallinity and very poor solubility. Here, we describe protocols based on recent advances in solid-state NMR spectroscopy to investigate the secondary structure, subunit-subunit protein interactions, symmetry parameters, and atomic architecture of bacterial filaments.
Collapse
|
13
|
Liu D, Liu X, Shang Z, Sindelar CV. Structural basis of cooperativity in kinesin revealed by 3D reconstruction of a two-head-bound state on microtubules. eLife 2017; 6. [PMID: 28504639 PMCID: PMC5459574 DOI: 10.7554/elife.24490] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/09/2017] [Indexed: 12/26/2022] Open
Abstract
The detailed basis of walking by dimeric molecules of kinesin along microtubules has remained unclear, partly because available structural methods have been unable to capture microtubule-bound intermediates of this process. Utilizing novel electron cryomicroscopy methods, we solved structures of microtubule-attached, dimeric kinesin bound to an ATP analog. We find that under these conditions, the kinesin dimer can attach to the microtubule with either one or two motor domains, and we present sub-nanometer resolution reconstructions of both states. The former structure reveals a novel kinesin conformation that revises the current understanding of how ATP binding is coupled to forward stepping of the motor. The latter structure indicates how tension between the two motor domains keeps their cycles out of phase in order to stimulate directional motility. The methods presented here pave the way for future structural studies of a variety of challenging macromolecules that bind to microtubules and other filaments.
Collapse
Affiliation(s)
- Daifei Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Xueqi Liu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Zhiguo Shang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| | - Charles V Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States
| |
Collapse
|
14
|
Grintsevich EE. Remodeling of Actin Filaments by Drebrin A and Its Implications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1006:61-82. [DOI: 10.1007/978-4-431-56550-5_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
15
|
Abstract
AbstractThere has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing. In spite of the great strides that have been made, quantitative analysis shows that there are still significant gains to be made provided that the problems associated with image degradation can be solved, possibly by minimising beam-induced specimen movement and charge build up during imaging. If this can be achieved, it should be possible to obtain near atomic resolution structures of smaller single particles, using fewer images and resolving more conformational states than at present, thus realising the full potential of the method. The recent popularity of cryoEM for molecular structure determination also highlights the need for lower cost microscopes, so we encourage development of an inexpensive, 100 keV electron cryomicroscope with a high-brightness field emission gun to make the method accessible to individual groups or institutions that cannot afford the investment and running costs of a state-of-the-art 300 keV installation. A key requisite for successful high-resolution structure determination by cryoEM includes interpretation of images and optimising the biochemistry and grid preparation to obtain nicely distributed macromolecules of interest. We thus include in this review a gallery of cryoEM micrographs that shows illustrative examples of single particle images of large and small macromolecular complexes.
Collapse
|
16
|
Coudray N, Lasala R, Zhang Z, Clark KM, Dumont ME, Stokes DL. Deducing the symmetry of helical assemblies: Applications to membrane proteins. J Struct Biol 2016; 195:167-178. [PMID: 27255388 DOI: 10.1016/j.jsb.2016.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/30/2022]
Abstract
Helical reconstruction represents a convenient and powerful approach for structure determination of macromolecules that assemble into helical arrays. In the case of membrane proteins, formation of tubular crystals with helical symmetry represents an attractive alternative, especially when their small size precludes the use of single-particle analysis. An essential first step for helical reconstruction is to characterize the helical symmetry. This process is often daunting, due to the complexity of helical diffraction and to the low signal-to-noise ratio in images of individual assemblies. Furthermore, the large diameters of the tubular crystals produced by membrane proteins exacerbates the innate ambiguities that, if not resolved, will produce incorrect structures. In this report, we describe a set of tools that can be used to eliminate ambiguities and to validate the choice of symmetry. The first approach increases the signal-to-noise ratio along layer lines by incoherently summing data from multiple helical assemblies, thus producing several candidate indexing schemes. The second approach compares the layer lines from images with those from synthetic models built with the various candidate schemes. The third approach uses unit cell dimensions measured from collapsed tubes to distinguish between these candidate schemes. These approaches are illustrated with tubular crystals from a boron transporter from yeast, Bor1p, and a β-barrel channel from the outer membrane of E. coli, OmpF.
Collapse
Affiliation(s)
- Nicolas Coudray
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Ralph Lasala
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Zhening Zhang
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Kathy M Clark
- Department of Pediatrics and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14652, United States
| | - Mark E Dumont
- Department of Pediatrics and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14652, United States
| | - David L Stokes
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| |
Collapse
|
17
|
Thompson RF, Walker M, Siebert CA, Muench SP, Ranson NA. An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology. Methods 2016; 100:3-15. [PMID: 26931652 PMCID: PMC4854231 DOI: 10.1016/j.ymeth.2016.02.017] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/11/2016] [Accepted: 02/25/2016] [Indexed: 11/22/2022] Open
Abstract
Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150 kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a ‘resolution revolution’, owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.
Collapse
Affiliation(s)
- Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Matt Walker
- MLW Consulting, 11 Race Hill, Launceston, Cornwall PL15 9BB, United Kingdom
| | - C Alistair Siebert
- Electron Bio-Imaging Centre, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Stephen P Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| |
Collapse
|
18
|
Fromm S, Sachse C. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction. Methods Enzymol 2016; 579:307-28. [DOI: 10.1016/bs.mie.2016.05.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
19
|
Subramaniam S, Kühlbrandt W, Henderson R. CryoEM at IUCrJ: a new era. IUCRJ 2016; 3:3-7. [PMID: 26870375 PMCID: PMC4704073 DOI: 10.1107/s2052252515023738] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 05/22/2023]
Abstract
In this overview, we briefly outline recent advances in electron cryomicroscopy (cryoEM) and explain why the journal IUCrJ, published by the International Union of Crystallography, could provide a natural home for publications covering many present and future developments in the cryoEM field.
Collapse
Affiliation(s)
- Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, 60538, Germany
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| |
Collapse
|
20
|
Yang S, Woodhead JL, Zhao FQ, Sulbarán G, Craig R. An approach to improve the resolution of helical filaments with a large axial rise and flexible subunits. J Struct Biol 2015; 193:45-54. [PMID: 26592473 DOI: 10.1016/j.jsb.2015.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/12/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022]
Abstract
Single particle analysis is widely used for three-dimensional reconstruction of helical filaments. Near-atomic resolution has been obtained for several well-ordered filaments. However, it is still a challenge to achieve high resolution for filaments with flexible subunits and a large axial rise per subunit relative to pixel size. Here, we describe an approach that improves the resolution in such cases. In filaments with a large axial rise, many segments must be shifted a long distance along the filament axis to match with a reference projection, potentially causing loss of alignment accuracy and hence resolution. In our study of myosin filaments, we overcame this problem by pre-determining the axial positions of myosin head crowns within segments to decrease the alignment error. In addition, homogeneous, well-ordered segments were selected from the raw data set by checking the assigned azimuthal rotation angle of segments in each filament against those expected for perfect helical symmetry. These procedures improved the resolution of the filament reconstruction from 30 Å to 13 Å. This approach could be useful in other helical filaments with a large axial rise and/or flexible subunits.
Collapse
Affiliation(s)
- Shixin Yang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - John L Woodhead
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Fa-Qing Zhao
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Guidenn Sulbarán
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Roger Craig
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| |
Collapse
|
21
|
Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W. EMDataBank unified data resource for 3DEM. Nucleic Acids Res 2015; 44:D396-403. [PMID: 26578576 PMCID: PMC4702818 DOI: 10.1093/nar/gkv1126] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/10/2023] Open
Abstract
Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.
Collapse
Affiliation(s)
- Catherine L Lawson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Corey Hryc
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Eduardo Sanz Garcia
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Ingvar Lagerstedt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Grigore Pintilie
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| | - Raul Sala
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - John D Westbrook
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wah Chiu
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
| |
Collapse
|
22
|
Valpuesta JM, Carrascosa JL. Electron microscopy: the coming of age of a structural biology technique. Arch Biochem Biophys 2015; 581:1-2. [DOI: 10.1016/j.abb.2015.06.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|