Single particle analysis: Difference between revisions

Revision as of 17:09, 6 November 2024

Revision as of 13:05, 18 November 2024

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Various software [[Software tools for molecular microscopy|programs]] are available that allow viewing the 3D maps. These often enable the user to manually dock in protein coordinates (structures from [[X-ray crystallography]] or NMR) of subunits into the electron density. Several programs can also fit subunits computationally.<ref>{{cite web |title=Cryo-EM structure solution with Phenix |url=https://phenix-online.org/documentation/overviews/cryo-em_index.html |website=phenix-online.org}}</ref><ref>{{cite journal |last1=Nicholls |first1=RA |last2=Tykac |first2=M |last3=Kovalevskiy |first3=O |last4=Murshudov |first4=GN |title=Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM. |journal=Acta Crystallographica Section D |date=1 June 2018 |volume=74 |issue=Pt 6 |pages=492–505 |doi=10.1107/S2059798318007313 |pmid=29872001|pmc=6096485 |bibcode=2018AcCrD..74..492N |doi-access=free }}</ref>

For higher-resolution structures, it is possible to build the macromolecule directly, without prior structural knowledge from other methods. Computer algorithms have also been developed for this task.<ref>{{cite journal |doi=10.1038/s41586-024-07215-4 |biorxiv=10.1101/2023.05.16.541002 |title=Automated model building and protein identification in cryo-EM maps |date=2024 |last1=Jamali |first1=Kiarash |last2=Käll |first2=Lukas |last3=Zhang |first3=Rui |last4=Brown |first4=Alan |last5=Kimanius |first5=Dari |last6=Scheres |first6=Sjors H. W. |journal=Nature |volume=628 |issue=8007 |pages=450–457 |pmid=38408488 |pmc=10245678 |bibcode=2024Natur.628..450J }}</ref>

As high-resolution cryo-EM models are relative new, quality control tools are not as plentiful as it is for X-ray models. Nevertheless, cryo-EM ("real space") versions of the [[difference density map]],<ref>{{cite journal |last1=Yamashita |first1=Keitaro |last2=Palmer |first2=Colin M. |last3=Burnley |first3=Tom |last4=Murshudov |first4=Garib N. |title=Cryo-EM single-particle structure refinement and map calculation using Servalcat |journal=Acta Crystallographica Section D |date=1 October 2021 |volume=77 |issue=10 |pages=1282–1291 |doi=10.1107/S2059798321009475 |pmid=34605431 |pmc=8489229 |bibcode=2021AcCrD..77.1282Y |doi-access=free |quote=}}</ref> cross-validation using a "free" map (comparable to the use of a free [[R-factor]]),<ref>{{cite journal |last1=Falkner |first1=B |last2=Schröder |first2=GF |title=Cross-validation in cryo-EM-based structural modeling. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=28 May 2013 |volume=110 |issue=22 |pages=8930–5 |doi=10.1073/pnas.1119041110 |pmid=23674685|pmc=3670386 |bibcode=2013PNAS..110.8930F |doi-access=free }}</ref><ref>{{cite journal |last1=Beckers |first1=Maximilian |last2=Mann |first2=Daniel |last3=Sachse |first3=Carsten |title=Structural interpretation of cryo-EM image reconstructions |journal=Progress in Biophysics and Molecular Biology |date=March 2021 |volume=160 |pages=26–36 |doi=10.1016/j.pbiomolbio.2020.07.004 |pmid=32735944 |doi-access=free}}</ref> and various [[structure validation]] tools have begun to appear.

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===Single particle ICP-MS===

Single particle-induced coupled plasma-mass spectroscopy (SP-ICP-MS) is used in several areas where there is the possibility of detecting and quantifying suspended particles in samples of environmental fluids, assessing their migration, assessing the size of particles and their distribution, and also determining their stability in a given environment. SP-ICP-MS was designed for particle suspensions in 2000 by Claude Degueldre. He first tested this new methodology at the Forel Institute of the University of Geneva and presented this new analytical approach at the 'Colloid 2oo2' symposium during the spring 2002 meeting of the EMRS, and in the proceedings in 2003.<ref>{{cite journal | doi=10.1016/S0927-7757(02)00568-X | title=Colloid analysis by single particle inductively coupled plasma-mass spectroscopy: A feasibility study | date=2003 | last1=Degueldre | first1=C. | last2=Favarger | first2=P.-Y. | journal=Colloids and Surfaces A: Physicochemical and Engineering Aspects | volume=217 | issue=1–3 | pages=137–142 }}</ref> This study presents the theory of SP ICP-MS and the results of tests carried out on clay particles (montmorillonite) as well as other suspensions of colloids. This method was then tested on thorium dioxide nanoparticles by Degueldre & Favarger (2004),<ref>{{cite journal | doi=10.1016/j.talanta.2003.10.016 | title=Thorium colloid analysis by single particle inductively coupled plasma-mass spectrometry | date=2004 | last1=Degueldre | first1=C. | journal=Talanta | volume=62 | issue=5 | pages=1051–1054 | pmid=18969397 }}</ref> zirconium dioxide by Degueldre et al (2004)<ref>{{cite journal | doi=10.1016/j.aca.2004.04.015 | title=Zirconia colloid analysis by single particle inductively coupled plasma–mass spectrometry | date=2004 | last1=Degueldre | first1=C. | last2=Favarger | first2=P.-Y. | last3=Bitea | first3=C. | journal=Analytica Chimica Acta | volume=518 | issue=1–2 | pages=137–142 | bibcode=2004AcAC..518..137D }}</ref> and gold nanoparticles, which are used as a substrate in nanopharmacy, and published by Degueldre et al (2006).<ref>{{cite journal | doi=10.1016/j.aca.2005.09.021 | title=Gold colloid analysis by inductively coupled plasma-mass spectrometry in a single particle mode | date=2006 | last1=Degueldre | first1=C. | last2=Favarger | first2=P.-Y. | last3=Wold | first3=S. | journal=Analytica Chimica Acta | volume=555 | issue=2 | pages=263–268 | bibcode=2006AcAC..555..263D }}</ref> Subsequently, the study of uranium dioxide nano- and micro-particles gave rise to a detailed publication, Degueldre et al (2006).<ref>{{cite journal | doi=10.1016/j.talanta.2005.05.006 | title=Uranium colloid analysis by single particle inductively coupled plasma-mass spectrometry | date=2006 | last1=Degueldre | first1=C. | last2=Favarger | first2=P.-Y. | last3=Rossé | first3=R. | last4=Wold | first4=S. | journal=Talanta | volume=68 | issue=3 | pages=623–628 | pmid=18970366 }}</ref> Since 2010 the interest for SP ICP-MS has exploded.

==Examples==