Literature DB >> 22152946

Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions.

Niels Volkmann1.   

Abstract

A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 22152946      PMCID: PMC3294126          DOI: 10.1016/j.ceb.2011.11.002

Source DB:  PubMed          Journal:  Curr Opin Cell Biol        ISSN: 0955-0674            Impact factor:   8.382


  94 in total

1.  Multi-resolution contour-based fitting of macromolecular structures.

Authors:  Pablo Chacón; Willy Wriggers
Journal:  J Mol Biol       Date:  2002-03-29       Impact factor: 5.469

2.  Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.

Authors:  Haixiao Gao; Joachim Frank
Journal:  Structure       Date:  2005-03       Impact factor: 5.006

3.  Structure determination in situ by averaging of tomograms.

Authors:  Friedrich Förster; Reiner Hegerl
Journal:  Methods Cell Biol       Date:  2007       Impact factor: 1.441

4.  Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations.

Authors:  Craig C Jolley; Stephen A Wells; Petra Fromme; M F Thorpe
Journal:  Biophys J       Date:  2007-11-09       Impact factor: 4.033

5.  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

6.  Direct phase determination in protein electron crystallography: the pseudo-atom approximation.

Authors:  D L Dorset
Journal:  Proc Natl Acad Sci U S A       Date:  1997-03-04       Impact factor: 11.205

7.  Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography.

Authors:  Friedrich Förster; Ohad Medalia; Nathan Zauberman; Wolfgang Baumeister; Deborah Fass
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-17       Impact factor: 11.205

8.  Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonance.

Authors:  K Wüthrich; M Billeter; W Braun
Journal:  J Mol Biol       Date:  1983-10-05       Impact factor: 5.469

9.  Three-dimensional structure of vinculin bound to actin filaments.

Authors:  Mandy E W Janssen; Eldar Kim; Hongjun Liu; L Miya Fujimoto; Andrey Bobkov; Niels Volkmann; Dorit Hanein
Journal:  Mol Cell       Date:  2006-01-20       Impact factor: 17.970

10.  Visual proteomics of the human pathogen Leptospira interrogans.

Authors:  Martin Beck; Johan A Malmström; Vinzenz Lange; Alexander Schmidt; Eric W Deutsch; Ruedi Aebersold
Journal:  Nat Methods       Date:  2009-10-18       Impact factor: 28.547

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  7 in total

Review 1.  Piecing it together: Unraveling the elusive structure-function relationship in single-pass membrane receptors.

Authors:  Christopher C Valley; Andrew K Lewis; Jonathan N Sachs
Journal:  Biochim Biophys Acta Biomembr       Date:  2017-01-12       Impact factor: 3.747

2.  Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.

Authors:  Javier Velázquez-Muriel; Keren Lasker; Daniel Russel; Jeremy Phillips; Benjamin M Webb; Dina Schneidman-Duhovny; Andrej Sali
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-29       Impact factor: 11.205

3.  Efficient Extraction of Macromolecular Complexes from Electron Tomograms Based on Reduced Representation Templates.

Authors:  Xiao-Ping Xu; Christopher Page; Niels Volkmann
Journal:  Comput Anal Images Patterns       Date:  2015-08-25

Review 4.  Electron crystallography--the waking beauty of structural biology.

Authors:  Christopher R Pope; Vinzenz M Unger
Journal:  Curr Opin Struct Biol       Date:  2012-04-21       Impact factor: 6.809

5.  PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements.

Authors:  Sean M Law; Aaron T Frank; Charles L Brooks
Journal:  J Comput Chem       Date:  2014-07-04       Impact factor: 3.376

6.  Few-shot learning for classification of novel macromolecular structures in cryo-electron tomograms.

Authors:  Ran Li; Liangyong Yu; Bo Zhou; Xiangrui Zeng; Zhenyu Wang; Xiaoyan Yang; Jing Zhang; Xin Gao; Rui Jiang; Min Xu
Journal:  PLoS Comput Biol       Date:  2020-11-11       Impact factor: 4.475

7.  LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry.

Authors:  Jacob D Durrant; Rommie E Amaro
Journal:  PLoS Comput Biol       Date:  2014-07-17       Impact factor: 4.475

  7 in total

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