Inference of Joint Conformational Distributions from Separately Acquired Experimental Measurements

Flexible proteins serve vital roles in a multitude of biological processes. However, determining their full conformational ensembles is extremely difficult because this requires detailed knowledge about the heterogeneity of the protein's degrees of freedom. Label-based experiments such as double electron-electron resonance (DEER) are very useful in studying flexible proteins, as they provide distributional data on heterogeneity. These experiments are typically performed separately, so information about correlation between distributions is lost. We have developed a method to recover correlation information using nonequilibrium work estimates in molecular dynamics refinement. We tested this method on a simple model of an alternating-access transporter for which the true joint distributions are known, and it successfully recovered the true joint distribution. We also applied our method to the protein syntaxin-1a, where it discarded physically implausible conformations. Our method thus provides a way to recover correlation structure in separate experimental measurements of conformational ensembles and refines the resulting structural ensemble.