Literature DB >> 28811371

Angular reconstitution-based 3D reconstructions of nanomolecular structures from superresolution light-microscopy images.

Desirée Salas1, Antoine Le Gall1, Jean-Bernard Fiche1, Alessandro Valeri1, Yonggang Ke2,3, Patrick Bron1, Gaetan Bellot4, Marcelo Nollmann5.   

Abstract

Superresolution light microscopy allows the imaging of labeled supramolecular assemblies at a resolution surpassing the classical diffraction limit. A serious limitation of the superresolution approach is sample heterogeneity and the stochastic character of the labeling procedure. To increase the reproducibility and the resolution of the superresolution results, we apply multivariate statistical analysis methods and 3D reconstruction approaches originally developed for cryogenic electron microscopy of single particles. These methods allow for the reference-free 3D reconstruction of nanomolecular structures from two-dimensional superresolution projection images. Since these 2D projection images all show the structure in high-resolution directions of the optical microscope, the resulting 3D reconstructions have the best possible isotropic resolution in all directions.

Keywords:  3D reconstruction; DNA origami; multivariate statistical analysis; structural biology; superresolution microscopy

Year:  2017        PMID: 28811371      PMCID: PMC5584428          DOI: 10.1073/pnas.1704908114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  43 in total

1.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

Authors:  Peter B Rosenthal; Richard Henderson
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

2.  Folding DNA to create nanoscale shapes and patterns.

Authors:  Paul W K Rothemund
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

3.  Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure.

Authors:  Gleb Shtengel; James A Galbraith; Catherine G Galbraith; Jennifer Lippincott-Schwartz; Jennifer M Gillette; Suliana Manley; Rachid Sougrat; Clare M Waterman; Pakorn Kanchanawong; Michael W Davidson; Richard D Fetter; Harald F Hess
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-06       Impact factor: 11.205

4.  Single particle electron cryomicroscopy: trends, issues and future perspective.

Authors:  Kutti R Vinothkumar; Richard Henderson
Journal:  Q Rev Biophys       Date:  2016-07-22       Impact factor: 5.318

5.  The 70S Escherichia coli ribosome at 23 A resolution: fitting the ribosomal RNA.

Authors:  H Stark; F Mueller; E V Orlova; M Schatz; P Dube; T Erdemir; F Zemlin; R Brimacombe; M van Heel
Journal:  Structure       Date:  1995-08-15       Impact factor: 5.006

6.  The correlation averaging of a regularly arranged bacterial cell envelope protein.

Authors:  W O Saxton; W Baumeister
Journal:  J Microsc       Date:  1982-08       Impact factor: 1.758

7.  Resolution improvement by 3D particle averaging in localization microscopy.

Authors:  Jordi Broeken; Hannah Johnson; Diane S Lidke; Sheng Liu; Robert P J Nieuwenhuizen; Sjoerd Stallinga; Keith A Lidke; Bernd Rieger
Journal:  Methods Appl Fluoresc       Date:  2015-03       Impact factor: 3.009

8.  Structure of a type IV secretion system.

Authors:  Harry H Low; Francesca Gubellini; Angel Rivera-Calzada; Nathalie Braun; Sarah Connery; Annick Dujeancourt; Fang Lu; Adam Redzej; Rémi Fronzes; Elena V Orlova; Gabriel Waksman
Journal:  Nature       Date:  2014-03-09       Impact factor: 49.962

9.  Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes.

Authors:  Andrew G York; Alireza Ghitani; Alipasha Vaziri; Michael W Davidson; Hari Shroff
Journal:  Nat Methods       Date:  2011-02-13       Impact factor: 28.547

10.  Recruitment, assembly, and molecular architecture of the SpoIIIE DNA pump revealed by superresolution microscopy.

Authors:  Jean-Bernard Fiche; Diego I Cattoni; Nele Diekmann; Julio Mateos Langerak; Caroline Clerte; Catherine A Royer; Emmanuel Margeat; Thierry Doan; Marcelo Nöllmann
Journal:  PLoS Biol       Date:  2013-05-07       Impact factor: 8.029

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  10 in total

1.  Single-molecule localization microscopy.

Authors:  Mickaël Lelek; Melina T Gyparaki; Gerti Beliu; Florian Schueder; Juliette Griffié; Suliana Manley; Ralf Jungmann; Markus Sauer; Melike Lakadamyali; Christophe Zimmer
Journal:  Nat Rev Methods Primers       Date:  2021-06-03

2.  Deciphering a hexameric protein complex with Angstrom optical resolution.

Authors:  Hisham Mazal; Franz-Ferdinand Wieser; Vahid Sandoghdar
Journal:  Elife       Date:  2022-05-26       Impact factor: 8.713

Review 3.  The emergence of phase separation as an organizing principle in bacteria.

Authors:  Christopher A Azaldegui; Anthony G Vecchiarelli; Julie S Biteen
Journal:  Biophys J       Date:  2020-09-28       Impact factor: 4.033

4.  3D particle averaging and detection of macromolecular symmetry in localization microscopy.

Authors:  Hamidreza Heydarian; Maarten Joosten; Adrian Przybylski; Florian Schueder; Ralf Jungmann; Ben van Werkhoven; Jan Keller-Findeisen; Jonas Ries; Sjoerd Stallinga; Mark Bates; Bernd Rieger
Journal:  Nat Commun       Date:  2021-05-14       Impact factor: 14.919

5.  Deformed alignment of super-resolution images for semi-flexible structures.

Authors:  Xiaoyu Shi; Galo Garcia; Yina Wang; Jeremy F Reiter; Bo Huang
Journal:  PLoS One       Date:  2019-03-13       Impact factor: 3.240

6.  CENP-A nucleosome clusters form rosette-like structures around HJURP during G1.

Authors:  Leonid Andronov; Khalid Ouararhni; Isabelle Stoll; Bruno P Klaholz; Ali Hamiche
Journal:  Nat Commun       Date:  2019-09-30       Impact factor: 14.919

7.  Nanoscale Pattern Extraction from Relative Positions of Sparse 3D Localizations.

Authors:  Alistair P Curd; Joanna Leng; Ruth E Hughes; Alexa J Cleasby; Brendan Rogers; Chi H Trinh; Michelle A Baird; Yasuharu Takagi; Christian Tiede; Christian Sieben; Suliana Manley; Thomas Schlichthaerle; Ralf Jungmann; Jonas Ries; Hari Shroff; Michelle Peckham
Journal:  Nano Lett       Date:  2020-11-30       Impact factor: 11.189

Review 8.  Mapping molecular complexes with super-resolution microscopy and single-particle analysis.

Authors:  Afonso Mendes; Hannah S Heil; Simao Coelho; Christophe Leterrier; Ricardo Henriques
Journal:  Open Biol       Date:  2022-07-27       Impact factor: 7.124

9.  Multicolor single-particle reconstruction of protein complexes.

Authors:  Christian Sieben; Niccolò Banterle; Kyle M Douglass; Pierre Gönczy; Suliana Manley
Journal:  Nat Methods       Date:  2018-10-01       Impact factor: 28.547

10.  Isolation and Fluorescence Imaging for Single-particle Reconstruction of Chlamydomonas Centrioles.

Authors:  Nikolai Klena; Davide Gambarotto; Maeva Le Guennec; Susanne Borgers; Paul Guichard; Virginie Hamel
Journal:  J Vis Exp       Date:  2018-09-21       Impact factor: 1.355

  10 in total

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