Molecular Origin of DNA Kinking by Transcription Factors
| Autor: | Arnab Mukherjee, Reman K. Singh, Wilbee D. Sasikala |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
HMG-box
Chemistry Intercalation (chemistry) DNA DNA-binding domain Plasma protein binding Molecular Dynamics Simulation Small molecule Surfaces Coatings and Films Molecular dynamics chemistry.chemical_compound Crystallography Materials Chemistry Nucleic Acid Conformation Thermodynamics lipids (amino acids peptides and proteins) Amino Acids Physical and Theoretical Chemistry Transcription factor Transcription Factors |
| Zdroj: | The Journal of Physical Chemistry B. 119:11590-11596 |
| ISSN: | 1520-5207 1520-6106 |
| Popis: | Binding of transcription factor (TF) proteins with DNA may cause severe kinks in the latter. Here, we investigate the molecular origin of the DNA kinks observed in the TF-DNA complexes using small molecule intercalation pathway, crystallographic analysis, and free energy calculations involving four different transcription factor (TF) protein-DNA complexes. We find that although protein binding may bend the DNA, bending alone is not sufficient to kink the DNA. We show that partial, not complete, intercalation is required to form the kink at a particular place in the DNA. It turns out that while amino acid alone can induce the desired kink through partial intercalation, protein provides thermodynamic stabilization of the kinked state in TF-DNA complexes. |
| Databáze: | OpenAIRE |
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