ArticleProceedings of the National Academy of Sciences of the United States of America2008
Transition state for protein-DNA recognition.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Structural and functional roles of conserved residues of human papillomavirus (HPV) E2 protein and biological consequences.Virology journal · 2025Article
- Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways.Nature communications · 2025Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- Direct observation of a transient ternary complex during IκBα-mediated dissociation of NF-κB from DNA.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex.The journal of physical chemistry. A · 2013Article
- Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Quantifying the similarity of monotonic trajectories in rough and smooth fitness landscapes.Molecular bioSystems · 2013Article
- Cooperative binding of transcription factors promotes bimodal gene expression response.PloS one · 2012Article
- Protein flexibility directs DNA recognition by the papillomavirus E2 proteins.Nucleic acids research · 2011Article
- Mutational analysis of kinetic partitioning in protein folding and protein-DNA binding.Protein engineering, design & selection : PEDS · 2011Article
- Thermodynamics of cooperative DNA recognition at a replication origin and transcription regulatory site.Biochemistry · 2010Article
- Experimental snapshots of a protein-DNA binding landscape.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Contributions of the histidine side chain and the N-terminal alpha-amino group to the binding thermodynamics of oligopeptides to nucleic acids as a function of pH.Biochemistry · 2010Article
- Capillarity theory for the fly-casting mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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Authors and funding
3 authors.
Funding
Abstract
We describe the formation of protein-DNA contacts in the two-state route for DNA sequence recognition by a transcriptional regulator. Surprisingly, direct sequence readout establishes in the transition state and constitutes the bottleneck of complex formation. Although a few nonspecific ionic interactions are formed at this early stage, they mainly play a stabilizing role in the final consolidated complex. The interface is fairly plastic in the transition state, likely because of a high level of hydration. The overall picture of this two-state route largely agrees with a smooth energy landscape for binding that speeds up DNA recognition. This "direct" two-state route differs from the parallel multistep pathway described for this system, which involves nonspecific contacts and at least two intermediate species that must involve substantial conformational rearrangement in either or both macromolecules.
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