Verifying Self-Consistency of Protein Structure and Dynamics through MD Simulation and WAXS

Abstract

Molecular Dynamics (MD) simulations based on a crystal structure and selected force field represent a powerful approach to generate models for the internal motions of a protein in order to interpret the results of biological experiments and model the interactions between proteins and ligands. However, there are relatively few experimental probes that can be used to verify the results of MD, particularly with regard to slow, correlated motions of loops, folds or domains. Wide-angle X-ray solution scattering (WAXS) is sensitive to protein structure and dynamics including secondary, tertiary and quaternary structure and slow, correlated motions. Here, we present a method to utilize the crystal structure of a protein and its corresponding MD simulation to predict WAXS data from a protein. First, the WAXS pattern of a rigid protein is calculated using an explicit atom model of the hydration layer with the software package, XS. Second, MD trajectories are utilized to calculate a sigma-r plot (the standard deviation of interatomic distances averaged as a function of interatomic distance) which is subsequently combined with the results of the XS calculation to predict the scattering pattern of the dynamic protein. The difference between observed and calculated intensities is minimized by scaling the sigma-r plot with a single variable factor which provides a measure of the discrepancy between experimental and computational characterization of global dynamics. In examples presented here, we show that the correspondence between observed and calculated intensities are often excellent, providing direct experimental validation of the MD results. In other examples, we demonstrate how the approach can identify over or under-estimates of large scale motions in MD simulations that may arise from under-sampling of the structural ensemble or inappropriate choice of simulation parameters.