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

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

doi:10.1107/s1399004714013856

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 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.

Highlights

X-ray crystallography is arguably the most versatile and dominant technique for delivering atomic structures of biomolecules
We extended a previous hybrid method, molecular dynamics flexible fitting (MDFF), developed to solve atomic models from cryo-EM densities
The four refinements began with the same initial phasing model and were evaluated against the same target; the final refined structures were evaluated using the overall improvement in Rfree as well as the root-mean-squared deviation (r.m.s.d.) from the target model. xMDFF refinements improved the Rfree value dramatically at every resolution, with an initial value of 0.57 and a final value of 0.23 at a resolution of 3.5 A (Table 1)

Summary

Introduction

X-ray crystallography is arguably the most versatile and dominant technique for delivering atomic structures of biomolecules. Traditional methods for determining X-ray structures include least-squares with gradient descent (Hendrickson, 1985), maximum likelihood (Pannu & Read, 1996; Bricogne & Irwin, 1996; Murshudov et al, 1997), simulated annealing (Brunger, 1988) and knowledge-based conformational sampling (Depristo et al, 2005). Investigating the structure of large biomolecular complexes has posed a serious challenge to traditional crystallographic techniques. The inherent flexibility of such large systems and the presence of disordered solvent and lipids or ligands often cause the crystals to diffract at low resolutions. In the low-resolution limit the number of atomic coordinates to be determined often exceeds the number of observed diffraction intensities. Lower resolutions, >5 A , pose a greater challenge to refinement; even at $7 Aresolution there are in principle enough independent Bragg reflections to determine

Methods

Results

Conclusion