ArticleNucleic acids research2017
How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 23 citations in OpenAlex.
- DyProL: Dynamic Ensemble Representation Learning for Protein-Nucleic Acid Binding Site Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations.Nucleic acids research · 2023Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.European biophysics journal : EBJ · 2021Article
- Transcriptional regulation of telomeric repeat-containing RNA by acridine derivatives.RNA biology · 2021Article
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
- Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Hinge like domain motion facilitates human RBMS1 protein binding to proto-oncogene c-myc promoter.Nucleic acids research · 2021Article
- Dynamics of TRF1 organizing a single human telomere.Nucleic acids research · 2021Article
- Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.Nucleic acids research · 2020Article
- Tunable order-disorder continuum in protein-DNA interactions.Nucleic acids research · 2018Article
- Protein plasticity driven by disorder and collapse governs the heterogeneous binding of CytR to DNA.Nucleic acids research · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
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