title: Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs.
abstract: 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.
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA.
authors.forename: Steffen
authors.initials: S
authors.lastname: Lindert
authors.forename: Phoebe L
authors.initials: PL
authors.lastname: Stewart
authors.forename: Jens
authors.initials: J
authors.lastname: Meiler
mesh_terms: D000465:Algorithms; D020134:Catalytic Domain; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D051747:DNA-Activated Protein Kinase / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding
chemical_list: D051747:DNA-Activated Protein Kinase