Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs

DNA dependent protein kinase catalytic subunit (DNA-PKcs) is an important regulatory protein in non-homologous end joining a process used to repair DNA double strand breaks. Medium resolution structures both from cryoEM and X-ray crystallography show the general topology of the protein and positions of helices in parts of DNA-PKcs. EM-Fold, an algorithm developed for building protein models into medium resolution density maps has been used to generate models for the heat repeat-like “Ring structure” of the molecule. We were able to computationally corroborate placement of the N-terminus of the domain that supports a previously published hypothesis. Targeted experiments are suggested to test the model.

Graphical abstractFigure optionsDownload full-size imageDownload as PowerPoint slideHighlights► Computational determination of orientation of heat repeat domain of DNA-PKcs. ► Presentation of structural model for heat repeat domain to enable design of experiments. ► Adaption of EM-Fold to work with X-ray density maps.