Primary Citation PubMed: 18381292
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A combination of computational and experimental approaches identifies DNA sequence constraints associated with target site binding specificity of the transcription factor CSL.
(2014) Nucleic Acids Res 42
PubMed: 25114055 | PubMedCentral: PMC4176381 | DOI: 10.1093/nar/gku730
MATERIALS AND METHODS Preparation of the starting structure The starting structure for the analysis was mouse CSL bound to DNA (HES-1 ( hairy and enhancer of split-1 ) site 5’-TGTGGGAA-3 ... 9;; PDB code 3BRG, resolution 2.2 Å), which contains all of the CSL conserved features but lacks the variable N-terminal residues (52 residues in mouse).
For the modeling experiments, mutations were introduced into the CSL structure, bound to the consensus TGTGGGAA DNA sequence (PDB ID: 3BRG), using MODELLER 9v8.
Starting from the X-ray structure where CSL binds its highest-affinity DNA motif comprised of eight nucleotides CGTGGGAA (PDB code 3BRG ( 17 ), Figure 1B ), all 4 8 permutations of an 8-nt motif were tested and the resulting 65 536 relative binding energies calculated (Figure 1A ).
The unbound structure of the protein was created from the 3BRG crystallographic structure of the protein bound to DNA, by stripping DNA from the complex followed by optimization (energy minimization) in implicit solvent.
Publication Year: 2014
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