TY - JOUR
T1 - XMDFF
T2 - Molecular dynamics flexible fitting of low-resolution X-ray structures
AU - Mcgreevy, Ryan
AU - Singharoy, Abhishek
AU - Li, Qufei
AU - Zhang, Jingfen
AU - Xu, Dong
AU - Perozo, Eduardo
AU - Schulten, Klaus
N1 - Publisher Copyright:
© 2014 International Union of Crystallography.
PY - 2014/8/26
Y1 - 2014/8/26
N2 - 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.
AB - 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.
KW - molecular dynamics flexible fitting
KW - xMDFF
UR - http://www.scopus.com/inward/record.url?scp=84907009224&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84907009224&partnerID=8YFLogxK
U2 - 10.1107/S1399004714013856
DO - 10.1107/S1399004714013856
M3 - Article
C2 - 25195748
AN - SCOPUS:84907009224
SN - 0907-4449
VL - 70
SP - 2344
EP - 2355
JO - Acta Crystallographica Section D: Biological Crystallography
JF - Acta Crystallographica Section D: Biological Crystallography
IS - 9
ER -