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

Abstract

Major secondary structure elements such as α helices and β sheets can be computationally detected from cryoelectron microscopy (cryo-EM) density maps with medium resolutions of 5-10Å. However, a critical piece of information for modeling atomic structures is missing, because there are no tools to detect β strands from cryo-EM maps at medium resolutions. We propose a method, StrandTwister, to detect the traces of β strands through the analysis of twist, an intrinsic nature of a β sheet. StrandTwister has been tested using 100 β sheets simulated at10Å resolution and 39 β sheets computationally detected from cryo-EM density maps at 4.4-7.4Å resolutions. Although experimentally derived cryo-EM maps contain errors, StrandTwister's best detections over 39 cases were able to detect 81.87% of theβ strands, with an overall 1.66Å two-way distance between the detected and observed β traces. StrandTwister appears to detect the traces of β strands on major β sheets quite accurately, particularly at the central area of a β sheet.