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Ercius P, Alaidi O, Rames MJ, Ren G. Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5638-63. [PMID: 26087941 PMCID: PMC4710474 DOI: 10.1002/adma.201501015] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/22/2015] [Indexed: 05/23/2023]
Abstract
Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.
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Affiliation(s)
- Peter Ercius
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Osama Alaidi
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Matthew J. Rames
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
| | - Gang Ren
- Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, CA 94720, USA
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Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res 2013; 12:5923-33. [PMID: 24010795 PMCID: PMC3859183 DOI: 10.1021/pr4003867] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.
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Affiliation(s)
- Andrew N Holding
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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3
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Fractal dimension analysis and mathematical morphology of structural changes in actin filaments imaged by electron microscopy. J Struct Biol 2011; 176:1-8. [DOI: 10.1016/j.jsb.2011.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 06/01/2011] [Accepted: 07/13/2011] [Indexed: 11/20/2022]
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4
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Vicente-Alique E, Núñez-Ramírez R, Vega JF, Hu P, Martínez-Salazar J. Size and conformational features of ErbB2 and ErbB3 receptors: a TEM and DLS comparative study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:835-42. [PMID: 21476053 DOI: 10.1007/s00249-011-0699-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/11/2011] [Accepted: 03/17/2011] [Indexed: 11/28/2022]
Abstract
ErbB2 and ErbB3 receptors belong to the epidermal growth factor receptor family. The members of this family are able to form homo- and heterodimers that trigger diverse downstream signalling concerned to multiple cellular events. In the absence of a ligand, ErbB3 adopts a characteristic tethered conformation, which differs from ErbB2 extended conformation. In this work, transmission electron microscopy (TEM) and dynamic light scattering (DLS) have been used to characterize the conformational features and the size of ErBb2 and ErbB3 receptors. Two main objectives are presented. The first one is to evaluate the use of TEM as a tool for structural studies for this family of receptors. The low molecular weight of these proteins represents a challenging purpose for TEM studies. The other one is to search for a relationship between the results obtained by TEM and those obtained for the hydrodynamic size measured by DLS. This comparison has allowed us to identify the conformational differences of the receptors and to anticipate the use of these experimental techniques for the study of the ligand activated heterodimerization, a process related to a significant number of human malignancies.
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Affiliation(s)
- Ernesto Vicente-Alique
- Departamento de Física Macromolecular, Instituto de Estructura de la Materia, Madrid, Spain
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5
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Fang Y, Murugappan S, Ramani K. Estimating view parameters from random projections for Tomography using spherical MDS. BMC Med Imaging 2010; 10:12. [PMID: 20565859 PMCID: PMC2898708 DOI: 10.1186/1471-2342-10-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 06/18/2010] [Indexed: 12/01/2022] Open
Abstract
Background During the past decade, the computed tomography has been successfully applied to various fields especially in medicine. The estimation of view angles for projections is necessary in some special applications of tomography, for example, the structuring of viruses using electron microscopy and the compensation of the patient's motion over long scanning period. Methods This work introduces a novel approach, based on the spherical multidimensional scaling (sMDS), which transforms the problem of the angle estimation to a sphere constrained embedding problem. The proposed approach views each projection as a high dimensional vector with dimensionality equal to the number of sampling points on the projection. By using SMDS, then each projection vector is embedded onto a 1D sphere which parameterizes the projection with respect to view angles in a globally consistent manner. The parameterized projections are used for the final reconstruction of the image through the inverse radon transform. The entire reconstruction process is non-iterative and computationally efficient. Results The effectiveness of the sMDS is verified with various experiments, including the evaluation of the reconstruction quality from different number of projections and resistance to different noise levels. The experimental results demonstrate the efficiency of the proposed method. Conclusion Our study provides an effective technique for the solution of 2D tomography with unknown acquisition view angles. The proposed method will be extended to three dimensional reconstructions in our future work. All materials, including source code and demos, are available on https://engineering.purdue.edu/PRECISE/SMDS.
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Affiliation(s)
- Yi Fang
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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6
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Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2010; 17:1563-1572. [PMID: 20004160 DOI: 10.1016/j.str.2009.10.009] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/02/2009] [Accepted: 10/22/2009] [Indexed: 01/05/2023]
Abstract
The reference-free averaging of three-dimensional electron microscopy (3D-EM) reconstructions with empty regions in Fourier space represents a pressing problem in electron tomography and single-particle analysis. We present a maximum likelihood algorithm for the simultaneous alignment and classification of subtomograms or random conical tilt (RCT) reconstructions, where the Fourier components in the missing data regions are treated as hidden variables. The behavior of this algorithm was explored using tests on simulated data, while application to experimental data was shown to yield unsupervised class averages for subtomograms of groEL/groES complexes and RCT reconstructions of p53. The latter application served to obtain a reliable de novo structure for p53 that may resolve uncertainties about its quaternary structure.
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Scheres SHW, Núñez-Ramírez R, Gómez-Llorente Y, San Martín C, Eggermont PPB, Carazo JM. Modeling experimental image formation for likelihood-based classification of electron microscopy data. Structure 2007; 15:1167-77. [PMID: 17937907 DOI: 10.1016/j.str.2007.09.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 08/18/2007] [Accepted: 09/01/2007] [Indexed: 11/15/2022]
Abstract
The coexistence of multiple distinct structural states often obstructs the application of three-dimensional cryo-electron microscopy to large macromolecular complexes. Maximum likelihood approaches are emerging as robust tools for solving the image classification problems that are posed by such samples. Here, we propose a statistical data model that allows for a description of the experimental image formation within the formulation of 2D and 3D maximum-likelihood refinement. The proposed approach comprises a formulation of the probability calculations in Fourier space, including a spatial frequency-dependent noise model and a description of defocus-dependent imaging effects. The Expectation-Maximization-like algorithms presented are generally applicable to the alignment and classification of structurally heterogeneous projection data. Their effectiveness is demonstrated with various examples, including 2D classification of top views of the archaeal helicase MCM and 3D classification of 70S E. coli ribosome and Simian Virus 40 large T-antigen projections.
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Affiliation(s)
- Sjors H W Scheres
- Centro Nacional de Biotecnología CSIC, Cantoblanco, 28049, Madrid, Spain
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Arias-Palomo E, Recuero-Checa MA, Bustelo XR, Llorca O. 3D structure of Syk kinase determined by single-particle electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1493-9. [PMID: 18021750 DOI: 10.1016/j.bbapap.2007.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 10/15/2007] [Accepted: 10/15/2007] [Indexed: 02/02/2023]
Abstract
The cytoplasmic Syk kinase plays key roles in immune responses and comprises two N-terminal regulatory Src homology 2 (SH2) domains followed by a catalytic region. Atomic structures of these domains have only been solved in isolation. To gain insights into the three-dimensional structure of full-length Syk, we have used single-particle electron microscopy. Syk acquires a closed conformation resembling the inhibited structure of Zap-70, another member of the Syk family. Such configuration suggests an inhibition of the N-terminal domains on its catalytic activity. The phosphotyrosine binding pockets of both SH2 domains are not occluded and they could interact with other phosphoproteins.
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Affiliation(s)
- Ernesto Arias-Palomo
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (Spanish National Research Council, CSIC), Ramiro de Maeztu, 9, E28040 Madrid, Spain
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9
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Torreira E, Schoehn G, Fernández Y, Jorba N, Ruigrok RW, Cusack S, Ortín J, Llorca O. Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer. Nucleic Acids Res 2007; 35:3774-83. [PMID: 17517766 PMCID: PMC1920261 DOI: 10.1093/nar/gkm336] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The genome of influenza A virus is organized into eight ribonucleoprotein complexes (RNPs), each containing one RNA polymerase complex. This RNA polymerase has also been found non-associated to RNPs and is possibly involved in distinct functions in the infection cycle. We have expressed the virus RNA polymerase complex by co-tranfection of the PB1, PB2 and PA genes in mammalian cells and the heterotrimer was purified by the TAP tag procedure. Its 3D structure was determined by electron microscopy and single-particle image processing. The model obtained resembles the structure previously reported for the polymerase complex associated to viral RNPs but appears to be in a more open conformation. Detailed model comparison indicated that specific areas of the complex show important conformational changes as compared to the structure for the RNP-associated polymerase, particularly in regions known to interact with the adjacent NP monomers in the RNP. Also, the PB2 subunit seems to undergo a substantial displacement as a result of the association of the polymerase to RNPs. The structural model presented suggests that a core conformation of the polymerase in solution exists but the interaction with other partners, such as proteins or RNA, will trigger distinct conformational changes to activate new functional properties.
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Affiliation(s)
- Eva Torreira
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Guy Schoehn
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Yolanda Fernández
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Núria Jorba
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Rob W.H. Ruigrok
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Stephen Cusack
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
| | - Juan Ortín
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
- *To whom correspondence should be addressed. 34 91 837 3112 ext. 444634 91 536 0432 Correspondence may also be addressed to J. Ortín. 34 91 585 455734-91 585 4506
| | - Oscar Llorca
- Centro Nacional de Biotecnología (CSIC). Darwin 3, Campus de Cantoblanco. 28049 Madrid, Spain, Laboratoire de Virologie Moléculaire et Structurale, FRE 2854 CNRS-Université Joseph Fourier, Grenoble, France, EMBL Grenoble Outstation, c/o ILL, BP181, 38042 Grenoble Cedex 9, France and Centro de Investigaciones Biológicas (CSIC). Ramiro de Maeztu 9, Campus Universidad Complutense, 28040 Madrid, Spain
- *To whom correspondence should be addressed. 34 91 837 3112 ext. 444634 91 536 0432 Correspondence may also be addressed to J. Ortín. 34 91 585 455734-91 585 4506
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10
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Llorca O, Trujillo A, Blanco FJ, Bernabeu C. Structural model of human endoglin, a transmembrane receptor responsible for hereditary hemorrhagic telangiectasia. J Mol Biol 2006; 365:694-705. [PMID: 17081563 DOI: 10.1016/j.jmb.2006.10.015] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Revised: 09/08/2006] [Accepted: 10/05/2006] [Indexed: 12/15/2022]
Abstract
Endoglin is a type I membrane protein expressed as a disulphide-linked homodimer on human vascular endothelial cells whose haploinsufficiency is responsible for the dominant vascular dysplasia known as hereditary hemorrhagic telangiectasia (HHT). Structurally, endoglin belongs to the zona pellucida (ZP) family of proteins that share a ZP domain of approximately 260 amino acid residues at their extracellular region. Endoglin is a component of the TGF-beta receptor complex, interacts with the TGF-beta signalling receptors types I and II, and modulates cellular responses to TGF-beta. Here, we have determined for the first time the three-dimensional structure of the approximately 140 kDa extracellular domain of endoglin at 25 A resolution, using single-particle electron microscopy (EM). This reconstruction provides the general architecture of endoglin, which arranges as a dome made of antiparallel oriented monomers enclosing a cavity at one end. A high-resolution structure of endoglin has also been modelled de novo and found to be consistent with the experimental reconstruction. Each subunit comprises three well-defined domains, two of them corresponding to ZP regions, organised into an open U-shaped monomer. This domain arrangement was found to closely resemble the overall structure derived experimentally and the three modelled de novo domains were tentatively assigned to the domains observed in the EM reconstruction. This molecular model was further tested by tagging endoglin's C terminus with an IgG Fc fragment visible after 3D reconstruction of the labelled protein. Combined, these data provide the structural framework to interpret endoglin's functional domains and mutations found in HHT patients.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antigens, CD/chemistry
- Antigens, CD/ultrastructure
- CHO Cells
- Cricetinae
- Cricetulus
- Endoglin
- Humans
- Membrane Proteins/chemistry
- Membrane Proteins/ultrastructure
- Microscopy, Electron
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense/genetics
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/ultrastructure
- Receptors, Fc/chemistry
- Receptors, Fc/ultrastructure
- Recombinant Proteins/chemistry
- Recombinant Proteins/ultrastructure
- Sequence Homology
- Solubility
- Telangiectasia, Hereditary Hemorrhagic/genetics
- Telangiectasia, Hereditary Hemorrhagic/pathology
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Affiliation(s)
- Oscar Llorca
- Centro de Investigaciones Biologicas, Consejo Superior de Investigaciones Cientificas (CSIC), Ramiro de Maetzu 9, 28040 Madrid, Spain
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11
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Boskovic J, Arnold JN, Stilion R, Gordon S, Sim RB, Rivera-Calzada A, Wienke D, Isacke CM, Martinez-Pomares L, Llorca O. Structural Model for the Mannose Receptor Family Uncovered by Electron Microscopy of Endo180 and the Mannose Receptor. J Biol Chem 2006; 281:8780-7. [PMID: 16452473 DOI: 10.1074/jbc.m513277200] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular portion contains a similar domain arrangement: an N-terminal cysteine-rich domain (CysR) followed by a single fibronectin type II domain (FNII) and 8-10 C-type lectin-like domains (CTLDs). These proteins mediate diverse functions ranging from extracellular matrix turnover through collagen uptake to homeostasis and immunity based on sugar recognition. Endo180 and the MR are multivalent transmembrane receptors capable of interacting with multiple ligands; in both receptors FNII recognizes collagens, and a single CTLD retains lectin activity (CTLD2 in Endo180 and CTLD4 in MR). It is expected that the overall conformation of these multivalent molecules would deeply influence their function as the availability of their binding sites could be altered under different conditions. However, conflicting reports have been published on the three-dimensional arrangement of these receptors. Here, we have used single particle electron microscopy to elucidate the three-dimensional organization of the MR and Endo180. Strikingly, we have found that both receptors display distinct three-dimensional structures, which are, however, conceptually very similar: a bent and compact conformation built upon interactions of the CysR domain and the lone functional CTLD. Biochemical and electron microscopy experiments indicate that, under a low pH mimicking the endosomal environment, both MR and Endo180 experience large conformational changes. We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity.
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MESH Headings
- Hydrogen-Ion Concentration
- Imaging, Three-Dimensional
- Lectins, C-Type/chemistry
- Lectins, C-Type/ultrastructure
- Mannose Receptor
- Mannose-Binding Lectins/chemistry
- Mannose-Binding Lectins/ultrastructure
- Microscopy, Electron
- Models, Structural
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/ultrastructure
- Receptors, Mitogen/chemistry
- Receptors, Mitogen/ultrastructure
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Affiliation(s)
- Jasminka Boskovic
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, Campus Universidad Complutense, 28040 Madrid, Spain
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