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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.

SUBMITTER: Lindert S

PROVIDER: S-EPMC3540162 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature

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

Lindert Steffen S Stewart Phoebe L PL Meiler Jens J

Computational biology and chemistry 20121119

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 struct ...[more]

PMID: 23246775

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