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Binding of Nucleoid-Associated Protein Fis to DNA Is Regulated by DNA Breathing Dynamics
- Source :
- PLoS Computational Biology, PLoS Computational Biology, Vol 9, Iss 1, p e1002881 (2013)
- Publication Year :
- 2013
- Publisher :
- Public Library of Science, 2013.
-
Abstract
- Physicochemical properties of DNA, such as shape, affect protein-DNA recognition. However, the properties of DNA that are most relevant for predicting the binding sites of particular transcription factors (TFs) or classes of TFs have yet to be fully understood. Here, using a model that accurately captures the melting behavior and breathing dynamics (spontaneous local openings of the double helix) of double-stranded DNA, we simulated the dynamics of known binding sites of the TF and nucleoid-associated protein Fis in Escherichia coli. Our study involves simulations of breathing dynamics, analysis of large published in vitro and genomic datasets, and targeted experimental tests of our predictions. Our simulation results and available in vitro binding data indicate a strong correlation between DNA breathing dynamics and Fis binding. Indeed, we can define an average DNA breathing profile that is characteristic of Fis binding sites. This profile is significantly enriched among the identified in vivo E. coli Fis binding sites. To test our understanding of how Fis binding is influenced by DNA breathing dynamics, we designed base-pair substitutions, mismatch, and methylation modifications of DNA regions that are known to interact (or not interact) with Fis. The goal in each case was to make the local DNA breathing dynamics either closer to or farther from the breathing profile characteristic of a strong Fis binding site. For the modified DNA segments, we found that Fis-DNA binding, as assessed by gel-shift assay, changed in accordance with our expectations. We conclude that Fis binding is associated with DNA breathing dynamics, which in turn may be regulated by various nucleotide modifications.<br />Author Summary Cellular transcription factors (TFs) are proteins that regulate gene expression, and thereby cellular activity and fate, by binding to specific DNA segments. The physicochemical determinants of protein-DNA binding specificity are not completely understood. Here, we report that the propensity of transient opening and re-closing of the double helix, resulting from thermal fluctuations, aka “DNA breathing” or “DNA bubbles,” can be associated with binding affinity in the case of Fis, a well-studied nucleoid-associated protein in Escherichia coli. We found that a particular breathing profile is characteristic of high-affinity Fis binding sites and that DNA fragments known to bind Fis in vivo are statistically enriched for this profile. Furthermore, we used simulations of DNA breathing dynamics to guide design of gel-shift experiments aimed at testing the idea that local breathing influences Fis binding. As a result, we show that via nucleotide modifications but without modifying nucleotides that directly contact Fis, we were able to transform a low-affinity Fis binding site into a high-affinity site and vice versa. The nucleotide modifications were designed only based on DNA breathing simulations. Our study suggests that strong Fis-DNA binding depends on DNA breathing - a novel physicochemical characteristic that could be used for prediction and rational design of TF binding sites.
- Subjects :
- Models, Molecular
HMG-box
Biophysics
Biology
01 natural sciences
DNA-binding protein
Biochemistry
Biophysics Simulations
03 medical and health sciences
Cellular and Molecular Neuroscience
chemistry.chemical_compound
Nucleic Acids
0103 physical sciences
Genetics
Nucleoid
Binding site
010306 general physics
lcsh:QH301-705.5
Molecular Biology
Transcription factor
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
0303 health sciences
Binding Sites
Ecology
Escherichia coli Proteins
Proteins
Computational Biology
DNA
DNA binding site
DNA-Binding Proteins
lcsh:Biology (General)
Computational Theory and Mathematics
chemistry
Modeling and Simulation
Biophysic Al Simulations
Binding domain
Research Article
Protein Binding
Subjects
Details
- Language :
- English
- ISSN :
- 15537358 and 1553734X
- Volume :
- 9
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- PLoS Computational Biology
- Accession number :
- edsair.doi.dedup.....9121654dc4db223e6928eef7a682d434