ArticleNucleic acids research2016
Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 70 citations in OpenAlex.
- So close yet so far apart: distinct flanking sequence recognition by DNMT3A and DNMT3B.Communications biology · 2025Article
- Dynamics design of a non-natural transcription factor responding to androst-4-ene-3,17-dione.Synthetic and systems biotechnology · 2024Article
- Structural insights into the DNA recognition mechanism by the bacterial transcription factor PdxR.Nucleic acids research · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA.RSC chemical biology · 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
- A dynamical view of protein-protein complexes: Studies by molecular dynamics simulations.Frontiers in molecular biosciences · 2022Article
- Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.Nucleic acids research · 2021Article
- Factors underlying asymmetric pore dynamics of disaggregase and microtubule-severing AAA+ machines.Biophysical journal · 2021Article
- The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition.The journal of physical chemistry. B · 2021Article
- Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex.Scientific reports · 2021Article
- Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease.ACS omega · 2020Article
- The ancillary N-terminal region of the yeast AP-1 transcription factor Yap8 contributes to its DNA binding specificity.Nucleic acids research · 2020Article
- Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade inG3 (Bethesda, Md.) · 2020Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Arginine methylation of SKN-1 promotes oxidative stress resistance in Caenorhabditis elegans.Redox biology · 2019Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.Biophysical journal · 2018Article
- Decomposing protein-DNA binding and recognition using simplified protein models.Nucleic acids research · 2017Article
- How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations of the Caenorhabditis elegans transcription factor SKN-1 bound to its cognate DNA site show that the protein-DNA interface undergoes significant dynamics on the microsecond timescale. A detailed analysis of the simulation shows that movements of two key arginine side chains between the major groove and the backbone of DNA generate distinct conformational sub-states that each recognize only part of the consensus binding sequence of SKN-1, while the experimentally observed binding specificity results from a time-averaged view of the dynamic recognition occurring within this complex.
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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.