XMDFF: Molecular dynamics flexible fitting of low-resolution X-ray structures

Ryan Mcgreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, Klaus Schulten

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of d-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7Å resolution, xMDFF refinements together with electro physiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Original languageEnglish (US)
Pages (from-to)2344-2355
Number of pages12
JournalActa Crystallographica Section D: Biological Crystallography
Volume70
Issue number9
DOIs
StatePublished - Jan 1 2014
Externally publishedYes

Fingerprint

Molecular Dynamics Simulation
X-Rays
Proteins
Ribose
X Ray Crystallography
Carrier Proteins
Databases
Electrons

Keywords

  • molecular dynamics flexible fitting
  • xMDFF

ASJC Scopus subject areas

  • Structural Biology

Cite this

XMDFF : Molecular dynamics flexible fitting of low-resolution X-ray structures. / Mcgreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 70, No. 9, 01.01.2014, p. 2344-2355.

Research output: Contribution to journalArticle

Mcgreevy, Ryan ; Singharoy, Abhishek ; Li, Qufei ; Zhang, Jingfen ; Xu, Dong ; Perozo, Eduardo ; Schulten, Klaus. / XMDFF : Molecular dynamics flexible fitting of low-resolution X-ray structures. In: Acta Crystallographica Section D: Biological Crystallography. 2014 ; Vol. 70, No. 9. pp. 2344-2355.
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