Single particle analysis: Difference between revisions

Revision as of 16:11, 14 October 2020

Revision as of 17:01, 11 December 2020

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[[File:SingleParticleAnalysis.png|thumb|right|Single particle analysis segments and averages many particles from a sample, allowing for computer algorithms to process the individual images into a combined "representative" image. This allows for improvements in signal to noise, and can be combined with [[deconvolution]] to provide limited improvements to spatial resolution in the image.]]

'''Single particle analysis''' is a group of related computerized image processing techniques used to analyze images from [[Transmission electron microscope|transmission electron microscopy]] (TEM).<ref name="Frank">{{Cite book|first=Joachim |last=Frank |title=Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state |publisher=Oxford University Press |___location=Oxford |year=2006 |pages= |isbn=978-0-19-518218-7 |url=https://books.google.com/?id=vWaSRUjicbgC}}{{Page needed|date=August 2010}}</ref> These methods were developed to improve and extend the information obtainable from TEM images of particulate samples, typically [[proteins]] or other large biological entities such as [[virus]]es. Individual images of stained or unstained particles are very [[Signal noise|noisy]], and so hard to interpret. Combining several digitized images of similar particles together gives an image with stronger and more easily interpretable features. An extension of this technique uses single particle methods to build up a [[Transmission electron microscopy#Three dimensional imaging|three-dimensional reconstruction]] of the particle. Using [[cryogenic transmission electron microscopy|cryo-electron microscopy]] it has become possible to generate reconstructions with sub-[[Nanometre|nanometer]] [[Resolution (electron density)|resolution]] and near-atomic resolution<ref name="Zhou">{{Cite journal|author=Zhou ZH |title=Towards atomic resolution structural determination by single-particle cryo-electron microscopy |journal=Current Opinion in Structural Biology |volume=18 |issue=2 |pages=218–28 |date=April 2008 |pmid=18403197 |pmc=2714865 |doi=10.1016/j.sbi.2008.03.004}}</ref><ref name="Dynamics">{{Cite journal|vauthors=Wang Q, Matsui T, Domitrovic T, Zheng Y, Doerschuk PC, Johnson JE |title=Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps |journal=Journal of Structural Biology|volume=181|issue=3 |pages=195–206 |date=March 2013 |doi=10.1016/j.jsb.2012.11.005|pmid=23246781 |pmc=3870017}}</ref> first in the case of highly symmetric viruses, and now in smaller, asymmetric proteins as well.<ref name="Bartesaghi">{{Cite journal| doi = 10.1126/science.aab1576| issn = 1095-9203| volume = 348| issue = 6239| pages = 1147–1151| last1 = Bartesaghi| first1 = Alberto| last2 = Merk| first2 = Alan| last3 = Banerjee| first3 = Soojay| last4 = Matthies| first4 = Doreen| last5 = Wu| first5 = Xiongwu| last6 = Milne| first6 = Jacqueline L. S.| last7 = Subramaniam| first7 = Sriram| title = 2.2 Å resolution CryoTEM structure of β-galactosidase in complex with a cell-permeant inhibitor| journal = Science| date = 2015-06-05| pmid = 25953817| pmc = 6512338| bibcode = 2015Sci...348.1147B}}</ref>

==Techniques==

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==Examples==

* Important information on protein synthesis, [[Ligand (biochemistry)|ligand binding]] and RNA interaction can be obtained using this novel technique at medium resolutions of 7.5 to 25Å.<ref>{{cite journal |vauthors=Arias-Palomo E, Recuero-Checa MA, Bustelo XR, Llorca O |title=3D structure of Syk kinase determined by single-particle electron microscopy |journal=Biochim. Biophys. Acta |volume=1774 |issue=12 |pages=1493–9 |date=December 2007 |pmid=18021750 |pmc=2186377 |doi=10.1016/j.bbapap.2007.10.008 |url=}}</ref>

* ''[[Methanococcus maripaludis]]'' chaperonin,<ref>Japanese Protein databank http://www.pdbj.org/emnavi/emnavi_movie.php?id=5137</ref> reconstructed to 0.43 nanometer resolution.<ref name="Zhang J">{{Cite journal |vauthors=Zhang J, Baker ML, Schröder GF, etal |title=Mechanism of folding chamber closure in a group II chaperonin |journal=Nature |volume=463 |issue=7279 |pages=379–83 |date=January 2010 |pmid=20090755 |pmc=2834796 |doi=10.1038/nature08701|bibcode=2010Natur.463..379Z }}</ref> This bacterial protein complex is a machine for folding other proteins, which get trapped within the shell.

* [[Fatty acid synthase]]<ref>Japanese Protein databank http://www.pdbj.org/emnavi/emnavi_movie.php?id=1623</ref> from yeast at 0.59 nanometer resolution.<ref name="Gipson">{{Cite journal|vauthors=Gipson P, Mills DJ, Wouts R, Grininger M, Vonck J, Kühlbrandt W |title=Direct structural insight into the substrate-shuttling mechanism of yeast fatty acid synthase by electron cryomicroscopy |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=107 |issue=20 |pages=9164–9 |date=May 2010 |pmid=20231485 |pmc=2889056 |doi=10.1073/pnas.0913547107|bibcode=2010PNAS..107.9164G }}</ref> This huge enzyme complex is responsible for building the long chain fatty acids essential for cellular life.