ArticleProceedings of the National Academy of Sciences of the United States of America2010
Experimental snapshots of a protein-DNA binding landscape.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- Mutations to transcription factor MAX allosterically increase DNA selectivity by altering folding and binding pathways.Nature communications · 2025Article
- Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1.Biochemistry · 2016Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6.Journal of molecular biology · 2014Article
- Detecting repetitions and periodicities in proteins by tiling the structural space.The journal of physical chemistry. B · 2013Article
- Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Frustration in protein-DNA binding influences conformational switching and target search kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Mammalian testis-determining factor SRY and the enigma of inherited human sex reversal: frustrated induced fit in a bent protein-DNA complex.The Journal of biological chemistry · 2011Article
- Dancing on DNA: kinetic aspects of search processes on DNA.Chemphyschem : a European journal of chemical physics and physical chemistry · 2011Review
- 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
- Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes.BMC structural biology · 2010Article
- Nonnative interactions in coupled folding and binding processes of intrinsically disordered proteins.PloS one · 2010Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Protein recognition of DNA sites is a primary event for gene function. Its ultimate mechanistic understanding requires an integrated structural, dynamic, kinetic, and thermodynamic dissection that is currently limited considering the hundreds of structures of protein-DNA complexes available. We describe a protein-DNA-binding pathway in which an initial, diffuse, transition state ensemble with some nonnative contacts is followed by formation of extensive nonnative interactions that drive the system into a kinetic trap. Finally, nonnative contacts are slowly rearranged into native-like interactions with the DNA backbone. Dissimilar protein-DNA interfaces that populate along the DNA-binding route are explained by a temporary degeneracy of protein-DNA interactions, centered on "dual-role" residues. The nonnative species slow down the reaction allowing for extended functionality.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.