ArticleFEBS open bio2017
Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation.
Article in FEBS open bio, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 21 citations in OpenAlex.
- Voltage-Gated Sodium Channel Dysfunction in Epilepsy: Zebrafish Models for Therapeutics.Biomedicines · 2025Review
- Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms.RNA (New York, N.Y.) · 2024Article
- Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms.bioRxiv : the preprint server for biology · 2024Article
- Molecular basis for SOX2-dependent regulation of super-enhancer activity.Nucleic acids research · 2023Article
- C-B-A Test of DNA Force Fields.ACS omega · 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
- EditingInternational journal of molecular sciences · 2021Review
- Highlighting the potential utility of MBP crystallization chaperone for Arabidopsis BIL1/BZR1 transcription factor-DNA complex.Scientific reports · 2021Article
- The Interaction of Supramolecular Anticancer Drug Amphiphiles with Phospholipid Membranes.Nanoscale advances · 2021Article
- CRISPR/Cas System and Factors Affecting Its Precision and Efficiency.Frontiers in cell and developmental biology · 2021Review
- SOX2 and p53 Expression Control Converges in PI3K/AKT Signaling with Versatile Implications for Stemness and Cancer.International journal of molecular sciences · 2020Review
- The evolution of the 9aaTAD domain in Sp2 proteins: inactivation with valines and intron reservoirs.Cellular and molecular life sciences : CMLS · 2020Article
- SOX2 protein biochemistry in stemness, reprogramming, and cancer: the PI3K/AKT/SOX2 axis and beyond.Oncogene · 2020Review
- Structural mechanism of DNA-mediated Nanog-Sox2 cooperative interaction.RSC advances · 2019Article
- Folding a viral peptide in different membrane environments: pathway and sampling analyses.Journal of biological physics · 2018Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence-specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF-binding pattern in DNA. Sox2 recognizes a 6- to 7-base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2-DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The α2-helix of Sox2 was found to be the key player in the Sox2-DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions.
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