How a protein searches for its site on DNA: the mechanism of facilitated diffusion
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Summary
It is demonstrated that coupling of DNA recognition with conformational transition within the protein–DNA complex is essential for fast search, and a new mechanism for local distance-dependent search that is likely essential in bacteria is proposed.
- Type
- article
- Published
- 2009-10-13
- Cited by
- 364
- References
- 89
- OpenAlex
- https://openalex.org/W2074142433
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8316596
Keywords
Mechanism (biology), Diffusion, DNA, Facilitated diffusion, Computational biology
References
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Cited by
- Mechanistic stochastic model of histone modification pattern formation
- Optimizing mating encounters by sexually dimorphic movements
- Optimal search strategies on complex networks
- Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher
- Sequence heterogeneity accelerates protein search for targets on DNA.
- Searching target sites on DNA by proteins: Role of DNA dynamics under confinement
- Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes
- Facilitated diffusion of proteins on DNA
- Symbolic complexity for nucleotide sequences: a sign of the genome structure
- Effects of Hydrodynamic Interactions on the Apparent 1D Mobility of a Nonspecifically Bound Protein Following a Helical Path around DNA.
- Protein search for multiple targets on DNA.
- The helical structure of DNA facilitates binding
- Single molecule study of non-specific binding kinetics of LacI in mammalian cells.
- Formaldehyde Crosslinking: A Tool for the Study of Chromatin Complexes*
- Facilitated diffusion framework for transcription factor search with conformational changes
- Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble
- Protein-DNA electrostatics: toward a new paradigm for protein sliding.
- Coarse-grained modeling of protein unspecifically bound to DNA
- Structures and functions in the crowded nucleus: new biophysical insights
- Mapping DNA-Lac repressor interaction with ultra-fast optical tweezers
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