Literature DB >> 30605122

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

C O S Sorzano1, A Jiménez1, J Mota1, J L Vilas1, D Maluenda1, M Martínez1, E Ramírez-Aportela1, T Majtner1, J Segura1, R Sánchez-García1, Y Rancel1, L Del Caño1, P Conesa1, R Melero1, S Jonic2, J Vargas3, F Cazals4, Z Freyberg5, J Krieger5, I Bahar5, R Marabini6, J M Carazo1.   

Abstract

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Keywords:  continuous heterogeneity; electron microscopy; image processing; normal-mode analysis; single-particle analysis

Mesh:

Substances:

Year:  2019        PMID: 30605122      PMCID: PMC6317454          DOI: 10.1107/S2053230X18015108

Source DB:  PubMed          Journal:  Acta Crystallogr F Struct Biol Commun        ISSN: 2053-230X            Impact factor:   1.056


  16 in total

1.  Hybrid Electron Microscopy Normal Mode Analysis with Scipion.

Authors:  Mohamad Harastani; Carlos Oscar S Sorzano; Slavica Jonić
Journal:  Protein Sci       Date:  2019-11-20       Impact factor: 6.725

Review 2.  Towards gaining sight of multiscale events: utilizing network models and normal modes in hybrid methods.

Authors:  James M Krieger; Pemra Doruker; Ana Ligia Scott; David Perahia; Ivet Bahar
Journal:  Curr Opin Struct Biol       Date:  2020-07-01       Impact factor: 6.809

Review 3.  Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Authors:  Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Chem Rev       Date:  2022-07-04       Impact factor: 72.087

4.  Visualizing Conformational Space of Functional Biomolecular Complexes by Deep Manifold Learning.

Authors:  Zhaolong Wu; Enbo Chen; Shuwen Zhang; Yinping Ma; Youdong Mao
Journal:  Int J Mol Sci       Date:  2022-08-09       Impact factor: 6.208

5.  Continuum dynamics and statistical correction of compositional heterogeneity in multivalent IDP oligomers resolved by single-particle EM.

Authors:  Barmak Mostofian; Russell McFarland; Aidan Estelle; Jesse Howe; Elisar Barbar; Steve L Reichow; Daniel M Zuckerman
Journal:  J Mol Biol       Date:  2022-03-01       Impact factor: 6.151

6.  Cryo-EM reconstruction of continuous heterogeneity by Laplacian spectral volumes.

Authors:  Amit Moscovich; Amit Halevi; Joakim Andén; Amit Singer
Journal:  Inverse Probl       Date:  2020-01-28       Impact factor: 2.407

7.  Single-particle cryo-electron microscopy: Mathematical theory, computational challenges, and opportunities.

Authors:  Tamir Bendory; Alberto Bartesaghi; Amit Singer
Journal:  IEEE Signal Process Mag       Date:  2020-02-27       Impact factor: 12.551

8.  HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes.

Authors:  Mohamad Harastani; Mikhail Eltsov; Amélie Leforestier; Slavica Jonic
Journal:  Front Mol Biosci       Date:  2021-05-19

Review 9.  Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps.

Authors:  Eman Alnabati; Daisuke Kihara
Journal:  Molecules       Date:  2019-12-24       Impact factor: 4.411

10.  Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

Authors:  Roberto Melero; Carlos Oscar S Sorzano; Brent Foster; José-Luis Vilas; Marta Martínez; Roberto Marabini; Erney Ramírez-Aportela; Ruben Sanchez-Garcia; David Herreros; Laura Del Caño; Patricia Losana; Yunior C Fonseca-Reyna; Pablo Conesa; Daniel Wrapp; Pablo Chacon; Jason S McLellan; Hemant D Tagare; Jose-Maria Carazo
Journal:  bioRxiv       Date:  2020-07-08
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