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

Mosquera, Jesús; Jiménez-Balsa, Adrián; Dodero, Verónica Isabel; Vázquez, M. Eugenio; Mascareñas, José L.

doi:10.1038/ncomms2825

Cited by 38 publications

(21 citation statements)

References 47 publications

(47 reference statements)

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“…Additionally, an N‐terminal cap, acetamido benzoic acid (Aba) was added to the N‐terminus of the peptide. This aromatic moiety allows convenient UV‐monitoring and concentration determination as an internal standard,17b while efficiently blocking the N‐terminus during the introduction of the second amino acid sequence (Scheme ). We chose to immobilize earlier described and well‐studied GCN4 basic‐region peptides as DNA‐binding moieties from the simple bZIP rather than b‐HLH‐ZIP TF family.…”

Section: Resultsmentioning

confidence: 99%

Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design

2014

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A dipodal peptidosteroid based on a deoxycholic acid scaffold was designed as a transcription factor model to study, and ultimately interfere in, selective protein–DNA interactions. In this paper, the selective binding of such a dipodal peptidosteroid to its DNA binding site is described for the first time, thus proving the concept and confirming the potential of the design. To achieve this, two 25‐mer peptides were synthesized in parallel and in close proximity on a rigid amphiphilic scaffold, attached by flexible linkers. Peptide aggregation complicated the synthesis under conventional conditions to such an extent that optimization and the use of microwave assistance were required for a successful synthesis. As such, this synthesis is a good model to showcase the beneficial effects of microwave assistance in peptide synthesis.

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Section: Resultsmentioning

confidence: 99%

Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design

2014

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“…In this study, we exploited this feature to demonstrate the ability of HCM-bearing peptides to recognize and bind a biological target. Starting with the pioneering work by Kim, 54,61 several synthetic strategies have been developed for the dimerization of bZIP peptides, 55,62-64 including disulfide bonding, 54 metal coordination, 65-68 and crosslinking with metal-tunable 69 or photo-switchable linkers. 70-72 These studies have collectively shown the importance of the dimeric organization of the basic domains as well as their proper orientation for DNA binding and recognition.…”

Section: Discussionmentioning

confidence: 99%

Tunable helicity, stability and DNA-binding properties of short peptides with hybrid metal coordination motifs

et al. 2016

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Given the prevalent role of α-helical motifs on protein surfaces in mediating protein-protein and protein-DNA interactions, there have been significant efforts to develop strategies to induce α-helicity in short, unstructured peptides to interrogate such interactions. Toward this goal, we have recently introduced hybrid metal coordination motifs (HCMs). HCMs combine a natural metal-binding amino acid side chain with a synthetic chelating group that are appropriately positioned in a peptide sequence to stabilize an α-helical conformation upon metal coordination. Here, we present a series of short peptides modified with HCMs consisting of a His and a phenanthroline group at i and i+7 positions that can induce α-helicity in a metal-tunable fashion as well as direct the formation of discrete dimeric architectures for recognition of biological targets. We show that the induction of α-helicity can be further modulated by secondary sphere interactions between amino acids at the i+4 position and the HCM. A frequently cited drawback of the use of peptides as therapeutics is their propensity to be quickly digested by proteases; here, we observe an enhancement of up to ∼100-fold in the half-lifes of the metal-bound HCM-peptides in the presence of trypsin. Finally, we show that an HCM-bearing peptide sequence, which contains the DNA-recognition domain of a bZIP protein but is devoid of the obligate dimerization domain, can dimerize with the proper geometry and in an α-helical conformation to bind a cognate DNA sequence with high affinities (Kd≥ 65 nM), again in a metal-tunable manner.

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“…Building on this successful idea of miniaturisation, Morii, Schepartz, Mascareñas Q3 and our group have enforced the proof-of-concept by using a variety of small dimerizing moieties. [7][8][9][10][11][12] Subsequently, we have shown that the attachment of the basic region peptides to a rigid scaffold, a derivative of deoxycholic acid in this case, also allows selective recognition of DNA. Indeed, our previous work on cMyc-Max b-HLH-ZIP and GCN4-bZIP proteins showed that this type of steroid-based constructs show potential for binding DNA.…”

Section: Q4mentioning

confidence: 99%

Sequence-selective DNA recognition and enhanced cellular up-take by peptide–steroid conjugates

et al. 2015

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Several GCN4 bZIP TF models have previously been designed and synthesized. However, the synthetic routes towards these constructs are typically tedious and difficult. We here describe the substitution of the Leucine zipper domain of the protein by a deoxycholic acid derivative appending the two GCN4 binding region peptides through\ud an optimized double azide–alkyne cycloaddition click reaction. In addition to achieving sequence specific dsDNA binding, we have investigated the potential of these compounds to enter cells. Confocal microscopy and flow cytometry show the beneficial influence of the steroid on cell uptake. This unique synthetic model of the bZIP TF thus combines sequence specific dsDNA binding properties with enhanced cell-uptake. Given the unique properties of deoxycholic acid and the convergent nature of the synthesis, we believe this work represents a key achievement in the field of TF mimicry

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

Cited by 38 publications

References 47 publications

Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design

Peptidosteroid Tweezers Revisited: DNA Binding Through an Optimised Design

Tunable helicity, stability and DNA-binding properties of short peptides with hybrid metal coordination motifs

Sequence-selective DNA recognition and enhanced cellular up-take by peptide–steroid conjugates

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