RosettaEPR: An integrated tool for protein structure determination from sparse EPR data

Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is often used for the structural characterization of proteins that elude other techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR). However, high-resolution structures are difficult to obtain due to uncertainty in the spin label location and sparseness of experimental data. Here, we introduce RosettaEPR, which has been designed to improve de novo high-resolution protein structure prediction using sparse SDSL-EPR distance data. The “motion-on-a-cone” spin label model is converted into a knowledge-based potential, which was implemented as a scoring term in Rosetta. RosettaEPR increased the fractions of correctly folded models (RMSDCα < 7.5 Å) and models accurate at medium resolution (RMSDCα < 3.5 Å) by 25%. The correlation of score and model quality increased from 0.42 when using no restraints to 0.51 when using bounded restraints and again to 0.62 when using RosettaEPR. This allowed for the selection of accurate models by score. After full-atom refinement, RosettaEPR yielded a 1.7 Å model of T4-lysozyme, thus indicating that atomic detail models can be achieved by combining sparse EPR data with Rosetta. While these results indicate RosettaEPR's potential utility in high-resolution protein structure prediction, they are based on a single example. In order to affirm the method's general performance, it must be tested on a larger and more versatile dataset of proteins.