Cobalt(II)‐Responsive DNA Binding of a GCN4‐bZIP Protein Containing Cysteine Residues Functionalized with Iminodiacetic Acid

Azuma, Yusuke; Imanishi, Masahito; Yoshimura, Tetsuzo; Kawabata, Takeo; Futaki, Shiroh

doi:10.1002/anie.200902888

Cited by 20 publications

(10 citation statements)

References 21 publications

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“…However, upon photoirradiation (l ex = 365 nm, 10 minutes), a more intense band for the intact peptide-CRE DNA complex could be successfully distinguished, consistent with stronger binding of peptide dimers to CRE DNA, as has been previously reported for similar systems. 13 In the cases of NS and half CRE DNA, the gel appears similar to that obtained prior to irradiation, consistent with both weaker binding and the lack of photodimer formation (Fig. 6B).…”

supporting

confidence: 76%

“…A number of groups have focused on perturbing GCN4's native dimerization unit, the leucine zipper, by altering the protein folding within this region. 13 A light-triggered example was reported by Woolley and co-workers, who introduced an azobenzene into the leucine zipper to control DNA binding through trans-cis isomerization. 14 An alternative approach (similar to that used in this work) involves covalently linking two much shorter peptides that retain only the GCN4 residues directly responsible for sequence-selective DNA binding (the basic region).…”

mentioning

confidence: 99%

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Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

2015

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supporting

confidence: 76%

mentioning

confidence: 99%

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

2015

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“…Particularly relevant are those based on dimeric bZIP basic regions, in which the natural C/C-terminal leucine zipper is replaced by artificial dimerizers [14][15][16][17] . Some of these designs have gone even further and incorporate switchable elements that allow conditional off/on DNA binding by the application of external stimuli such as light or metal ions [18][19][20][21][22] . Despite advances in these and other switchable DNA binders 23,24 , designed systems capable of interacting with alternative DNA sites in an externally regulated manner are unknown.…”

mentioning

confidence: 99%

Stimuli-responsive selection of target DNA sequences by synthetic bZIP peptides

Mosquera¹,

Jiménez-Balsa²,

Dodero³

et al. 2013

Nat Commun

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One of the strategies used by nature to regulate gene expression relies on the stimulicontrolled combination of DNA-binding proteins. This in turn determines the target-binding site within the genome, and thereby whether a particular gene is activated or repressed. Here we demonstrate how a designed basic region leucine zipper-based peptide can be directed towards two different DNA sequences depending on its dimerization arrangement. While the monomeric peptide is non-functional, a C-terminal metallo-dimer recognizes the natural ATF/CREB-binding site (5 0 -ATGA cg TCAT-3 0 ), and a N-terminal disulphide dimer binds preferentially to the swapped sequence (5 0 -TCAT cg ATGA-3 0 ). As the dimerization mode can be efficiently controlled by appropriate external reagents, it is possible to reversibly drive the peptide to either DNA site in response to such specific inputs. This represents the first example of a designed molecule that can bind to more than one specific DNA sequence depending on changes in its environment.

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“…The GCN4 bZip is a common template for protein design (19,39,40). Our DNA looping peptides were inspired by the work from the Oakley laboratory in which the basic DNA-binding region was fused to the C-terminus of the leucine zipper instead, to make the reverseGCN4 peptide (29).…”

Section: Resultsmentioning

confidence: 99%

Rationally designed coiled-coil DNA looping peptides control DNA topology

Gowetski¹,

Kodis²,

Kahn³

2013

Nucleic Acids Research

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Artificial DNA looping peptides were engineered to study the roles of protein and DNA flexibility in controlling the geometry and stability of protein-mediated DNA loops. These LZD (leucine zipper dual-binding) peptides were derived by fusing a second, C-terminal, DNA-binding region onto the GCN4 bZip peptide. Two variants with different coiled-coil lengths were designed to control the relative orientations of DNA bound at each end. Electrophoretic mobility shift assays verified formation of a sandwich complex containing two DNAs and one peptide. Ring closure experiments demonstrated that looping requires a DNA-binding site separation of 310 bp, much longer than the length needed for natural loops. Systematic variation of binding site separation over a series of 10 constructs that cyclize to form 862-bp minicircles yielded positive and negative topoisomers because of two possible writhed geometries. Periodic variation in topoisomer abundance could be modeled using canonical DNA persistence length and torsional modulus values. The results confirm that the LZD peptides are stiffer than natural DNA looping proteins, and they suggest that formation of short DNA loops requires protein flexibility, not unusual DNA bendability. Small, stable, tunable looping peptides may be useful as synthetic transcriptional regulators or components of protein–DNA nanostructures.

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Cobalt(II)‐Responsive DNA Binding of a GCN4‐bZIP Protein Containing Cysteine Residues Functionalized with Iminodiacetic Acid

Cited by 20 publications

References 21 publications

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

Exploiting anthracene photodimerization within peptides: light induced sequence-selective DNA binding

Stimuli-responsive selection of target DNA sequences by synthetic bZIP peptides

Rationally designed coiled-coil DNA looping peptides control DNA topology

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