1
|
Zhao J, Yu X, Shentu X, Li D. The application and development of electron microscopy for three-dimensional reconstruction in life science: a review. Cell Tissue Res 2024; 396:1-18. [PMID: 38416172 DOI: 10.1007/s00441-024-03878-7] [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: 10/17/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.
Collapse
Affiliation(s)
- Jingjing Zhao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China
| | - Danting Li
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Science, China , Jiliang University, Hangzhou, 310018, China.
| |
Collapse
|
2
|
Weisbord I, Segal-Peretz T. Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions. ACS APPLIED MATERIALS & INTERFACES 2023; 15:58003-58022. [PMID: 37338172 DOI: 10.1021/acsami.3c02956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.
Collapse
Affiliation(s)
- Inbal Weisbord
- Chemical Engineering Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Tamar Segal-Peretz
- Chemical Engineering Department, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| |
Collapse
|
3
|
Gassner C, Vongsvivut J, Ng SH, Ryu M, Tobin MJ, Juodkazis S, Morikawa J, Wood BR. Linearly Polarized Infrared Spectroscopy for the Analysis of Biological Materials. APPLIED SPECTROSCOPY 2023; 77:977-1008. [PMID: 37464791 DOI: 10.1177/00037028231180233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The analysis of biological samples with polarized infrared spectroscopy (p-IR) has long been a widely practiced method for the determination of sample orientation and structural properties. In contrast to earlier works, which employed this method to investigate the fundamental chemistry of biological systems, recent interests are moving toward "real-world" applications for the evaluation and diagnosis of pathological states. This focal point review provides an up-to-date synopsis of the knowledge of biological materials garnered through linearly p-IR on biomolecules, cells, and tissues. An overview of the theory with special consideration to biological samples is provided. Different modalities which can be employed along with their capabilities and limitations are outlined. Furthermore, an in-depth discussion of factors regarding sample preparation, sample properties, and instrumentation, which can affect p-IR analysis is provided. Additionally, attention is drawn to the potential impacts of analysis of biological samples with inherently polarized light sources, such as synchrotron light and quantum cascade lasers. The vast applications of p-IR for the determination of the structure and orientation of biological samples are given. In conclusion, with considerations to emerging instrumentation, findings by other techniques, and the shift of focus toward clinical applications, we speculate on the future directions of this methodology.
Collapse
Affiliation(s)
- Callum Gassner
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Australia
| | - Jitraporn Vongsvivut
- Infrared Microspectroscopy (IRM) Beamline, ANSTO-Australian Synchrotron, Clayton, Australia
| | - Soon Hock Ng
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, Australia
| | - Meguya Ryu
- National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Mark J Tobin
- Infrared Microspectroscopy (IRM) Beamline, ANSTO-Australian Synchrotron, Clayton, Australia
| | - Saulius Juodkazis
- Optical Sciences Centre and ARC Training Centre in Surface Engineering for Advanced Materials (SEAM), School of Science, Swinburne University of Technology, Hawthorn, Australia
| | - Junko Morikawa
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Bayden R Wood
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, Australia
| |
Collapse
|
4
|
Assessing Collagen D-Band Periodicity with Atomic Force Microscopy. MATERIALS 2022; 15:ma15041608. [PMID: 35208148 PMCID: PMC8877100 DOI: 10.3390/ma15041608] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 02/01/2023]
Abstract
The collagen superfamily includes more than fifty collagen and/or collagen-like proteins with fibril-forming collagen type I being the most abundant protein within the extracellular matrix. Collagen type I plays a crucial role in a variety of functions, it has been associated with many pathological conditions and it is widely used due to its unique properties. One unique nano-scale characteristic of natural occurring collagen type I fibers is the so-called D-band periodicity, which has been associated with collagen natural structure and properties, while it seems to play a crucial role in the interactions between cells and collagen and in various pathological conditions. An accurate characterization of the surface and structure of collagen fibers, including D-band periodicity, on collagen-based tissues and/or (nano-)biomaterials can be achieved by Atomic Force Microscopy (AFM). AFM is a scanning probe microscope and is among the few techniques that can assess D-band periodicity. This review covers issues related to collagen and collagen D-band periodicity and the use of AFM for studying them. Through a systematic search in databases (PubMed and Scopus) relevant articles were identified. The study of these articles demonstrated that AFM can offer novel information concerning D-band periodicity. This study highlights the importance of studying collagen D-band periodicity and proves that AFM is a powerful tool for investigating a number of different properties related to collagen D-band periodicity.
Collapse
|
5
|
Farnush M. A Model for Heterogeneous Brain Tumor Cells that Cause Dizziness. CURRENT CANCER THERAPY REVIEWS 2019. [DOI: 10.2174/1573394714666180907152741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background::
Various models are used for brain tumors modeling. To our knowledge,
no earlier work has been done on modeling the heterogeneous brain tumor that causes dizziness.
However, specifying a cell using a model is not new. Unlike all earlier works in this regard, which
consider analog or analog-CPU computers in the cell model, the model presented in this work
fully utilizes processor computers.
Materials and Methods::
The purpose of this study is to offer a comprehensive approach for
heterogeneous modeling of brain tumor cells. The model uses a brain tumor cell in Matlab and
Simulink 3D software. Two heterogeneous models are presented for brain tumor cells: the imagebased
cell model and computer-generated cell model. The image-based cell model is obtained
through the figure altering on X-ray or ocular figures by recognizing the dissimilar states in the
tumors.
Results::
The computer-generated cell model works based on locating computer produced aggregate
cells into tumors. Some subdivisions for both the image-based and computer-generated cell
models are presented as well.
Conclusion::
The positive and negative points of the image-based cell models and computergenerated
cell models some scientific advices are presented in this work. Generally, the imagebased
cell models could offer analytical facts for each state, but they are expensive and timeconsuming;
besides, their performance is heavily influenced by deformation techniques. The
computer-generated cell model, on the other hand, provides a higher cost of production and simplicity,
but its main contribution is the overall performance and accuracy.
Collapse
Affiliation(s)
- Mohammad Farnush
- School of Metallurgy & Materials Engineering, College of Engineering, University of Tehran, Tehran, Iran
| |
Collapse
|
6
|
Marelja Z, Leimkühler S, Missirlis F. Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism. Front Physiol 2018; 9:50. [PMID: 29491838 PMCID: PMC5817353 DOI: 10.3389/fphys.2018.00050] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022] Open
Abstract
Iron sulfur (Fe-S) clusters and the molybdenum cofactor (Moco) are present at enzyme sites, where the active metal facilitates electron transfer. Such enzyme systems are soluble in the mitochondrial matrix, cytosol and nucleus, or embedded in the inner mitochondrial membrane, but virtually absent from the cell secretory pathway. They are of ancient evolutionary origin supporting respiration, DNA replication, transcription, translation, the biosynthesis of steroids, heme, catabolism of purines, hydroxylation of xenobiotics, and cellular sulfur metabolism. Here, Fe-S cluster and Moco biosynthesis in Drosophila melanogaster is reviewed and the multiple biochemical and physiological functions of known Fe-S and Moco enzymes are described. We show that RNA interference of Mocs3 disrupts Moco biosynthesis and the circadian clock. Fe-S-dependent mitochondrial respiration is discussed in the context of germ line and somatic development, stem cell differentiation and aging. The subcellular compartmentalization of the Fe-S and Moco assembly machinery components and their connections to iron sensing mechanisms and intermediary metabolism are emphasized. A biochemically active Fe-S core complex of heterologously expressed fly Nfs1, Isd11, IscU, and human frataxin is presented. Based on the recent demonstration that copper displaces the Fe-S cluster of yeast and human ferredoxin, an explanation for why high dietary copper leads to cytoplasmic iron deficiency in flies is proposed. Another proposal that exosomes contribute to the transport of xanthine dehydrogenase from peripheral tissues to the eye pigment cells is put forward, where the Vps16a subunit of the HOPS complex may have a specialized role in concentrating this enzyme within pigment granules. Finally, we formulate a hypothesis that (i) mitochondrial superoxide mobilizes iron from the Fe-S clusters in aconitase and succinate dehydrogenase; (ii) increased iron transiently displaces manganese on superoxide dismutase, which may function as a mitochondrial iron sensor since it is inactivated by iron; (iii) with the Krebs cycle thus disrupted, citrate is exported to the cytosol for fatty acid synthesis, while succinyl-CoA and the iron are used for heme biosynthesis; (iv) as iron is used for heme biosynthesis its concentration in the matrix drops allowing for manganese to reactivate superoxide dismutase and Fe-S cluster biosynthesis to reestablish the Krebs cycle.
Collapse
Affiliation(s)
- Zvonimir Marelja
- Imagine Institute, Université Paris Descartes-Sorbonne Paris Cité, Paris, France
| | - Silke Leimkühler
- Department of Molecular Enzymology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fanis Missirlis
- Departamento de Fisiología, Biofísica y Neurociencias, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| |
Collapse
|
7
|
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]
|
8
|
Opara N, Martiel I, Arnold SA, Braun T, Stahlberg H, Makita M, David C, Padeste C. Direct protein crystallization on ultrathin membranes for diffraction measurements at X-ray free-electron lasers. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717005799] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A new era of protein crystallography started when X-ray free-electron lasers (XFELs) came into operation, as these provide an intense source of X-rays that facilitates data collection in the `diffract-before-destroy' regime. In typical experiments, crystals sequentially delivered to the beam are exposed to X-rays and destroyed. Therefore, the novel approach of serial crystallography requires thousands of nearly identical samples. Currently applied sample-delivery methods, in particular liquid jets or drop-on-demand systems, suffer from significant sample consumption of the precious crystalline material. Direct protein microcrystal growth by the vapour diffusion technique inside arrays of nanolitre-sized wells is a method specifically tailored to crystallography at XFELs. The wells, with X-ray transparent Si3N4windows as bottoms, are fabricated in silicon chips. Their reduced dimensions can significantly decrease protein specimen consumption. Arrays provide crystalline samples positioned in an ordered way without the need to handle fragile crystals. The nucleation process inside these microfabricated cavities was optimized to provide high membrane coverage and a quasi-random crystal distribution. Tight sealing of the chips and protection of the crystals from dehydration were achieved, as confirmed by diffraction experiments at a protein crystallography beamline. Finally, the test samples were shown to be suitable for time-resolved measurements at an XFEL at femtosecond resolution.
Collapse
|
9
|
Sjöhamn J, Båth P, Neutze R, Hedfalk K. Applying bimolecular fluorescence complementation to screen and purify aquaporin protein:protein complexes. Protein Sci 2016; 25:2196-2208. [PMID: 27643892 PMCID: PMC5119558 DOI: 10.1002/pro.3046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022]
Abstract
Protein:protein interactions play key functional roles in the molecular machinery of the cell. A major challenge for structural biology is to gain high‐resolution structural insight into how membrane protein function is regulated by protein:protein interactions. To this end we present a method to express, detect, and purify stable membrane protein complexes that are suitable for further structural characterization. Our approach utilizes bimolecular fluorescence complementation (BiFC), whereby each protein of an interaction pair is fused to nonfluorescent fragments of yellow fluorescent protein (YFP) that combine and mature as the complex is formed. YFP thus facilitates the visualization of protein:protein interactions in vivo, stabilizes the assembled complex, and provides a fluorescent marker during purification. This technique is validated by observing the formation of stable homotetramers of human aquaporin 0 (AQP0). The method's broader applicability is demonstrated by visualizing the interactions of AQP0 and human aquaporin 1 (AQP1) with the cytoplasmic regulatory protein calmodulin (CaM). The dependence of the AQP0‐CaM complex on the AQP0 C‐terminus is also demonstrated since the C‐terminal truncated construct provides a negative control. This screening approach may therefore facilitate the production and purification of membrane protein:protein complexes for later structural studies by X‐ray crystallography or single particle electron microscopy.
Collapse
Affiliation(s)
- Jennie Sjöhamn
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, SE-405 30, Sweden
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, SE-405 30, Sweden
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, SE-405 30, Sweden
| | - Kristina Hedfalk
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, SE-405 30, Sweden
| |
Collapse
|
10
|
Grushin K, Miller J, Dalm D, Stoilova-McPhie S. Factor VIII organisation on nanodiscs with different lipid composition. Thromb Haemost 2015; 113:741-9. [PMID: 25589466 DOI: 10.1160/th14-09-0725] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/23/2014] [Indexed: 11/05/2022]
Abstract
Nanodiscs (ND) are lipid bilayer membrane patches held by amphiphilic scaffolding proteins (MSP) of ~10 nm in diameter. Nanodiscs have been developed as lipid nanoplatforms for structural and functional studies of membrane and membrane associated proteins. Their size and monodispersity have rendered them unique for electron microscopy (EM) and single particle analysis studies of proteins and complexes either spanning or associated to the ND membrane. Binding of blood coagulation factors and complexes, such as the Factor VIII (FVIII) and the Factor VIIIa - Factor IXa (intrinsic tenase) complex to the negatively charged activated platelet membrane is required for normal haemostasis. In this study we present our work on optimising ND, specifically designed to bind FVIII at close to physiological conditions. The binding of FVIII to the negatively charged ND rich in phosphatidylserine (PS) was followed by electron microscopy at three different PS compositions and two different membrane scaffolding protein (MSP1D1) to lipid ratios. Our results show that the ND with highest PS content (80 %) and lowest MSP1D1 to lipid ratio (1:47) are the most suitable for structure determination of the membrane-bound FVIII by single particle EM. Our preliminary FVIII 3D reconstruction as bound to PS containing ND demonstrates the suitability of the optimised ND for structural studies by EM. Further assembly of the activated FVIII form (FVIIIa) and the whole FVIIIa-FIXa complex on ND, followed by EM and single particle reconstruction will help to identify the protein-protein and protein-membrane interfaces critical for the intrinsic tenase complex assembly and function.
Collapse
Affiliation(s)
| | | | | | - Svetla Stoilova-McPhie
- Svetla Stoilova-McPhie, Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA, Tel: +1 979 319 1349, Fax: +1 409 747 2200, E-mail:
| |
Collapse
|
11
|
Abstract
OBJECTIVE To study the complex formed between Tat protein and Env soluble trimeric immunogen, and compare with previously determined structures of Env native trimers and Env-CD4m complexes. DESIGN The soluble Env trimer was used to mimic the spike glycoprotein on the virus surface for the study. To overcome limitations of other structural determination methods, cryoelectron microscopy was employed to image the complex, and single particle reconstruction was utilized to reconstruct the structure of the complex from collected micrographs. Molecular modeling of gp120-Tat was performed to provide atomic coordinates for docking. METHODS Images were preprocessed by multivariate statistical analysis to identify principal components of variation then submitted for reconstruction. Reconstructed structures were docked with modeled gp120-Tat atomic coordinates to study the positions of crucial epitopes. RESULTS Analysis of the Env-Tat complex demonstrated an intermediate structure between Env native trimers and Env-CD4m structures. Docking results indicate that the CD4-binding site and the V3 loop are exposed in the Env-Tat complex. The integrin-binding sequence in Tat was also exposed in Env-Tat docking. CONCLUSION The intermediate structure induced by Tat-interaction with Env could potentially provide an explanation for increased virus infection in the presence of Tat protein. Consequently, exposure of CD4-binding sites and a putative integrin-binding sequence on Tat in the complex may provide a new avenue for rational design of an effective HIV vaccine.
Collapse
|
12
|
Jeong HS, Park HN, Kim JG, Hyun JK. Critical importance of the correction of contrast transfer function for
transmission electron microscopy-mediated structural biology. J Anal Sci Technol 2013. [DOI: 10.1186/2093-3371-4-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstracts
Background
Transmission electron microscopy (TEM) is an excellent tool for studying
detailed biological structures. High-resolution structure determination is
now routinely performed using advanced sample preparation techniques and
image processing software. In particular, correction for contrast transfer
function (CTF) is crucial for extracting high-resolution information from
TEM image that is convoluted by imperfect imaging condition. Accurate
determination of defocus, one of the major elements constituting the CTF, is
mandatory for CTF correction.
Findings
To investigate the effect of correct estimation of image defocus and
subsequent CTF correction, we tested arbitrary CTF imposition onto the
images of two-dimensional crystals of Rous sarcoma virus capsid protein. The
morphology of the crystal in calculated projection maps from incorrect CTF
imposition was utterly distorted in comparison to an appropriately
CTF-corrected image.
Conclusion
This result demonstrates critical importance of CTF correction for producing
true representation of the specimen at high resolution.
Collapse
|
13
|
Esquivel-Rodríguez J, Kihara D. Computational methods for constructing protein structure models from 3D electron microscopy maps. J Struct Biol 2013; 184:93-102. [PMID: 23796504 DOI: 10.1016/j.jsb.2013.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 06/11/2013] [Accepted: 06/13/2013] [Indexed: 12/31/2022]
Abstract
Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided.
Collapse
Affiliation(s)
- Juan Esquivel-Rodríguez
- Department of Computer Science, College of Science, Purdue University, West Lafayette, IN 47907, USA
| | | |
Collapse
|
14
|
Yoshioka C, Lyumkis D, Carragher B, Potter CS. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. J Struct Biol 2013; 182:155-63. [PMID: 23428431 DOI: 10.1016/j.jsb.2013.02.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/22/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
Electron microscopy (EM) is an important tool for determining the composition, arrangement and structure of biological macromolecules. When studying structurally heterogeneous samples using EM, classification is a critical step toward achieving higher resolution and identifying biologically significant conformations. We have developed an interactive, web-based tool, called Maskiton, for creating custom masks and performing 2D classifications on aligned single-particle EM images. The Maskiton interface makes it considerably easier and faster to explore the significance of heterogeneity in single-particle datasets. Maskiton features include: resumable uploads to facilitate transfer of large datasets to the server, custom mask creation in the browser, continual progress updates, and interactive viewing of classification results. To demonstrate the value of this tool, we provide examples of its use on several experimental datasets and include analyses of the independent terminus mobility within the Ltn1 E3 ubiquitin ligase, the in vitro assembly of 30S ribosomal subunits, and classification complexity reduction within Immunoglobulin M. This work also serves as a proof-of-concept for the development of future cross-platform, interactive user interfaces for electron microscopy data processing.
Collapse
Affiliation(s)
- Craig Yoshioka
- National Resource for Automated Molecular Microscopy, Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | | | |
Collapse
|
15
|
Boehm M, Yu J, Krynicka V, Barker M, Tichy M, Komenda J, Nixon PJ, Nield J. Subunit organization of a synechocystis hetero-oligomeric thylakoid FtsH complex involved in photosystem II repair. THE PLANT CELL 2012; 24:3669-83. [PMID: 22991268 PMCID: PMC3480294 DOI: 10.1105/tpc.112.100891] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
FtsH metalloproteases are key components of the photosystem II (PSII) repair cycle, which operates to maintain photosynthetic activity in the light. Despite their physiological importance, the structure and subunit composition of thylakoid FtsH complexes remain uncertain. Mutagenesis has previously revealed that the four FtsH homologs encoded by the cyanobacterium Synechocystis sp PCC 6803 are functionally different: FtsH1 and FtsH3 are required for cell viability, whereas FtsH2 and FtsH4 are dispensable. To gain insights into FtsH2, which is involved in selective D1 protein degradation during PSII repair, we used a strain of Synechocystis 6803 expressing a glutathione S-transferase (GST)-tagged derivative (FtsH2-GST) to isolate FtsH2-containing complexes. Biochemical analysis revealed that FtsH2-GST forms a hetero-oligomeric complex with FtsH3. FtsH2 also interacts with FtsH3 in the wild-type strain, and a mutant depleted in FtsH3, like ftsH2(-) mutants, displays impaired D1 degradation. FtsH3 also forms a separate heterocomplex with FtsH1, thus explaining why FtsH3 is more important than FtsH2 for cell viability. We investigated the structure of the isolated FtsH2-GST/FtsH3 complex using transmission electron microscopy and single-particle analysis. The three-dimensional structural model obtained at a resolution of 26 Å revealed that the complex is hexameric and consists of alternating FtsH2/FtsH3 subunits.
Collapse
Affiliation(s)
- Marko Boehm
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jianfeng Yu
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vendula Krynicka
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Myles Barker
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin Tichy
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Peter J. Nixon
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
- Address correspondence to
| | - Jon Nield
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| |
Collapse
|
16
|
Radjainia M, Huang B, Bai B, Schmitz M, Yang SH, Harris PWR, Griffin MDW, Brimble MA, Wang Y, Mitra AK. A highly conserved tryptophan in the N-terminal variable domain regulates disulfide bond formation and oligomeric assembly of adiponectin. FEBS J 2012; 279:2495-507. [DOI: 10.1111/j.1742-4658.2012.08630.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
17
|
BAKER LINDSAYA, RUBINSTEIN JOHNL. SINGLE PARTICLE ELECTRON MICROSCOPY OF THE MITOCHONDRIAL ATP SYNTHASE. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048010001135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mitochondrial ATP synthase is a large, membrane-bound protein complex that plays a central role in cellular metabolism. Since the identification of this assembly in micrographs of mitochondrial membranes, electron microscopy has been crucial in elucidating the structure and mechanism of the enzyme. This review addresses the recent use of single particle electron microscopy for structure determination of ATP synthase, including subunit localization, the challenges posed by the protein, and areas in which further work is needed.
Collapse
Affiliation(s)
- LINDSAY A. BAKER
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 555 University Ave, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8, Canada
| | - JOHN L. RUBINSTEIN
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 555 University Ave, Toronto, Ontario M5G 1X8, Canada
- Department of Biochemistry, University of Toronto, 555 University Ave, Toronto, Ontario M5G 1X8, Canada
| |
Collapse
|
18
|
Gallyamov MO. Scanning Force Microscopy as Applied to Conformational Studies in Macromolecular Research. Macromol Rapid Commun 2011; 32:1210-46. [DOI: 10.1002/marc.201100150] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/06/2011] [Indexed: 01/17/2023]
|
19
|
Gan SW, Vararattanavech A, Nordin N, Eshaghi S, Torres J. A cost-effective method for simultaneous homo-oligomeric size determination and monodispersity conditions for membrane proteins. Anal Biochem 2011; 416:100-6. [PMID: 21624344 DOI: 10.1016/j.ab.2011.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 04/29/2011] [Accepted: 05/04/2011] [Indexed: 10/18/2022]
Abstract
The use of blue native polyacrylamide gel electrophoresis (BN-PAGE) has been reported in the literature to retain both water-soluble and membrane protein complexes in their native hetero-oligomeric state and to determine the molecular weight of membrane proteins. However, membrane proteins show abnormal mobility when compared with water-soluble markers. Although one could use membrane proteins as markers or apply a conversion factor to the observed molecular weight to account for the bound Coomassie blue dye, when one just wants to assess homo-oligomeric size, these methods appear to be too time-consuming or might not be generally applicable. Here, during detergent screening studies to identify the best detergent for achieving a monodisperse sample, we observed that under certain conditions membrane proteins tend to form ladders of increasing oligomeric size. Although the ladders themselves contain no indication of which band represents the correct oligomeric size, they provide a scale that can be compared with a single band, representing the native homo-oligomeric size, obtained in other conditions of the screen. We show that this approach works for three membrane proteins: CorA (42 kDa), aquaporin Z (25 kDa), and small hydrophobic (SH) protein from respiratory syncytial virus (8 kDa). In addition, polydispersity results and identification of the most suitable detergent correlate optimally not only with size exclusion chromatography (SEC) but also with results from sedimentation velocity and equilibrium experiments. Because it involves minute quantities of sample and detergent, this method can be used in high-throughput approaches as a low-cost technique.
Collapse
Affiliation(s)
- Siok Wan Gan
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | | | | | | | | |
Collapse
|
20
|
Iwanczyk J, Leong V, Ortega J. Factors defining the functional oligomeric state of Escherichia coli DegP protease. PLoS One 2011; 6:e18944. [PMID: 21526129 PMCID: PMC3081313 DOI: 10.1371/journal.pone.0018944] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 03/24/2011] [Indexed: 12/04/2022] Open
Abstract
Escherichia coli DegP protein is a periplasmic protein that functions both as a protease and as a chaperone. In the absence of substrate, DegP oligomerizes as a hexameric cage but in its presence DegP reorganizes into 12 and 24-mer cages with large chambers that house the substrate for degradation or refolding. Here, we studied the factors that determine the oligomeric state adopted by DegP in the presence of substrate. Using size exclusion chromatography and electron microscopy, we found that the size of the substrate molecule is the main factor conditioning the oligomeric state adopted by the enzyme. Other factors such as temperature, a major regulatory factor of the activity of this enzyme, did not influence the oligomeric state adopted by DegP. In addition, we observed that substrate concentration exerted an effect only when large substrates (full-length proteins) were used. However, small substrate molecules (peptides) always triggered the same oligomeric state regardless of their concentration. These results clarify important aspects of the regulation of the oligomeric state of DegP.
Collapse
Affiliation(s)
- Jack Iwanczyk
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Vivian Leong
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
| | - Joaquin Ortega
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| |
Collapse
|
21
|
Nield J, Moriya M, Ochiai M. Calmodulin binding-heat shock proteins form a ring structure in the rat testis. Mol Reprod Dev 2010; 77:738. [PMID: 20734430 DOI: 10.1002/mrd.21231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
22
|
Busch A, Nield J, Hippler M. The composition and structure of photosystem I-associated antenna from Cyanidioschyzon merolae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:886-97. [PMID: 20230507 DOI: 10.1111/j.1365-313x.2010.04202.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Red algae contain two types of light-harvesting antenna systems, the phycobilisomes and chlorophyll a binding polypeptides (termed Lhcr), which expand the light-harvesting capacity of the photosynthetic reaction centers. In this study, photosystem I (PSI) and its associated light-harvesting proteins were isolated from the red alga Cyanidioschyzon merolae. The structural and functional properties of the largest PSI particles observed were investigated by biochemical characterization, mass spectrometry, fluorescence emission and excitation spectroscopy, and transmission electron microscopy. Our data provide strong evidence for a stable PSI complex in red algae that possesses two distinct types of functional peripheral light-harvesting antenna complex, comprising both Lhcr and a PSI-linked phycobilisome sub-complex. We conclude that the PSI antennae system of red algae represents an evolutionary intermediate between the prokaryotic cyanobacteria and other eukaryotes, such as green algae and vascular plants.
Collapse
Affiliation(s)
- Andreas Busch
- Department of Biology, Institute of Plant Biochemistry and Biotechnology, University of Münster, Hindenburgplatz 55, 48143 Münster, Germany
| | | | | |
Collapse
|
23
|
Inforzato A, Baldock C, Jowitt TA, Holmes DF, Lindstedt R, Marcellini M, Rivieccio V, Briggs DC, Kadler KE, Verdoliva A, Bottazzi B, Mantovani A, Salvatori G, Day AJ. The angiogenic inhibitor long pentraxin PTX3 forms an asymmetric octamer with two binding sites for FGF2. J Biol Chem 2010; 285:17681-92. [PMID: 20363749 DOI: 10.1074/jbc.m109.085639] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The inflammation-associated long pentraxin PTX3 plays key roles in innate immunity, female fertility, and vascular biology (e.g. it inhibits FGF2 (fibroblast growth factor 2)-mediated angiogenesis). PTX3 is composed of multiple protomers, each composed of distinct N- and C-terminal domains; however, it is not known how these are organized or contribute to its functional properties. Here, biophysical analyses reveal that PTX3 is composed of eight identical protomers, associated through disulfide bonds, forming an elongated and asymmetric, molecule with two differently sized domains interconnected by a stalk. The N-terminal region of the protomer provides the main structural determinant underlying this quaternary organization, supporting formation of a disulfide-linked tetramer and a dimer of dimers (a non-covalent tetramer), giving rise to the asymmetry of the molecule. Furthermore, the PTX3 octamer is shown to contain two FGF2 binding sites, where it is the tetramers that act as the functional units in ligand recognition. Thus, these studies provide a unifying model of the PTX3 oligomer, explaining both its quaternary organization and how this is required for its antiangiogenic function.
Collapse
Affiliation(s)
- Antonio Inforzato
- Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Jung HS. Technical approaches of single particle analysis following electron microscopy to pre-screening biological candidates targeted on high resolution studies. J Anal Sci Technol 2010. [DOI: 10.5355/jast.2010.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
|
25
|
Graham HK, Hodson NW, Hoyland JA, Millward-Sadler SJ, Garrod D, Scothern A, Griffiths CEM, Watson REB, Cox TR, Erler JT, Trafford AW, Sherratt MJ. Tissue section AFM: In situ ultrastructural imaging of native biomolecules. Matrix Biol 2010; 29:254-60. [PMID: 20144712 PMCID: PMC2877882 DOI: 10.1016/j.matbio.2010.01.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 01/29/2010] [Accepted: 01/29/2010] [Indexed: 11/12/2022]
Abstract
Conventional approaches for ultrastructural high-resolution imaging of biological specimens induce profound changes in bio-molecular structures. By combining tissue cryo-sectioning with non-destructive atomic force microscopy (AFM) imaging we have developed a methodology that may be applied by the non-specialist to both preserve and visualize bio-molecular structures (in particular extracellular matrix assemblies) in situ. This tissue section AFM technique is capable of: i) resolving nm–µm scale features of intra- and extracellular structures in tissue cryo-sections; ii) imaging the same tissue region before and after experimental interventions; iii) combining ultrastructural imaging with complimentary microscopical and micromechanical methods. Here, we employ this technique to: i) visualize the macro-molecular structures of unstained and unfixed fibrillar collagens (in skin, cartilage and intervertebral disc), elastic fibres (in aorta and lung), desmosomes (in nasal epithelium) and mitochondria (in heart); ii) quantify the ultrastructural effects of sequential collagenase digestion on a single elastic fibre; iii) correlate optical (auto fluorescent) with ultrastructural (AFM) images of aortic elastic lamellae.
Collapse
Affiliation(s)
- Helen K Graham
- Unit of Cardiac Physiology, School of Biomedicine, The University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Structural and mutational analysis of band 7 proteins in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 2009; 191:6425-35. [PMID: 19684140 DOI: 10.1128/jb.00644-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Band 7 proteins, which encompass members of the stomatin, prohibitin, flotillin, and HflK/C protein families, are integral membrane proteins that play important physiological roles in eukaryotes but are poorly characterized in bacteria. We have studied the band 7 proteins encoded by the cyanobacterium Synechocystis sp. strain PCC 6803, with emphasis on their structure and proposed role in the assembly and maintenance of the photosynthetic apparatus. Mutagenesis revealed that none of the five band 7 proteins (Slr1106, Slr1128, Slr1768, Sll0815, and Sll1021) was essential for growth under a range of conditions (including high light, salt, oxidative, and temperature stresses), although motility was compromised in an Slr1768 inactivation mutant. Accumulation of the major photosynthetic complexes in the thylakoid membrane and repair of the photosystem II complex following light damage were similar in the wild type and a quadruple mutant. Cellular fractionation experiments indicated that three of the band 7 proteins (Slr1106, Slr1768, and Slr1128) were associated with the cytoplasmic membrane, whereas Slr1106, a prohibitin homologue, was also found in the thylakoid membrane fraction. Blue native gel electrophoresis indicated that these three proteins, plus Sll0815, formed large (>669-kDa) independent complexes. Slr1128, a stomatin homologue, has a ring-like structure with an approximate diameter of 16 nm when visualized by negative stain electron microscopy. No evidence for band 7/FtsH supercomplexes was found. Overall, our results indicate that the band 7 proteins form large homo-oligomeric complexes but do not play a crucial role in the biogenesis of the photosynthetic apparatus in Synechocystis sp. strain PCC 6803.
Collapse
|
27
|
Walsh CP, Davies A, Butcher AJ, Dolphin AC, Kitmitto A. Three-dimensional structure of CaV3.1: comparison with the cardiac L-type voltage-gated calcium channel monomer architecture. J Biol Chem 2009; 284:22310-22321. [PMID: 19520861 PMCID: PMC2755954 DOI: 10.1074/jbc.m109.017152] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calcium entry through voltage-gated calcium channels has widespread cellular effects upon a host of physiological processes including neuronal excitability, muscle excitation-contraction coupling, and secretion. Using single particle analysis methods, we have determined the first three-dimensional structure, at 23 A resolution, for a member of the low voltage-activated voltage-gated calcium channel family, CaV3.1, a T-type channel. CaV3.1 has dimensions of approximately 115x85x95 A, composed of two distinct segments. The cytoplasmic densities form a vestibule below the transmembrane domain with the C terminus, unambiguously identified by the presence of a His tag being approximately 65 A long and curling around the base of the structure. The cytoplasmic assembly has a large exposed surface area that may serve as a signaling hub with the C terminus acting as a "fishing rod" to bind regulatory proteins. We have also determined a three-dimensional structure, at a resolution of 25 A, for the monomeric form of the cardiac L-type voltage-gated calcium (high voltage-activated) channel with accessory proteins beta and alpha2delta bound to the ion channel polypeptide CaV1.2. Comparison with the skeletal muscle isoform finds a good match particularly with respect to the conformation, size, and shape of the domain identified as that formed by alpha2. Furthermore, modeling of the CaV3.1 structure (analogous to CaV1.2 at these resolutions) into the heteromeric L-type voltage-gated calcium channel complex volume reveals multiple interaction sites for beta-CaV1.2 binding and for the first time identifies the size and organization of the alpha2delta polypeptides.
Collapse
Affiliation(s)
- Conor P Walsh
- Cardiovascular Medicine, School of Clinical and Laboratory Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9NT
| | - Anthony Davies
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Adrian J Butcher
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Annette C Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Ashraf Kitmitto
- Cardiovascular Medicine, School of Clinical and Laboratory Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9NT
| |
Collapse
|
28
|
Abstract
Integrins are a family of heterodimeric, cell-surface receptors that mediate interactions between the cytoskeleton and the extracellular matrix. We have used electron microscopy and single-particle image analysis combined with molecular modeling to investigate the structures of the full-length integrin alpha(IIb)beta(3) and the ectodomain of alpha(V)beta(3) in a complex with fibronectin. The full-length integrin alpha(IIb)beta(3) is purified from human platelets by ion exchange and gel filtration chromatography in buffers containing the detergent octyl-beta-D-glucopyranoside, whereas the recombinant ectodomain of alpha(V)beta(3) is soluble in aqueous buffer. Transmission electron microscopy is performed either in negative stain, where the protein is embedded in a heavy metal such as uranyl acetate, or in the frozen-hydrated state, where the sample is flash-frozen such that the buffer is vitrified and native conditions are preserved. Individual integrin particles are selected from low-dose micrographs, either by manual identification or an automated method using a cross-correlation search of the micrograph against a set of reference images. Due to the small size of integrin heterodimers (approximately 250 kDa) and the low electron dose required to minimize beam damage, the signal-to-noise level of individual particles is quite low, both by negative-stain electron microscopy and electron cryomicroscopy. Consequently, it is necessary to average many particle images with equivalent views. The particle images are subjected to reference-free alignment and classification, in which the particles are aligned to a common view and further grouped by statistical methods into classes with common orientations. Assessment of the structure from a set of two-dimensional averaged projections is often difficult, and a further three-dimensional (3D) reconstruction analysis is performed to classify each particle as belonging to a specific projection from a single 3D model. The 3D reconstruction algorithm is an iterative projection-matching routine in which the classified particles are used to construct a new, 3D map for the next iteration. Docking of known high-resolution structures of individual subdomains within the molecular envelope of the 3D EM map is used to derive a pseudoatomic model of the integrin complex. This approach of 3D EM image analysis and pseudoatomic modeling is a powerful strategy for exploring the structural biology of transmembrane signaling by integrins because it is likely that multiple conformational states will be difficult to crystallize, whereas the different states should be amenable to electron cryomicroscopy.
Collapse
Affiliation(s)
- Brian D Adair
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California, USA
| | | |
Collapse
|
29
|
Gutmann DAP, Mizohata E, Newstead S, Ferrandon S, Postis V, Xia X, Henderson PJF, van Veen HW, Byrne B. A high-throughput method for membrane protein solubility screening: the ultracentrifugation dispersity sedimentation assay. Protein Sci 2007; 16:1422-8. [PMID: 17567744 PMCID: PMC2206705 DOI: 10.1110/ps.072759907] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
One key to successful crystallization of membrane proteins is the identification of detergents that maintain the protein in a soluble, monodispersed state. Because of their hydrophobic nature, membrane proteins are particularly prone to forming insoluble aggregates over time. This nonspecific aggregation of the molecules reduces the likelihood of the regular association of the protein molecules essential for crystal lattice formation. Critical buffer components affecting the aggregation of membrane proteins include detergent choice, salt concentration, and presence of glycerol. The optimization of these parameters is often a time- and protein-consuming process. Here we describe a novel ultracentrifugation dispersity sedimentation (UDS) assay in which ultracentrifugation of very small (5 microL) volumes of purified, soluble membrane protein is combined with SDS-PAGE analysis to rapidly assess the degree of protein aggregation. The results from the UDS method correlate very well with established methods like size-exclusion chromatography (SEC), while consuming considerably less protein. In addition, the UDS method allows rapid screening of detergents for membrane protein crystallization in a fraction of the time required by SEC. Here we use the UDS method in the identification of suitable detergents and buffer compositions for the crystallization of three recombinant prokaryotic membrane proteins. The implications of our results for membrane protein crystallization prescreening are discussed.
Collapse
Affiliation(s)
- Daniel A P Gutmann
- Membrane Protein Crystallography Group, Division of Molecular Biosciences, Imperial College London, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Woolford D, Ericksson G, Rothnagel R, Muller D, Landsberg MJ, Pantelic RS, McDowall A, Pailthorpe B, Young PR, Hankamer B, Banks J. SwarmPS: rapid, semi-automated single particle selection software. J Struct Biol 2006; 157:174-88. [PMID: 16774837 DOI: 10.1016/j.jsb.2006.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/23/2006] [Accepted: 04/03/2006] [Indexed: 10/24/2022]
Abstract
Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that approximately 10(4)-10(5) particle projections are required to attain a 3A resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present Swarm(PS), a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (approximately 10(2)), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. Swarm(PS) is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.
Collapse
Affiliation(s)
- David Woolford
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Wang WX, Dgany O, Wolf SG, Levy I, Algom R, Pouny Y, Wolf A, Marton I, Altman A, Shoseyov O. Aspen SP1, an exceptional thermal, protease and detergent-resistant self-assembled nano-particle. Biotechnol Bioeng 2006; 95:161-8. [PMID: 16732592 DOI: 10.1002/bit.21010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Stable protein 1 (SP1) is a homo-oligomeric protein isolated from aspen (Populus tremula aspen) plants which forms a ring-shape dodecameric particle with a central cavity. The oligomeric form of SP1 is an exceptionally stable structure that is resistant to proteases (e.g., trypsin, V8, and proteinase K), high temperatures, organic solvents, and high levels of ionic detergent. Analytical ultra-centrifugation, chemical cross-linking, matrix-assisted laser-desorption time-of-flight mass spectrometry (MALDI-TOF-MS), and transmission electron microscopy were used to further characterize the SP1 dodecamer. Introduction of a single cysteine at the N-terminus of SP1 enabled the formation of disulfide bridges within the SP1 dodecamer, concurrent with increased melting point. A six-histidine tag was introduced at the N-terminus of SP1 to generate 6HSP1, and the DeltaNSP1 mutant was generated by a deletion of amino acids 2-6 at the N-terminus. Both 6HSP1 and DeltaNSP1 maintained their ability to assemble a stable dodecamer. Remarkably, these SP1 homo-dodecamers were able to re-assemble into stable hetero-dodecamers following co-electro-elution from SDS-PAGE. The exceptional stability of the SP1-nano ring and its ability to self-assemble hetero-complexes paves the way to further research in utilizing this unique protein in nano-biotechnology.
Collapse
Affiliation(s)
- Wang-Xia Wang
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, and the Otto Warburg Center for Agricultural Biotechnology, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Kargul J, Turkina MV, Nield J, Benson S, Vener AV, Barber J. Light-harvesting complex II protein CP29 binds to photosystem I of Chlamydomonas reinhardtii under State 2 conditions. FEBS J 2005; 272:4797-806. [PMID: 16156798 DOI: 10.1111/j.1742-4658.2005.04894.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The State 1 to State 2 transition in the photosynthetic membranes of plants and green algae involves the functional coupling of phosphorylated light-harvesting complexes of photosystem II (LHCII) to photosystem I (PSI). We present evidence suggesting that in Chlamydomonas reinhardtii this coupling may be aided by a hyper-phosphorylated form of the LHCII-like CP29 protein (Lhcbm4). MS analysis of CP29 showed that Thr6, Thr16 and Thr32, and Ser102 are phosphorylated in State 2, whereas in State 1-exposed cells only phosphorylation of Thr6 and Thr32 could be detected. The LHCI-PSI supercomplex isolated from the alga in State 2 was found to contain strongly associated CP29 in phosphorylated form. Electron microscopy suggests that the binding site for this highly phosphorylated CP29 is close to the PsaH protein. It is therefore postulated that redox-dependent multiple phosphorylation of CP29 in green algae is an integral part of the State transition process in which the structural changes of CP29, induced by reversible phosphorylation, determine the affinity of LHCII for either of the two photosystems.
Collapse
Affiliation(s)
- Joanna Kargul
- Wolfson Laboratories, Division of Molecular Biosciences, Imperial College London, UK
| | | | | | | | | | | |
Collapse
|
33
|
Vacha F, Bumba L, Kaftan D, Vacha M. Microscopy and single molecule detection in photosynthesis. Micron 2005; 36:483-502. [PMID: 15951188 DOI: 10.1016/j.micron.2005.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Revised: 04/18/2005] [Accepted: 04/19/2005] [Indexed: 11/30/2022]
Abstract
Progress in various fields of microscopy techniques brought up enormous possibilities to study the photosynthesis down to the level of individual pigment-protein complexes. The aim of this review is to present recent developments in the photosynthesis research obtained using such highly advanced techniques. Three areas of microscopy techniques covering optical microscopy, electron microscopy and scanning probe microscopy are reviewed. Whereas the electron microscopy and scanning probe microscopy are used in photosynthesis mainly for structural studies of photosynthetic pigment-protein complexes, the optical microscopy is used also for functional studies.
Collapse
Affiliation(s)
- Frantisek Vacha
- Institute of Physical Biology, University of South Bohemia, Budejovice, Czech Republic.
| | | | | | | |
Collapse
|
34
|
Unser M, Sorzano C, Thévenaz P, Jonić S, El-Bez C, De Carlo S, Conway J, Trus B. Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions. J Struct Biol 2005; 149:243-55. [PMID: 15721578 PMCID: PMC1464087 DOI: 10.1016/j.jsb.2004.10.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 09/22/2004] [Indexed: 11/20/2022]
Abstract
Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.
Collapse
Affiliation(s)
- M. Unser
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - C.O.S. Sorzano
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
- Escuela Politécnica Superior, Universidad San Pablo-CEU, Campus Urb. Montepríncipe s/n, 28668 Boadilla del Monte, Madrid, Spain
- Biocomputing Unit, National Center of Biotechnology (CSIC), Campus Univ. Autónoma s/n, 28047 Cantoblanco, Madrid, Spain
- Corresponding author. Fax: +34 91 585 4506. E-mail address: (C.O.S. Sorzano)
| | - P Thévenaz
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - S. Jonić
- Biomedical Imaging Group, Swiss Federal Institute of Technology Lausanne, CH-1015 Lausanne VD, Switzerland
| | - C. El-Bez
- Laboratoire d’analyse ultrastructurale, Université de Lausanne, CH-1015 Lausanne VD, Switzerland
| | - S. De Carlo
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - J.F. Conway
- Laboratoire de Microscopie Electronique Structurale, Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027 Grenoble, Cedex 1, France
| | - B.L. Trus
- Imaging Sciences Laboratory, Center of Information Technology (NIH/DHHS), 12 Center Drive, MSC 5624, Bethesda, MD 20892-5624, USA
| |
Collapse
|
35
|
Nield J, Redding K, Hippler M. Remodeling of light-harvesting protein complexes in chlamydomonas in response to environmental changes. EUKARYOTIC CELL 2005; 3:1370-80. [PMID: 15590812 PMCID: PMC539040 DOI: 10.1128/ec.3.6.1370-1380.2004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jon Nield
- Department of Biological Sciences, Imperial College London, London, UK
| | | | | |
Collapse
|
36
|
Sorzano COS, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SHW, Carazo JM, Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol 2005; 148:194-204. [PMID: 15477099 DOI: 10.1016/j.jsb.2004.06.006] [Citation(s) in RCA: 353] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 06/04/2004] [Indexed: 11/30/2022]
Abstract
X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.
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
|
37
|
Marco S, Boudier T, Messaoudi C, Rigaud JL. Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2005; 69:1219-25. [PMID: 15627375 DOI: 10.1007/s10541-005-0067-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electron tomography allows computing three-dimensional (3D) reconstructions of objects from their projections recorded at several angles. Combined with transmission electron microscopy, electron tomography has contributed greatly to the understanding of subcellular structures and organelles. Performed on frozen-hydrated samples, electron tomography has yielded useful information about complex biological structures. Combined with energy filtered transmission electron microscopy (EFTEM) it can be used to analyze the spatial distribution of chemical elements in biological or material sciences samples. In the present review, we present an overview of the requirements, applications, and perspectives of electron tomography in structural biology.
Collapse
Affiliation(s)
- S Marco
- Institut Curie, Section Recherche, UMR-CNRS 168 et LRC-CEA 34V 11, 75005 Paris, France.
| | | | | | | |
Collapse
|
38
|
Collins RF, Frye SA, Balasingham S, Ford RC, Tønjum T, Derrick JP. Interaction with type IV pili induces structural changes in the bacterial outer membrane secretin PilQ. J Biol Chem 2005; 280:18923-30. [PMID: 15753075 DOI: 10.1074/jbc.m411603200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Type IV pili are cell surface organelles found on many Gram-negative bacteria. They mediate a variety of functions, including adhesion, twitching motility, and competence for DNA uptake. The type IV pilus is a helical polymer of pilin protein subunits and is capable of rapid polymerization or depolymerization, generating large motor forces in the process. Here we show that a specific interaction between the outer membrane secretin PilQ and the type IV pilus fiber can be detected by far-Western analysis and sucrose density gradient centrifugation. Transmission electron microscopy of preparations of purified pili, to which the purified PilQ oligomer had been added, showed that PilQ was uniquely located at one end of the pilus fiber, effectively forming a "mallet-type" structure. Determination of the three-dimensional structure of the PilQ-type IV pilus complex at 26-angstroms resolution showed that the cavity within the protein complex was filled. Comparison with a previously determined structure of PilQ at 12-angstroms resolution indicated that binding of the pilus fiber induced a dissociation of the "cap" feature and lateral movement of the "arms" of the PilQ oligomer. The results demonstrate that the PilQ structure exhibits a dynamic response to the binding of its transported substrate and suggest that the secretin could play an active role in type IV pilus assembly as well as secretion.
Collapse
Affiliation(s)
- Richard F Collins
- Faculty of Life Sciences, The University of Manchester, Faculty of Life Sciences, Sackville Street, P. O. Box 88, Manchester M60 1QD, United Kingdom
| | | | | | | | | | | |
Collapse
|
39
|
Heymann JB, Conway JF, Steven AC. Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy. J Struct Biol 2005; 147:291-301. [PMID: 15450298 DOI: 10.1016/j.jsb.2004.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Revised: 02/04/2004] [Indexed: 11/23/2022]
Abstract
Cryo-electron microscopy of single particles offers a unique opportunity to detect and quantify conformational variation of protein complexes. Different conformers may, in principle, be distinguished by classification of individual projections in which image differences arising from viewing geometry are disentangled from variability in the underlying structures by "multiple particle analysis"--MPA. If the various conformers represent dynamically related states of the same complex, MPA has the potential to visualize transition states, and eventually to yield movies of the dynamic process. Ordering the various conformers into a time series is facilitated if cryo-EM data are taken at successive times from a system that is known to be developing in time. Virus maturation represents a relatively tractable dynamic process because the changes are large and irreversible and the rate of the natural process may be conveniently slowed in vitro by adjusting the environmental conditions. We describe the strategy employed in a recent analysis of herpes simplex virus procapsid maturation (Nat. Struct. Biol. 10 (2003) 334-341), compare it with previous work on the maturation of bacteriophage HK97 procapsid, and discuss various factors that impinge on the feasibility of performing similar experimental analyses of molecular dynamics in the general case.
Collapse
Affiliation(s)
- J Bernard Heymann
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | |
Collapse
|
40
|
Sorzano COS, de la Fraga LG, Clackdoyle R, Carazo JM. Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy. Ultramicroscopy 2004; 101:129-38. [PMID: 15450658 DOI: 10.1016/j.ultramic.2004.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Revised: 04/08/2004] [Accepted: 04/13/2004] [Indexed: 10/26/2022]
Abstract
In the process of three-dimensional reconstruction of single particle biological macromolecules several hundreds, or thousands, of projection images are taken from tens or hundreds of independently digitized micrographs. These different micrographs show differences in the background grey level and particle contrast and, therefore, have to be normalized by scaling their pixel values before entering the reconstruction process. In this work several normalization procedures are studied using a statistical comparison framework. We finally show that the use of the different normalization methods affects the reconstruction quality, providing guidance on the choice of normalization procedures.
Collapse
Affiliation(s)
- C O S Sorzano
- Biocomputing Unit, National Center of Biotechnology (CSIC), Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | | | | | | |
Collapse
|
41
|
Electron tomography of biological samples. BIOCHEMISTRY (MOSCOW) 2004. [DOI: 10.1007/pl00021757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
|
42
|
Cong Y, Kovacs JA, Wriggers W. 2D fast rotational matching for image processing of biophysical data. J Struct Biol 2004; 144:51-60. [PMID: 14643208 DOI: 10.1016/j.jsb.2003.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In 3D single particle reconstruction, which involves the translational and rotational matching of a large number of electron microscopy (EM) images, the algorithmic performance is largely dependent on the efficiency and accuracy of the underlying 2D image alignment kernel. We present a novel fast rotational matching kernel for 2D images (FRM2D) that significantly reduces the cost of this alignment. The alignment problem is formulated using one translational and two rotational degrees of freedom. This allows us to take advantage of fast Fourier transforms (FFTs) in rotational space to accelerate the search of the two angular parameters, while the remaining translational parameter is explored, within a limited range, by exhaustive search. Since there are no boundary effects in FFTs of cyclic angular variables, we avoid the expensive zero padding associated with Fourier transforms in linear space. To verify the robustness of our method, efficiency and accuracy tests were carried out over a range of noise levels in realistic simulations of EM images. Performance tests against two standard alignment methods, resampling to polar coordinates and self-correlation, demonstrate that FRM2D compares very favorably to the traditional methods. FRM2D exhibits a comparable or higher robustness against noise and a significant gain in efficiency that depends on the fineness of the angular sampling and linear search range.
Collapse
Affiliation(s)
- Yao Cong
- School of Health Information Sciences and Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 7000 Fannin St, Suite 600, Houston, TX 77030, USA
| | | | | |
Collapse
|
43
|
Horowitz-Scherer RA, Woodcock CL. Visualization and 3D structure determination of defined sequence chromatin and chromatin remodeling complexes. Methods Enzymol 2004; 376:29-48. [PMID: 14975297 DOI: 10.1016/s0076-6879(03)76003-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
|
44
|
Wang MC, Dolphin A, Kitmitto A. L-type voltage-gated calcium channels: understanding function through structure. FEBS Lett 2004; 564:245-50. [PMID: 15111104 DOI: 10.1016/s0014-5793(04)00253-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2003] [Accepted: 02/23/2004] [Indexed: 11/19/2022]
Abstract
L-type voltage-gated calcium channels (VGCCs) are multisubunit membrane proteins that regulate calcium influx into excitable cells. Within the last two years there have been four separate reports describing the structure of the skeletal muscle VGCC determined by electron microscopy and single particle analysis methods. There are some discrepancies between the structures, as well as reports for both monomeric and dimeric forms of the channel. This article considers each of the VGCC structures in terms of similarities and differences with an emphasis upon translation of data into a biological context.
Collapse
Affiliation(s)
- Ming-Chuan Wang
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, UK
| | | | | |
Collapse
|
45
|
Hankamer BD, Elderkin SL, Buck M, Nield J. Organization of the AAA+ Adaptor Protein PspA Is an Oligomeric Ring. J Biol Chem 2004; 279:8862-6. [PMID: 14688274 DOI: 10.1074/jbc.m307889200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 25.3 kDa "adaptor" protein, PspA (phage shock protein A), is found in the cytoplasm and in association with the inner membrane of certain bacteria. PspA plays critical roles in negatively regulating the phage shock response and maintaining membrane integrity, especially during the export of proteins such as virulence factors. Homologues of PspA function exist for thylakoid biogenesis. Here we report the first three-dimensional reconstruction of a PspA assembly from Escherichia coli, visualized by electron microscopy and single particle analysis to a resolution of 30 Angstroms. The assembly forms a 9-fold rotationally symmetric ring with an outer diameter of 200 Angstroms, an inner diameter of 95 Angstroms, and a height of approximately 85 Angstroms. The molecular mass of the complex was calculated to be 1023 kDa by size exclusion chromatography, suggesting that each of the nine domains is likely to be composed of four PspA subunits. The functional implications of this PspA structure are discussed in terms of its interaction with the protein export machinery of the bacterial cell and its AAA(+) protein partner, PspF.
Collapse
Affiliation(s)
- Ben D Hankamer
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | | | | | | |
Collapse
|
46
|
Iwata M, Imamura H, Stambouli E, Ikeda C, Tamakoshi M, Nagata K, Makyio H, Hankamer B, Barber J, Yoshida M, Yokoyama K, Iwata S. Crystal structure of a central stalk subunit C and reversible association/dissociation of vacuole-type ATPase. Proc Natl Acad Sci U S A 2004; 101:59-64. [PMID: 14684831 PMCID: PMC314138 DOI: 10.1073/pnas.0305165101] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2003] [Indexed: 11/18/2022] Open
Abstract
The vacuole-type ATPases (V-ATPases) exist in various intracellular compartments of eukaryotic cells to regulate physiological processes by controlling the acidic environment. The crystal structure of the subunit C of Thermus thermophilus V-ATPase, homologous to eukaryotic subunit d of V-ATPases, has been determined at 1.95-A resolution and located into the holoenzyme complex structure obtained by single particle analysis as suggested by the results of subunit cross-linking experiments. The result shows that V-ATPase is substantially longer than the related F-type ATPase, due to the insertion of subunit C between the V(1) (soluble) and the V(o) (membrane bound) domains. Subunit C, attached to the V(o) domain, seems to have a socket like function in attaching the central-stalk subunits of the V(1) domain. This architecture seems essential for the reversible association/dissociation of the V(1) and the V(o) domains, unique for V-ATPase activity regulation.
Collapse
Affiliation(s)
- Momi Iwata
- ATP System Project, Exploratory Research for Advanced Technology, Japan Science and Technology Corporation, 5800-3 Nagatsuta, Midori-ku, Yokohama 226-0026, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Meissner U, Martin AG, Schwarz BO, Stohr M, Gebauer W, Harris JR, Markl J. 3-D reconstruction of hemocyanins and other invertebrate hemolymph proteins by cryo-TEM: an overview. Micron 2004; 35:7-9. [PMID: 15040394 DOI: 10.1016/j.micron.2003.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Ulrich Meissner
- Institute of Zoology, Johannes Gutenberg--University, D-55099, Mainz, Germany.
| | | | | | | | | | | | | |
Collapse
|
48
|
Grünewald K, Medalia O, Gross A, Steven AC, Baumeister W. Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophys Chem 2003; 100:577-91. [PMID: 12646392 DOI: 10.1016/s0301-4622(02)00307-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electron cryotomography has unique potential for three-dimensional visualization of macromolecular complexes at work in their natural environment. This approach is based on reconstructing three-dimensional volumes from tilt series of electron micrographs of cells preserved in their native states by vitrification. Resolutions of 5-8 nm have already been achieved and the prospects for further improvement are good. Since many intracellular activities are conducted by complexes in the megadalton range with dimensions of 20-50 nm, current resolutions should suffice to identify many of them in tomograms. However, residual noise and the dense packing of cellular constituents hamper interpretation. Recently, tomographic data have been collected on vitrified eukaryotic cells (Medalia et al., Science (2002) in press). Their cytoplasm was found to be markedly less crowded than in the prokaryotes previously studied, in accord with differences in crowding between prokaryotic and eukaryotic cells documented by other (indirect) biophysical methods. The implications of this observation are twofold. First, complexes should be more easily identifiable in tomograms of eukaryotic cytoplasm. This applies both to recognizing known complexes and characterizing novel complexes. An example of the latter-a 5-fold symmetric particle is-given. Second, electron cryotomography offers an incisive probe to examine crowding in different cellular compartments.
Collapse
Affiliation(s)
- Kay Grünewald
- Department of Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18a, D-82152 Martinsried, Germany
| | | | | | | | | |
Collapse
|
49
|
Bibby TS, Nield J, Chen M, Larkum AWD, Barber J. Structure of a photosystem II supercomplex isolated from Prochloron didemni retaining its chlorophyll a/b light-harvesting system. Proc Natl Acad Sci U S A 2003; 100:9050-4. [PMID: 12837938 PMCID: PMC166436 DOI: 10.1073/pnas.1532271100] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prochlorophytes are a class of cyanobacteria that do not use phycobiliproteins as light-harvesting systems, but contain chlorophyll (Chl) a/b-binding Pcb proteins. Recently it was shown that Pcb proteins form an 18-subunit light-harvesting antenna ring around the photosystem I (PSI) trimeric reaction center complex of the prochlorophyte Prochlorococcus marinus SS120. Here we have investigated whether the symbiotic prochlorophyte Prochloron didemni also contains the same supermolecular complex. Using cells isolated directly from its ascidian host, we found no evidence for the presence of the Pcb-PSI supercomplex. Instead we have identified and characterized a supercomplex composed of photosystem II (PSII) and Pcb proteins. We show that 10-Pcb subunits associate with the PSII dimeric reaction center core to form a giant complex having an estimated Mr of 1,500 kDa with dimensions of 210 x 290 A. Five-Pcb subunits flank each long side of the dimer and assuming each binds 13 Chl molecules, increase the antenna size of PSII by approximately 200%. Fluorescence emission studies indicate that energy transfer occurs efficiently from the Pcb antenna. Modeling using the x-ray structure of cyanobacterial PSII suggests that energy transfer to the PSII reaction center is via the Chls bound to the CP47 and CP43 proteins.
Collapse
Affiliation(s)
- Thomas S Bibby
- Wolfson Laboratories, Department of Biological Sciences, Imperial College, London SW7 2AZ, United Kingdom
| | | | | | | | | |
Collapse
|
50
|
Kargul J, Nield J, Barber J. Three-dimensional reconstruction of a light-harvesting complex I-photosystem I (LHCI-PSI) supercomplex from the green alga Chlamydomonas reinhardtii. Insights into light harvesting for PSI. J Biol Chem 2003; 278:16135-41. [PMID: 12588873 DOI: 10.1074/jbc.m300262200] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A supercomplex containing the photosystem I (PSI) and chlorophyll a/b light-harvesting complex I (LHCI) has been isolated using a His-tagged mutant of Chlamydomonas reinhardtii. This LHCI-PSI supercomplex contained approximately 215 chlorophyll molecules of which 175 were estimated to be chlorophyll a and 40 to be chlorophyll b, based on P700 oxidation and chlorophyll a/b ratio measurements. Its room temperature long wavelength absorption peak was at 680 nm, and it emitted chlorophyll fluorescence maximally at 715 nm (77 K). The LHCI was composed of four or more different types of Lhca polypeptides including Lhca3. No LHCII proteins or other phosphoproteins were detected in the LHCI-PSI supercomplexes suggesting that the cells from which they were isolated were in State 1. Electron microscopy of negatively stained samples followed by image analysis revealed the LHCI-PSI supercomplex to have maximal dimensions of 220 A by 180 A and to be approximately 105 A thick. An averaged top view was used to model in x-ray and electron crystallographic data for PSI and Lhca proteins respectively. We conclude that the supercomplex consists of a PSI reaction center monomer with 11 Lhca proteins arranged along the side where the PSI proteins, PsaK, PsaJ, PsaF, and PsaG are located. The estimated molecular mass for the complex is 700 kDa including the bound chlorophyll molecules. The assignment of 11 Lhca proteins is consistent with a total chlorophyll level of 215 assuming that the PSI reaction center core binds approximately 100 chlorophylls and that each Lhca subunit binds 10 chlorophylls. There was no evidence for oligomerization of Chlamydomonas PSI in contrast to the trimerization of PSI in cyanobacteria.
Collapse
Affiliation(s)
- Joanna Kargul
- Wolfson Laboratories, Department of Biological Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, United Kingdom
| | | | | |
Collapse
|