ArticleProceedings of the National Academy of Sciences of the United States of America2001
The role of rigidity in DNA looping-unlooping by AraC.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 56 citations in OpenAlex.
- Review
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- RNA Polymerase and Transcription Mechanisms: The Forefront of Physicochemical Studies of Chemical Reactions.Biomolecules · 2020Review
- Arabinose Alters Both Local and Distal H-D Exchange Rates in the Escherichia coli AraC Transcriptional Regulator.Biochemistry · 2019Article
- Understanding the basis of a class of paradoxical mutations in AraC through simulations.Proteins · 2013Article
- Mutational analysis of the N-terminal domain of UreR, the positive transcriptional regulator of urease gene expression.Microbiological research · 2012Article
- Active role of the interdomain linker of AraC.Journal of bacteriology · 2011Article
- Understanding apparent DNA flexibility enhancement by HU and HMGB architectural proteins.Journal of molecular biology · 2011Article
- Gene repression by minimal lac loops in vivo.Nucleic acids research · 2010Article
- Computational predictions of the mutant behavior of AraC.Journal of molecular biology · 2010Article
- A DNA-assisted binding assay for weak protein-protein interactions.Journal of molecular biology · 2009Article
- Article
- Opposite allosteric mechanisms in TetR and CAP.Protein science : a publication of the Protein Society · 2009Article
- Constitutive mutations in the Escherichia coli AraC protein.Journal of bacteriology · 2009Article
- Functional modes of the regulatory arm of AraC.Proteins · 2009Article
- Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation.Nucleic acids research · 2008Article
- Geometry of mediating protein affects the probability of loop formation in DNA.Biophysical journal · 2008Article
- Differences in the mechanism of the allosteric l-rhamnose responses of the AraC/XylS family transcription activators RhaS and RhaR.Molecular microbiology · 2008Article
- DNA tape measurements of AraC.Nucleic acids research · 2008Article
- Specific interactions by the N-terminal arm inhibit self-association of the AraC dimerization domain.Protein science : a publication of the Protein Society · 2006Article
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3 authors at 2 institutions in 1 country.
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Abstract
We applied two experiments useful in the study of ligand-regulated DNA binding proteins to AraC, the dimeric regulator of the Escherichia coli l-arabinose operon. In the absence of arabinose, AraC prefers to loop DNA by binding to two half-sites that are separated by 210 base pairs, and in the presence of arabinose it prefers to bind to adjacently located half-sites. The basis for this ligand-regulated shift in binding appears to result from a shift in the rigidity of the system, where rigidity both in AraC protein in the absence of arabinose, and in the DNA are required to generate the free energy differences that produce the binding preferences. Eliminating the dimerization domains and connecting the two DNA binding domains of AraC by a flexible peptide linker should provide a protein whose behavior mimics that of AraC when there is no interaction between its dimerization and DNA binding domains. The resulting protein bound to adjacent half-sites on the DNA, like AraC protein in the presence of arabinose. When the two double-stranded DNA half-sites were connected by 24 bases of single-stranded, flexible DNA, wild-type AraC protein bound to the DNA in the presence and absence of arabinose with equal affinity, showing that AraC modulates its DNA binding affinity in response to arabinose by shifting the relative positions of its DNA binding domains. These results are consistent with the light switch mechanism for the action of AraC, refine the model, and extend the range of experimental tests to which it has been subjected.
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