1
|
Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf) 2015; 65:43-56. [PMID: 26671944 DOI: 10.1093/jmicro/dfv369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/06/2015] [Indexed: 11/12/2022] Open
Abstract
Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.
Collapse
Affiliation(s)
- Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Anchi Cheng
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| |
Collapse
|
2
|
Semiautomatic, high-throughput, high-resolution protocol for three-dimensional reconstruction of single particles in electron microscopy. Methods Mol Biol 2013; 950:171-93. [PMID: 23086876 DOI: 10.1007/978-1-62703-137-0_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
In this chapter we describe the steps needed for reconstructing the three-dimensional structure of a macromolecular complex starting from its projections collected in electron micrographs. The concepts are shown through the use of Xmipp 3.0, a software suite specifically designed for the image processing of biological structures imaged with electron or X-ray microscopy. We illustrate the image processing workflow by applying it to the images of Bovine Papilloma virus published in Wolf et al. (Proc Natl Acad Sci USA 107:6298-6303, 2010). We show that in the case of high-quality, homogeneous datasets with a priori knowledge about the initial volume, we can have a high-resolution 3D reconstruction in less than 1 day using a computer cluster with only 32 processors.
Collapse
|
3
|
Vargas J, Otón J, Marabini R, Jonic S, de la Rosa-Trevín JM, Carazo JM, Sorzano COS. FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. J Struct Biol 2012; 181:136-48. [PMID: 23261401 DOI: 10.1016/j.jsb.2012.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 12/07/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Abstract
In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].
Collapse
Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco, Madrid, Spain.
| | | | | | | | | | | | | |
Collapse
|
4
|
Tatischeff I, Larquet E, Falcón-Pérez JM, Turpin PY, Kruglik SG. Fast characterisation of cell-derived extracellular vesicles by nanoparticles tracking analysis, cryo-electron microscopy, and Raman tweezers microspectroscopy. J Extracell Vesicles 2012; 1:19179. [PMID: 24009887 PMCID: PMC3760651 DOI: 10.3402/jev.v1i0.19179] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/21/2012] [Accepted: 09/23/2012] [Indexed: 12/12/2022] Open
Abstract
The joint use of 3 complementary techniques, namely, nanoparticle tracking analysis (NTA), cryo-electron microscopy (Cryo-EM) and Raman tweezers microspectroscopy (RTM), is proposed for a rapid characterisation of extracellular vesicles (EVs) of various origins. NTA is valuable for studying the size distribution and concentration, Cryo-EM is outstanding for the morphological characterisation, including observation of vesicle heterogeneity, while RTM provides the global chemical composition without using any exogenous label. The capabilities of this approach are evaluated on the example of cell-derived vesicles of Dictyostelium discoideum, a convenient general model for eukaryotic EVs. At least 2 separate species differing in chemical composition (relative amounts of DNA, lipids and proteins, presence of carotenoids) were found for each of the 2 physiological states of this non-pathogenic microorganism, that is, cell growth and starvation-induced aggregation. These findings demonstrate the specific potency of RTM. In addition, the first Raman spectra of human urinary exosomes are reported, presumably constituting the primary step towards Raman characterisation of EVs for the purpose of human diseases diagnoses.
Collapse
Affiliation(s)
- Irène Tatischeff
- Laboratoire Jean Perrin, FRE 3231 CNRS, Université Pierre et Marie Curie, Paris, France
| | | | | | | | | |
Collapse
|
5
|
Vulović M, Franken E, Ravelli RB, van Vliet LJ, Rieger B. Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy. Ultramicroscopy 2012. [DOI: 10.1016/j.ultramic.2012.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
6
|
Processing of Transmission Electron Microscopy Images for Single-Particle Analysis of Macromolecular Complexes. Methods Cell Biol 2012. [DOI: 10.1016/b978-0-12-405914-6.00016-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
|
7
|
Karimi Nejadasl F, Karuppasamy M, Koster AJ, Ravelli RBG. Defocus estimation from stroboscopic cryo-electron microscopy data. Ultramicroscopy 2011; 111:1592-8. [PMID: 21945999 DOI: 10.1016/j.ultramic.2011.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 06/09/2011] [Accepted: 08/18/2011] [Indexed: 11/25/2022]
Abstract
Defocus estimation is an important step for improving the resolution of single particle reconstructions. It can be troublesome to estimate the defocus from low-dose cryo-electron microscopy (cryo-EM) data, particularly if there is not sufficient contrast present in the Fourier transform of the micrograph. Most existing approaches estimate the defocus from the presence of Thon rings within the power spectrum, employing image enhancement techniques to highlight these rings. In this paper, an approach to estimating the defocus from a stroboscopic image series is described. The image series is used to obtain two statistical metrics: figure of merit (FOM) and Q-factor. These metrics have been used to estimate the defoci from low-dose stroboscopic cryo-EM data consisting of a variable number of images.
Collapse
Affiliation(s)
- Fatemeh Karimi Nejadasl
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | | | | | | |
Collapse
|
8
|
Sorzano COS, Otero A, Olmos EM, Carazo JM. Error analysis in the determination of the electron microscopical contrast transfer function parameters from experimental power Spectra. BMC STRUCTURAL BIOLOGY 2009; 9:18. [PMID: 19321015 PMCID: PMC2683171 DOI: 10.1186/1472-6807-9-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 03/26/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The transmission electron microscope is used to acquire structural information of macromolecular complexes. However, as any other imaging device, it introduces optical aberrations that must be corrected if high-resolution structural information is to be obtained. The set of all aberrations are usually modeled in Fourier space by the so-called Contrast Transfer Function (CTF). Before correcting for the CTF, we must first estimate it from the electron micrographs. This is usually done by estimating a number of parameters specifying a theoretical model of the CTF. This estimation is performed by minimizing some error measure between the theoretical Power Spectrum Density (PSD) and the experimentally observed PSD. The high noise present in the micrographs, the possible local minima of the error function for estimating the CTF parameters, and the cross-talking between CTF parameters may cause errors in the estimated CTF parameters. RESULTS In this paper, we explore the effect of these estimation errors on the theoretical CTF. For the CTF model proposed in 1 we show which are the most sensitive CTF parameters as well as the most sensitive background parameters. Moreover, we provide a methodology to reveal the internal structure of the CTF model (which parameters influence in which parameters) and to estimate the accuracy of each model parameter. Finally, we explore the effect of the variability in the detection of the CTF for CTF phase and amplitude correction. CONCLUSION We show that the estimation errors for the CTF detection methodology proposed in 1 does not show a significant deterioration of the CTF correction capabilities of subsequent algorithms. All together, the methodology described in this paper constitutes a powerful tool for the quantitative analysis of CTF models that can be applied to other models different from the one analyzed here.
Collapse
Affiliation(s)
- Carlos Oscar S Sorzano
- Escuela Politécnica Superior, Universidad San Pablo-CEU, Campus Urb, Montepríncipe s/n, E-28668 Boadilla del Monte, Madrid, Spain.
| | | | | | | |
Collapse
|
9
|
JONIĆ S, SORZANO C, BOISSET N. Comparison of single-particle analysis and electron tomography approaches: an overview. J Microsc 2008; 232:562-79. [DOI: 10.1111/j.1365-2818.2008.02119.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
10
|
High-resolution single-particle 3D analysis on GroEL prepared by cryo-negative staining. Micron 2008; 39:934-43. [DOI: 10.1016/j.micron.2007.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 11/05/2007] [Accepted: 11/06/2007] [Indexed: 11/23/2022]
|
11
|
Scheres SHW, Núñez-Ramírez R, Sorzano COS, Carazo JM, Marabini R. Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc 2008; 3:977-90. [PMID: 18536645 DOI: 10.1038/nprot.2008.62] [Citation(s) in RCA: 291] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.
Collapse
Affiliation(s)
- Sjors H W Scheres
- Centro Nacional de Biotecnología CSIC, Unidad de Biocomputación, Cantoblanco, 28049 Madrid, Spain
| | | | | | | | | |
Collapse
|
12
|
Vanoni MA, Curti B. Structure-function studies of glutamate synthases: a class of self-regulated iron-sulfur flavoenzymes essential for nitrogen assimilation. IUBMB Life 2008; 60:287-300. [PMID: 18421771 DOI: 10.1002/iub.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Glutamate synthases play with glutamine synthetase an essential role in nitrogen assimilation processes in microorganisms, plants, and lower animals by catalyzing the net synthesis of one molecule of L-glutamate from L-glutamine and 2-oxoglutarate. They exhibit a modular architecture with a common subunit or region, which is responsible for the L-glutamine-dependent glutamate synthesis from 2-oxoglutarate. Here, a PurF- (Type II- or Ntn-) type amidotransferase domain is coupled to the synthase domain, a (beta/alpha)8 barrel containing FMN and one [3Fe-4S]0,+1 cluster, through a approximately 30 angstroms-long intramolecular tunnel for the transfer of ammonia between the sites. In bacterial and eukaryotic GltS, reducing equivalents are provided by reduced pyridine nucleotides thanks to the stable association with a second subunit or region, which acts as a FAD-dependent NAD(P)H oxidoreductase and is responsible for the formation of the two low potential [4Fe-4S]+1,+2 clusters of the enzyme. In photosynthetic cells, reduced ferredoxin is the physiological reductant. This review focus on the mechanism of cross-activation of the synthase and glutaminase reactions in response to the bound substrates and the redox state of the enzyme cofactors, as well as on recent information on the structure of the alphabeta protomer of the NADPH-dependent enzyme, which sheds light on the intramolecular electron transfer pathway between the flavin cofactors.
Collapse
Affiliation(s)
- Maria Antonietta Vanoni
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano, Via Celoria 26, Milano, Italy.
| | | |
Collapse
|
13
|
Cottevieille M, Larquet E, Jonic S, Petoukhov MV, Caprini G, Paravisi S, Svergun DI, Vanoni MA, Boisset N. The subnanometer resolution structure of the glutamate synthase 1.2-MDa hexamer by cryoelectron microscopy and its oligomerization behavior in solution: functional implications. J Biol Chem 2008; 283:8237-49. [PMID: 18199747 DOI: 10.1074/jbc.m708529200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The three-dimensional structure of the hexameric (alphabeta)(6) 1.2-MDa complex formed by glutamate synthase has been determined at subnanometric resolution by combining cryoelectron microscopy, small angle x-ray scattering, and molecular modeling, providing for the first time a molecular model of this complex iron-sulfur flavoprotein. In the hexameric species, interprotomeric alpha-alpha and alpha-beta contacts are mediated by the C-terminal domain of the alpha subunit, which is based on a beta helical fold so far unique to glutamate synthases. The alphabeta protomer extracted from the hexameric model is fully consistent with it being the minimal catalytically active form of the enzyme. The structure clarifies the electron transfer pathway from the FAD cofactor on the beta subunit, to the FMN on the alpha subunit, through the low potential [4Fe-4S](1+/2+) centers on the beta subunit and the [3Fe-4S](0/1+) cluster on the alpha subunit. The (alphabeta)(6) hexamer exhibits a concentration-dependent equilibrium with alphabeta monomers and (alphabeta)(2) dimers, in solution, the hexamer being destabilized by high ionic strength and, to a lower extent, by the reaction product NADP(+). Hexamerization seems to decrease the catalytic efficiency of the alphabeta protomer only 3-fold by increasing the K(m) values measured for l-Gln and 2-OG. However, it cannot be ruled out that the (alphabeta)(6) hexamer acts as a scaffold for the assembly of multienzymatic complexes of nitrogen metabolism or that it provides a means to regulate the activity of the enzyme through an as yet unknown ligand.
Collapse
Affiliation(s)
- Magali Cottevieille
- Département de Biologie Structurale, IMPMC-UMR 7590, CNRS, Universités Paris 6 et Paris 7, IPGP, Paris, France
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Sorzano COS, Jonic S, Núñez-Ramírez R, Boisset N, Carazo JM. Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J Struct Biol 2007; 160:249-62. [PMID: 17911028 DOI: 10.1016/j.jsb.2007.08.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 08/18/2007] [Accepted: 08/22/2007] [Indexed: 01/24/2023]
Abstract
Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called contrast transfer function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.
Collapse
Affiliation(s)
- C O S Sorzano
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain.
| | | | | | | | | |
Collapse
|
15
|
Attia J, Rémita S, Jonic S, Lacaze E, Fauré MC, Larquet E, Goldmann M. Radiation-induced synthesis and cryo-TEM characterization of silver nanoshells on linoleate spherical micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:9523-6. [PMID: 17696459 DOI: 10.1021/la701366f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We combine the self-assembly properties of amphiphilic molecules with the radiolysis method to produce specific sizes and shapes of metallic nano-objects. Radiolysis is used to synthesize core--shell structures consisting of nanometric linoleate spherical micelles as the core and silver as the shell. The validity of the technique is asserted by cryoelectron microscopy, which is an adequate technique for low density contrasts and core--shell structures. The shells are found to be homogeneous with a size of a few nanometers. Images are used to bring forward the hypothesis of the fabrication process.
Collapse
Affiliation(s)
- J Attia
- Institut des Nanosciences de Paris, Université Pierre et Marie Curie, INSP-UMR7588, Paris, F-75005 France
| | | | | | | | | | | | | |
Collapse
|
16
|
Sorzano COS, Jonic S, Cottevieille M, Larquet E, Boisset N, Marco S. 3D electron microscopy of biological nanomachines: principles and applications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:995-1013. [PMID: 17611751 DOI: 10.1007/s00249-007-0203-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 06/01/2007] [Accepted: 06/11/2007] [Indexed: 11/21/2022]
Abstract
Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.
Collapse
Affiliation(s)
- C O S Sorzano
- Bioengineering Lab, Escuela Politécnica Superior, Univ. San Pablo CEU, Campus Urb, Montepríncipe s/n, 28668, Boadilla del Monte, Madrid, Spain.
| | | | | | | | | | | |
Collapse
|