Algorithmic robustness to preferred orientations in single particle analysis by CryoEM.

Autor: Sorzano COS; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain. Electronic address: carazo@cnb.csic.es., Semchonok D; ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany., Lin SC; Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan., Lo YC; Dept. Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan., Vilas JL; Dept. of Biomedical Engineering, Yale University, New Haven, United States., Jiménez-Moreno A; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Gragera M; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Vacca S; Dept. of Biochemistry, Univ. Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland., Maluenda D; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Martínez M; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Ramírez-Aportela E; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Melero R; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Cuervo A; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Conesa JJ; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Conesa P; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Losana P; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Caño LD; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., de la Morena JJ; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Fonseca YC; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Sánchez-García R; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Strelak D; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Fernández-Giménez E; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., de Isidro F; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Herreros D; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Kastritis PL; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain., Marabini R; Escuela Politecnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain., Bruce BD; Dept. Biochemistry & Cellular and Molecular Biology, Univ. Tennessee Knoxville, Knoxville, TN 37996, United States., Carazo JM; Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain.
Jazyk: angličtina
Zdroj: Journal of structural biology [J Struct Biol] 2021 Mar; Vol. 213 (1), pp. 107695. Date of Electronic Publication: 2021 Jan 07.
DOI: 10.1016/j.jsb.2020.107695
Abstrakt: The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.
(Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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