Single Particle Electron Microscopy

Overview

Journal Photosynth Res

Publisher Springer

Date 2009 Jun 11

PMID 19513809

Citations 6

Authors

Egbert J Boekema

Mihaela Folea

Roman Kouril

Affiliations

Soon will be listed here.

Abstract

Electron microscopy (EM) in combination with image analysis is a powerful technique to study protein structures at low, medium, and high resolution. Since electron micrographs of biological objects are very noisy, improvement of the signal-to-noise ratio by image processing is an integral part of EM, and this is performed by averaging large numbers of individual projections. Averaging procedures can be divided into crystallographic and non-crystallographic methods. The crystallographic averaging method, based on two-dimensional (2D) crystals of (membrane) proteins, yielded in solving atomic protein structures in the last century. More recently, single particle analysis could be extended to solve atomic structures as well. It is a suitable method for large proteins, viruses, and proteins that are difficult to crystallize. Because it is also a fast method to reveal the low-to-medium resolution structures, the impact of its application is growing rapidly. Technical aspects, results, and possibilities are presented.

Citing Articles

The Assembly of Super-Complexes in the Plant Chloroplast.

Qin K, Fernie A, Zhang Y Biomolecules. 2021; 11(12).

PMID: 34944483 PMC: 8699064. DOI: 10.3390/biom11121839.

Unique organization of photosystem II supercomplexes and megacomplexes in Norway spruce.

Kouril R, Nosek L, Opatikova M, Arshad R, Semchonok D, Chamrad I Plant J. 2020; 104(1):215-225.

PMID: 32654240 PMC: 7590091. DOI: 10.1111/tpj.14918.

Molecular Mechanisms of Photoadaptation of Photosystem I Supercomplex from an Evolutionary Cyanobacterial/Algal Intermediate.

Haniewicz P, Abram M, Nosek L, Kirkpatrick J, El-Mohsnawy E, Janna Olmos J Plant Physiol. 2017; 176(2):1433-1451.

PMID: 29187568 PMC: 5813541. DOI: 10.1104/pp.17.01022.

Conservation of core complex subunits shaped the structure and function of photosystem I in the secondary endosymbiont alga Nannochloropsis gaditana.

Alboresi A, Le Quiniou C, Yadav S, Scholz M, Meneghesso A, Gerotto C New Phytol. 2016; 213(2):714-726.

PMID: 27620972 PMC: 5216901. DOI: 10.1111/nph.14156.

Out with the old and in with the new: rapid specimen preparation procedures for electron microscopy of sectioned biological material.

McDonald K Protoplasma. 2013; 251(2):429-48.

PMID: 24258967 DOI: 10.1007/s00709-013-0575-y.

References

De Carlo S, Boisset N, Hoenger A . High-resolution single-particle 3D analysis on GroEL prepared by cryo-negative staining. Micron. 2007; 39(7):934-43. DOI: 10.1016/j.micron.2007.11.003. View

Frank J . Single-particle imaging of macromolecules by cryo-electron microscopy. Annu Rev Biophys Biomol Struct. 2002; 31:303-19. DOI: 10.1146/annurev.biophys.31.082901.134202. View

Kouril R, Arteni A, Lax J, Yeremenko N, DHaene S, Rogner M . Structure and functional role of supercomplexes of IsiA and Photosystem I in cyanobacterial photosynthesis. FEBS Lett. 2005; 579(15):3253-7. DOI: 10.1016/j.febslet.2005.03.051. View

Arteni A, Nowaczyk M, Lax J, Kouril R, Rogner M, Boekema E . Single particle electron microscopy in combination with mass spectrometry to investigate novel complexes of membrane proteins. J Struct Biol. 2005; 149(3):325-31. DOI: 10.1016/j.jsb.2004.12.002. View

Mitra K, Frank J . Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu Rev Biophys Biomol Struct. 2006; 35:299-317. DOI: 10.1146/annurev.biophys.35.040405.101950. View

Bibby T, Nield J, Barber J . Three-dimensional model and characterization of the iron stress-induced CP43'-photosystem I supercomplex isolated from the cyanobacterium Synechocystis PCC 6803. J Biol Chem. 2001; 276(46):43246-52. DOI: 10.1074/jbc.M106541200. View

Zhang X, Settembre E, Xu C, Dormitzer P, Bellamy R, Harrison S . Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci U S A. 2008; 105(6):1867-72. PMC: 2542862. DOI: 10.1073/pnas.0711623105. View

Yamaguchi M, Danev R, Nishiyama K, Sugawara K, Nagayama K . Zernike phase contrast electron microscopy of ice-embedded influenza A virus. J Struct Biol. 2008; 162(2):271-6. DOI: 10.1016/j.jsb.2008.01.009. View

Bottcher B, Graber P, Boekema E . The structure of Photosystem I from the thermophilic cyanobacterium Synechococcus sp. determined by electron microscopy of two-dimensional crystals. Biochim Biophys Acta. 1992; 1100(2):125-36. DOI: 10.1016/0005-2728(92)90073-b. View

10.

Adrian M, Dubochet J, Lepault J, McDowall A . Cryo-electron microscopy of viruses. Nature. 1984; 308(5954):32-6. DOI: 10.1038/308032a0. View

11.

Kuhlbrandt W, Wang D, Fujiyoshi Y . Atomic model of plant light-harvesting complex by electron crystallography. Nature. 1994; 367(6464):614-21. DOI: 10.1038/367614a0. View

12.

Heinemeyer J, Braun H, Boekema E, Kouril R . A structural model of the cytochrome C reductase/oxidase supercomplex from yeast mitochondria. J Biol Chem. 2007; 282(16):12240-8. DOI: 10.1074/jbc.M610545200. View

13.

Henderson R . The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules. Q Rev Biophys. 1995; 28(2):171-93. DOI: 10.1017/s003358350000305x. View

14.

Massover W, Lai P, Marsh P . Negative staining permits 4.0 A resolution with low-dose electron diffraction of catalase crystals. Ultramicroscopy. 2002; 90(1):7-12. DOI: 10.1016/s0304-3991(01)00131-0. View

15.

Arteni A, Zhang P, Battchikova N, Ogawa T, Aro E, Boekema E . Structural characterization of NDH-1 complexes of Thermosynechococcus elongatus by single particle electron microscopy. Biochim Biophys Acta. 2006; 1757(11):1469-75. DOI: 10.1016/j.bbabio.2006.05.042. View

16.

Carragher B, Potter C, Sigworth F . Software tools for macromolecular microscopy. J Struct Biol. 2006; 157(1):1-2. DOI: 10.1016/j.jsb.2006.11.001. View

17.

Yeager M, Unger V, Mitra A . Three-dimensional structure of membrane proteins determined by two-dimensional crystallization, electron cryomicroscopy, and image analysis. Methods Enzymol. 1999; 294:135-80. DOI: 10.1016/s0076-6879(99)94010-7. View

18.

Yeremenko N, Kouril R, Ihalainen J, DHaene S, van Oosterwijk N, Andrizhiyevskaya E . Supramolecular organization and dual function of the IsiA chlorophyll-binding protein in cyanobacteria. Biochemistry. 2004; 43(32):10308-13. DOI: 10.1021/bi048772l. View

19.

Henderson R, Baldwin J, Ceska T, Zemlin F, Beckmann E, Downing K . Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J Mol Biol. 1990; 213(4):899-929. DOI: 10.1016/S0022-2836(05)80271-2. View

20.

Ludtke S, Baker M, Chen D, Song J, Chuang D, Chiu W . De novo backbone trace of GroEL from single particle electron cryomicroscopy. Structure. 2008; 16(3):441-8. DOI: 10.1016/j.str.2008.02.007. View