1. Structural Biology and Molecular Biophysics
  2. Computational and Systems Biology
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Molecular dynamics-based model refinement and validation for sub-5 Å cryo-electron microscopy maps

  1. Abhishek Singharoy  Is a corresponding author
  2. Ivan Teo
  3. Ryan McGreevy
  4. John E Stone
  5. Jianhua Zhao
  6. Klaus Schulten  Is a corresponding author
  1. University of Illinois at Urbana Champaign, United States
  2. University of Illinois at Urbana-Champaign, United States
  3. University of California, San Francisco, United States
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Cite this article as: eLife 2016;5:e16105 doi: 10.7554/eLife.16105

Abstract

Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5-Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods, denoted cascade MDFF and resolution exchange MDFF, sequentially re-refine a search model against a series of maps of progressively higher resolutions, which ends with the original experimental resolution. Application of sequential re-refinement enables MDFF to achieve a convergence radius of ~25Å demonstrated with the accurate modeling of β-galactosidase and TRPV1 proteins at 3.2Å and 3.4Å resolution. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the respective macromolecules studied, captured employing local root mean square fluctuations. The MDFF tools are made available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Data availability

The following previously published data sets were used

Article and author information

Author details

  1. Abhishek Singharoy

    Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, United States
    For correspondence
    singharo@illinois.edu
    Competing interests
    The authors declare that no competing interests exist.
  2. Ivan Teo

    Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Ryan McGreevy

    Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. John E Stone

    Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jianhua Zhao

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Klaus Schulten

    Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
    For correspondence
    kschulte@ks.uiuc.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7192-9632

Reviewing Editor

  1. Axel T Brunger, Howard Hughes Medical Institute, Stanford University, United States

Publication history

  1. Received: March 16, 2016
  2. Accepted: July 6, 2016
  3. Accepted Manuscript published: July 7, 2016 (version 1)
  4. Accepted Manuscript updated: July 8, 2016 (version 2)
  5. Version of Record published: August 18, 2016 (version 3)
  6. Version of Record updated: October 7, 2016 (version 4)

Copyright

© 2016, singharoy et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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