Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors
| Autor: | Gaofei He, Gregory M.K. Poon, James K. Bashkin, Ana Tolic |
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| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular HMG-box DNA footprinting Biology DNA sequencing Proto-Oncogene Protein c-ets-1 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Structural Biology Proto-Oncogene Proteins Genetics Binding site Transcription factor 030304 developmental biology 0303 health sciences Binding Sites DNA DNA-binding domain Protein Structure Tertiary DNA binding site chemistry 030220 oncology & carcinogenesis Trans-Activators Protein Binding |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| DOI: | 10.1093/nar/gkv267 |
| Popis: | The ETS family of transcription factors exemplifies current uncertainty in how eukaryotic genetic regulators with overlapping DNA sequence preferences achieve target site specificity. PU.1 and Ets-1 represent archetypes for studying site discrimination by ETS proteins because their DNA-binding domains are the most divergent in sequence, yet they share remarkably superimposable DNA-bound structures. To gain insight into the contrasting thermodynamics and kinetics of DNA recognition by these two proteins, we investigated the structure and dynamics of site discrimination by their DNA-binding domains. Electrophoretic mobilities of complexes formed by the two homologs with circularly permuted binding sites showed significant dynamic differences only for DNA complexes of PU.1. Free solution measurements by dynamic light scattering showed PU.1 to be more dynamic than Ets-1; moreover, dynamic changes are strongly coupled to site discrimination by PU.1, but not Ets-1. Interrogation of the protein/DNA interface by DNA footprinting showed similar accessibility to dimethyl sulfate for PU.1/DNA and Ets-1/DNA complexes, indicating that the dynamics of PU.1/DNA complexes reside primarily outside that interface. An information-based analysis of the two homologs' binding motifs suggests a role for dynamic coupling in PU.1's ability to enforce a more stringent sequence preference than Ets-1 and its proximal sequence homologs. |
| Databáze: | OpenAIRE |
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