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Conformational selection or induced fit for Brinker and DNA recognitionElectronic supplementary information (ESI) available: Transition state and related information. See DOI: 10.1039/c0cp00701c.
- Source :
- Physical Chemistry Chemical Physics (PCCP); Jan2011, Vol. 13 Issue 4, p1407-1412, 6p
- Publication Year :
- 2011
-
Abstract
- Brinker is the key target protein of the Drosophila Decapentaplegic morphogen signalling pathway. Brinker is widely expressed and can bind with DNA. NMR spectra suggest that apo-Brinker is intrinsically unstructured and undergoes a folding transition upon DNA-binding. However, the coupled mechanism of binding and folding is poorly understood. Here, we performed molecular dynamics (MD) simulations for both bound and apo-Brinker to study the mechanism. Room-temperature MD simulations suggest that Brinker becomes more rigid and stable upon DNA-binding. Kinetic analysis of high-temperature MD simulations shows that both bound and apo-Brinker unfold viaa two-state process. The time scale of tertiary unfolding is significantly different between bound and apo-Brinker. The predicted Φ-values suggest that there are more residues with native-like transition state ensembles (TSEs) for bound Brinker than for apo-Brinker. The average RMSD differences between bound and apo-Brinker and Kolmogorov-Smirnov (KS) test analysis illustrate that Brinker folding upon DNA-binding might obey induced-fit mechanism based on MD simulations. These methods can be used for the research of other biomolecular folding upon ligand-binding. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 14639076
- Volume :
- 13
- Issue :
- 4
- Database :
- Complementary Index
- Journal :
- Physical Chemistry Chemical Physics (PCCP)
- Publication Type :
- Academic Journal
- Accession number :
- 57512175
- Full Text :
- https://doi.org/10.1039/c0cp00701c