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

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 5–10 A˚ . 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 at 10 A˚ resolution and 39 β sheets computationally detected from cryo-EM density maps at 4.4–7.4 A˚ resolutions. Although experimentally derived cryoEMmaps contain errors, StrandTwister’s best detections over 39 cases were able to detect 81.87% of the β strands, with an overall 1.66 A˚ 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

Modeling Beta-Traces for Beta-Barrels from Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) has produced density maps of various resolutions. Although ά-helices can be detected from density maps at 5-8 angstrom resolutions, β-strands are challenging to detect at such density maps due to close-spacing of β-strands. The variety of shapes of β-sheets adds the complexity of β-strands detection from density maps. We propose a new approach to model traces of β-strands for β-barrel density regions that are extracted from cryo-EM density maps. In the test containing eight β-barrels extracted from experimental cryo-EM density maps at 5.5 angstrom-8.25 angstrom resolution, StrandRoller detected about 74.26% of the amino acids in the β-strands with an overall 2.05 angstrom 2-way distance between the detected β-traces and the observed ones, if the best of the fifteen detection cases is considered