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

Lindert S, Stewart PL, Meiler J
Comput Biol Chem. 2013 42: 1-4

PMID: 23246775 · PMCID: PMC3540162 · DOI:10.1016/j.compbiolchem.2012.11.001

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.

Copyright © 2012 Elsevier Ltd. All rights reserved.

MeSH Terms (7)

Algorithms Catalytic Domain Computer Simulation Crystallography, X-Ray DNA-Activated Protein Kinase Models, Molecular Protein Folding

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