DNA Bending and Binding by Metallo-Zipper Models of bZIP Proteins

Palmer, C. Rodgers; Sloan, Leslie S.; Adrian, James C.; Cuenoud, Bernard; Paolella, David N.; Schepartz, Alanna

doi:10.1021/ja00140a002

Cited by 39 publications

(28 citation statements)

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“… 4 Metal complexation by bipyridine (bipy) and terpyridine (terpy) have previously been exploited as allosteric switches in organic solvents, 5 , 6 and have been inserted into a range of macromolecules including polymers 7 and DNA. 8 A number of reports describe their insertion into peptide sequences, 9 – 11 however, the majority focus on using them to achieve dimerisation on metal ion complexation. Only a small fraction takes advantage of a cisoïd-transoïd conformational transition on metal ion complexation, in an effort to achieve allosteric regulation.…”

Section: Introductionmentioning

confidence: 99%

Conformational Study of an Artificial Metal‐Dependent Regulation Site for Use in Designer Proteins

Oheix

Spencer

Gethings

et al. 2013

Zeitschrift anorg allge chemie

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This report describes the dimerisation of glutathione, and by extension, other cysteine-containing peptides or protein fragments, with a 5, 5’-disubstituted-2, 2’-bipyridine or 6, 6”-disubstituted-2, 2’:6’,2”-terpyridine unit. The resulting bipy-GS2 and terpy-GS2 were investigated as potential metal ion dependent switches in aqueous solution, and were found to predominantly adopt the transoïd conformation at physiological pH. Metal complexation with CuII and ZnII at this pH has been studied by UV/Vis, CD, NMR and ion-mobility mass spectrometry. ZnII titrations are consistent with the formation of a 1:1 ZnII:terpy-GS2 complex at pH 7.4, but bipy-GS2 was shown to form both 1:1 and 1:2 complexes with the former being predominant under dilute micromolar conditions. Formation constants for the resulting 1:1 complexes were determined to be log KM 6.86 (bipy-GS2) and 6.22 (terpy-GS2), consistent with a higher affinity for the unconstrained bipyridine, compared to the strained terpyridine. CuII coordination involves the initial formation of 1:1 complexes, followed by 1.5Cu:1bipy-GS2 and 2Cu:1terpy-GS2 complexes at micromolar concentrations. Binding constants for formation of the 1:1 complexes (log KM 12.5 (bipy-GS2); 8.04 and 7.14 (terpy-GS2)) indicate a higher affinity for CuII than ZnII. Finally, ion-mobility MS studies detected the free ligands in their protonated form, and were consistent with the formation of two different Cu adducts with different conformations in the gas-phase. We illustrate that the bipyridine and terpyridine dimerisation units can behave like conformational switches in response to Cu/Zn complexation, and propose that in future these can be employed in synthetic biology with larger peptide or protein fragments, to control large scale folding and related biological function.

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Section: Introductionmentioning

confidence: 99%

Conformational Study of an Artificial Metal‐Dependent Regulation Site for Use in Designer Proteins

Oheix

Spencer

Gethings

et al. 2013

Zeitschrift anorg allge chemie

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“…Moreover their small size means that they cannot target more than 2-3 bp and consequently are not suitable scaffolds for sequence-specific recognition. There have been a very few studies, primarily from two American groups, in which these noncovalent binding metal complexes are conjugated to other biomolecular recognition motifs to create hybrid systems (14)(15)(16), and to date these have not shown enhanced sequence selectivity over the parent recognition motifs because of the poor recognition properties of the small metallo-units used.…”

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confidence: 99%

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: Differential binding of P and M helical enantiomers

Meistermann

Moreno

Prieto

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

185

119

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We have designed a synthetic tetracationic metallo-supramolecular cylinder that targets the major groove of DNA with a binding constant in excess of 10 7 M ؊1 and induces DNA bending and intramolecular coiling. The two enantiomers of the helical molecule bind differently to DNA and have different structural effects. We report the characterization of the interactions by a range of biophysical techniques. The M helical cylinder binds to the major groove and induces dramatic intramolecular coiling. The DNA bending is less dramatic for the P enantiomer.W hile DNA encodes the essential blueprint for life, within biological systems its structure and function is regulated by proteins. In the postgenomic environment the goal is to understand the processing of the genetic code and how to stimulate or prevent this processing. To achieve this end a variety of different types of molecular tools will be required that recognize the genetic code in a sequence-selective fashion. Within biological systems, sequencespecific code recognition is generally achieved by the surface motifs of proteins, which generally interact noncovalently with the major groove of DNA (1-3). The major groove is particularly attractive for DNA recognition because the size and shape of the major groove of B-DNA varies most with base sequence. For example, transcriptional regulators often involve cylindrical binding units, such as ␣-helices or zinc fingers, that insert into the major groove and may kink the DNA (1-3).Oligonucleotides (synthetic and natural) can selectively recognize DNA by forming triplexes through binding in the major groove (4). Neutral oligonucleotide analogues (e.g., peptide nucleic acids) can achieve similar effects, although more commonly they achieve sequence selectivity through strand displacement (5).Such biomacromolecule recognition of DNA contrasts with synthetic small molecule recognition agents. Synthetic molecules that achieve sequence selectivity include well-known minor groove binders such as amide-linked imidazole͞pyrole oligomers and polymers (6), which in common with many small-molecule DNA-binding agents target the minor groove (7). Alternatively small molecules can act by means of intercalation (8, 9). Synthetic agents that target the major groove of DNA with recognition through noncovalent surface motifs have the potential to be a powerful new tool in the armory of reagents that is being developed to tackle the postgenomic challenge. However, to date little progress has been made in this direction, caused in large part by the size of the molecular surfaces required.DNA binding by metal complexes through formation of metal-ligand bonds (e.g., cisplatin) has been extensively studied and usually focuses on binding to N7 of G and A residues (ref. 10 and references therein). By contrast, noncovalent binding of metal complexes to DNA is a less well-developed area and has primarily centered around approximately spherical ruthenium polypyridyl complexes, complexes bearing planar intercalating units, or combinations thereof ...

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“…Our approach was to take advantage of the reactivity of the cysteine (Cys) thiol side‐chain to couple di(bromomethyl) derivatives of bipyridine and terpyridine, through a nucleophilic substitution reaction. The two metal chelating linker units selected, 5,5′‐dibromomethyl‐2,2′‐bipyridine and 6,6′′‐dibromomethyl‐2,2′:6′,2′′‐terpyridine, were synthesised as reported previously,14c, 27 and subsequently reacted with the single Cys amino acid introduced for this purpose towards the C terminus of peptide sequences based on GCN4.…”

Section: Resultsmentioning

confidence: 99%

Metal‐Ion‐Regulated Miniature DNA‐Binding Proteins Based on GCN4 and Non‐native Regulation Sites

Oheix

Peacock

2014

Chemistry A European J

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The design of artificial peptide dimers containing polypyridine switching domains, for which metal-ion coordination is shown to regulate DNA binding, is reported. Short peptides, based on the basic domain of the GCN4 transcription factor (GCN4bd), dimerised with either 2,2'-bipyridine (bipy(GCN4bd) 2 ) or 2,2':6',2''-terpyridine (terpy(GCN4bd) 2 ) linker units, undergo a conformational rearrangement on Cu II and Zn II coordination. Depending on the linker substitution pattern, this is proposed to alter the relative alignment of the two peptide moieties, and in turn regulate DNA binding. Circular dichroism and UV-visible spectroscopy reveal that Cu II and Zn II coordination promotes binding to DNA containing the CRE target site, but to a differing and opposite degree for the two linkers, and that the metal-ion affinity for terpy(GCN4bd) 2 is enhanced in the presence of CRE DNA. Binding to DNA containing the shorter AP1 target site, which lacks a single nucleobase pair compared to CRE, as well as half-CRE, which contains only half of the CRE target site, was also investigated. Cu II and Zn II coordination to terpy(GCN4bd) 2 promotes binding to AP1 DNA, and to a lesser extent half-CRE DNA. Whereas, bipy(GCN4bd) 2 , for which interpeptide distances are largely independent of metal-ion coordination and less suitable for binding to these shorter sites, displays allosteric ineffective behaviour in these cases. These findings for the first time demonstrate that biomolecular recognition, and specifically sequence-selective DNA binding, can be controlled by metal-ion coordination to designed switching units, non-native regulation sites, in artificial biomolecules. We believe that in the future these could find a wide range of applications in biotechnology.

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DNA Bending and Binding by Metallo-Zipper Models of bZIP Proteins

Cited by 39 publications

References 0 publications

Conformational Study of an Artificial Metal‐Dependent Regulation Site for Use in Designer Proteins

Conformational Study of an Artificial Metal‐Dependent Regulation Site for Use in Designer Proteins

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: Differential binding of P and M helical enantiomers

Metal‐Ion‐Regulated Miniature DNA‐Binding Proteins Based on GCN4 and Non‐native Regulation Sites

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