xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures

By Ryan McGreevy, Abhishek Singharoy, Qufei Li, Jingfen Zhang, Dong Xu, Eduardo Perozo, and Klaus Schulten.

Published in Acta Crystallogr D Biol Crystallogr. 2014 Sep;70(Pt 9):2344-55. PMID: 25195748. PMCID: PMC4157446. Link to publication page.

Core Facilities: Membrane Protein Expression and Purification and Computational Modeling.

Figure 1. xMDFF re-refinement characteristics for six structures. The structures with diffraction data between 4 and 4.5 Å resolution had been deposited earlier in the Protein Data Bank and were used as initial models for xMDFF refinement. Improvements were evaluated using the R free values of the xMDFF-refined structures (shown in red) against their respective starting values taken from the deposited structure (blue). In addition, the increase in the percentage of favored Ramachandran angles owing to xMDFF refinement and other structural statistics, as summarized by the overall MolProbity score, were used to measure the improvement in structural geometries.


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 7 Å resolution, xMDFF refinements together with electro­physiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.


Figure 2. Overview of the xMDFF workflow.

Figure 3. Test xMDFF refinement of the ‘closed’ conformation of d-ribose-binding protein using its ‘open’ conformation as the initial phasing model.

Figure 4. Refinement of the highly flexible region in the case of PDB entry 1xdv.

Figure 5. xMDFF refinement of the voltage-sensing protein Ci-VSP.