Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps

Abhishek Singharoy, Ivan Teo, Ryan McGreevy, John E. Stone, Jianhua Zhao, Klaus Schulten

Research output: Contribution to journalArticle

44 Citations (Scopus)

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 radius of convergence of ~25 Å demonstrated with the accurate modeling of b-galactosidase and TRPV1 proteins at 3.2 Å and 3.4 Å resolution, respectively. The MDFF refinements uniquely offer map-model validation and B-factor determination criteria based on the inherent dynamics of the macromolecules studied, captured by means of local root mean square fluctuations. The MDFF tools described are available to researchers through an easy-to-use and cost-effective cloud computing resource on Amazon Web Services.

Original languageEnglish (US)
Article numbere16105
JournaleLife
Volume5
Issue numberJULY
DOIs
StatePublished - Jul 7 2016
Externally publishedYes

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Cryoelectron Microscopy
Molecular Dynamics Simulation
Electron microscopy
Molecular dynamics
Galactosidases
Cloud computing
Macromolecules
Web services
Research Personnel
Costs and Cost Analysis
Costs
Proteins

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

Cite this

Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. / Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan; Stone, John E.; Zhao, Jianhua; Schulten, Klaus.

In: eLife, Vol. 5, No. JULY, e16105, 07.07.2016.

Research output: Contribution to journalArticle

Singharoy, Abhishek ; Teo, Ivan ; McGreevy, Ryan ; Stone, John E. ; Zhao, Jianhua ; Schulten, Klaus. / Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps. In: eLife. 2016 ; Vol. 5, No. JULY.
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