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Evidence for a bind-then-bend mechanism for architectural DNA binding protein yNhp6A.
- Source :
-
Nucleic acids research [Nucleic Acids Res] 2019 Apr 08; Vol. 47 (6), pp. 2871-2883. - Publication Year :
- 2019
-
Abstract
- The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60°. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are 'captured' by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18-base-pair DNA oligomer indeed remains bound to yNhp6A while unbent. In 100 mM NaCl, yNhp6A-bound DNA unbends as the temperature is raised, with no significant dissociation of the complex detected up to ∼45°C. In 200 mM NaCl, DNA unbending in the intact yNhp6A complex is again detected up to ∼35°C. Microseconds-resolved laser temperature-jump perturbation of the yNhp6a-DNA complex revealed relaxation kinetics that yielded unimolecular DNA bending/unbending rates on timescales of 500 μs-1 ms. These data provide the first direct observation of bending/unbending dynamics of DNA in complex with yNhp6A, suggesting a bind-then-bend mechanism for this protein.<br /> (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Subjects :
- Chromatin Assembly and Disassembly genetics
Fluorescence Resonance Energy Transfer
HMGN Proteins physiology
Models, Molecular
Molecular Dynamics Simulation
Protein Binding
Protein Structure, Quaternary
Saccharomyces cerevisiae genetics
Saccharomyces cerevisiae Proteins physiology
DNA, Fungal chemistry
DNA, Fungal metabolism
HMGN Proteins chemistry
HMGN Proteins metabolism
Nucleic Acid Conformation
Saccharomyces cerevisiae Proteins chemistry
Saccharomyces cerevisiae Proteins metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1362-4962
- Volume :
- 47
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Nucleic acids research
- Publication Type :
- Academic Journal
- Accession number :
- 30698746
- Full Text :
- https://doi.org/10.1093/nar/gkz022