Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions

Major secondary structure elements such as alpha helices and beta sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5-10 angstrom. However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect b strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of beta strands through the analysis of twist, an intrinsic nature of a beta sheet. StrandTwister has been tested using 100 beta sheets simulated at 10 angstrom resolution and 39 beta sheets computationally detected from cryo-EM density maps at 4.4-7.4 angstrom resolutions. Although experimentally derived cryo-EM maps contain errors, StrandTwister's best detections over 39 cases were able to detect 81.87% of the beta strands, with an overall 1.66 angstrom two-way distance between the detected and observed beta traces. StrandTwister appears to detect the traces of beta strands on major beta sheets quite accurately, particularly at the central area of a beta sheet.