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Nucleic Acids Res. 2014 Apr;42(6):3783-91. doi: 10.1093/nar/gkt1327. Epub 2014 Jan 6.

Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins.

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Department of Materials Science, Northwestern University, 2220 Cook Dr. Evanston, IL 60208, USA, Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA and Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.


Recent work has demonstrated concentration-dependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (2011) (Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res., 39:2249)]. The physical origin of this concentration-dependence is unexplained. We use a combination of coarse-grained simulation and theory to demonstrate that this behavior can be explained by taking into account the dimeric nature of the protein, which permits partial dissociation and exchange with other proteins in solution. Concentration-dependent unbinding is generated by this simple model, quantitatively explaining experimental data. This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules.

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