ArticleBiophysical journal2008
Monte carlo simulations of protein assembly, disassembly, and linear motion on DNA.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Who cites it
7 citing papers in PubMed.
- NProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA.Nature structural & molecular biology · 2024Article
- Visualization and quantification of nascent RAD51 filament formation at single-monomer resolution.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Effect of the BRCA2 CTRD domain on RAD51 filaments analyzed by an ensemble of single molecule techniques.Nucleic acids research · 2011Article
- Torsional regulation of hRPA-induced unwinding of double-stranded DNA.Nucleic acids research · 2010Article
- Dynamics of RecA filaments on single-stranded DNA.Nucleic acids research · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use Monte Carlo simulations to analyze the simultaneous interactions of multiple proteins to a long DNA molecule. We study the time dependence of protein organization on DNA for different regimes that comprise (non)cooperative sequence-independent protein assembly, dissociation, and linear motion. A range of different behaviors is observed for the dynamics, final coverage, and cluster size distributions. We observe that the DNA substrate is almost never completely covered by protein when taking into account only (non)cooperative binding, because gaps remain on the substrate that are smaller than the binding site size of the protein. Due to these gaps, the apparent binding size of a protein during noncooperative binding can be overestimated by up to 30%. During dissociation of cooperatively bound proteins, the dissociation curve can be exponentially shaped even when allowing only end-dependent dissociation. We discuss the potential of our method for the analysis of a number of single-molecule experiments, for example, the binding of the DNA-repair proteins RecA and Rad51 to DNA.
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Registered trials
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