The role of zinc finger linkers in zinc finger protein binding to DNA

Journal of Computer-Aided Molecular Design - Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains...     

Influence of structure on binding of chlorophylls to peptide ligands

Four classes of chlorophyll (Chl), a, b, c, and d, are involved in photosynthesis within cyanobacteria, algae, and plants. These classes have different evolutionary origins, chemical properties, and biological functions. Our results demonstrate that peptide-bound ligands provided by the imidazole group of histidine and the charge-compensated glutamate-arginine ion pair readily form coordination bonds with Chls a and d but do not interact significantly with Chls b and c. These ligands are apparently not sufficiently strong Lewis bases to displace strongly coordinated water from Chls b and c. These differences determine specificity of binding of Chls in light-harvesting complexes and play an important role in assembly of stable Chl-protein complexes, which has had a profound impact on the evolution of photosynthetic organisms.     

Hydrolytic reaction by zinc finger mutant peptides: successful redesign of structural zinc sites into catalytic zinc sites

To redesign a metal site originally required for the stabilization of a folded protein structure into a functional metal site, we constructed a series of zinc finger mutant peptides such as zf(CCHG) and zf(GCHH), in which one zinc-coordinating residue is substituted into a noncoordinating one. The mutant peptides having water bound to the zinc ion catalyzed the hydrolysis of 4-nitrophenyl acetate as well as the enantioselective hydrolysis of amino acid esters. All the zinc complexes of the mutant peptides showed hydrolytic activity, depending on their peptide sequences. In contrast, the zinc complex of the wild-type, zf(CCHH), and zinc ion alone exhibited no hydrolytic ability. These results clearly indicate that the catalytic abilities are predominantly attributed to the zinc center in the zinc complexes of the mutant peptides. Kinetic studies of the mutant peptides demonstrated that the catalytic hydrolysis is affected by the electron-donating ability of the protein ligands and the coordination environment. In addition, the pH dependence of the hydrolysis strongly suggests that the zinc-coordinated hydroxide ion participates the catalytic reaction. This report is the first successful study of catalytically active zinc finger peptides.     

Site-selective metal binding by designed alpha-helical peptides

It is known that the designed alpha-helical peptide family TRI [(Ac-G(LKALEEK)4G-CONH2)], containing single site substitution of a cysteine for a leucine, is capable of binding Cd(II) within a three-stranded coiled coil. The binding affinity of cadmium is dependent upon the site of substitution, with cysteine incorporated at the a site leading to cadmium complexes of higher affinity than when a d site was modified. In this work we have examined whether this differential binding affinity can be expressed in a di-cysteine-substituted peptide in order to develop site specificity within a designed system. The peptide TRI L9CL19C was used to determine whether significant differences in binding affinities at nearly proximal sites could be achieved in a short designed peptide. On the basis of 113Cd, 1H NMR, and circular dichroic spectroscopies, we have shown that 1 equiv of Cd(II) binds exclusively at the a site. Only after that position is filled does the second site become populated. Thus, the TRI system represents the first example where stoichiometrically equivalent peptides with different sequences form the framework for designing molecular assemblies that show site-specific ion recognition. We propose that the distinct metal affinities are due to the cysteine conformers at different substitution points along the peptide. Furthermore, we have shown that site selectivity in biomolecules can be encoded into relatively short peptides with helical sequences and, therefore, do not necessarily require the extensive protein scaffolds found in natural systems.     

Influences of peptide side chains on the metal ion binding site in metal ion-cationized peptides: Participation of aromatic rings in metal chelation

Aromatic side chains on amino acids influence the fragmentations of cationic complexes of doubly charged metal ions and singly deprotonated peptides. The metal ion interacts with an aromatic side chain and binds to adjacent amide nitrogens. When fragmentation occurs, this bonding leads to the formation of abundant metal-containing a-type ions by reactions that occur at the sites of amino acids that contain the aromatic side chain. Furthermore, formation of metal-containing immonium ions of the amino acids that contain the aromatic side chain also are formed. The abundant a-type ions may be useful in interpretation strategies in which it is necessary to locate in a peptide the position of an amino acid that bears an aromatic side chain.     

Coordination properties of zinc finger peptides revisited: ligand competition studies reveal higher affinities for zinc and cobalt

Zinc fingers are ubiquitous small protein domains which have a Zn(Cys)(4-x)(His)(x) site. They possess great diversity in their structure and amino acid composition. Using a family of six peptides, it was possible to assess the influence of hydrophobic amino acids on the metal-peptide affinities and on the rates of metal association and dissociation. A model of a treble-clef zinc finger, a model of the zinc finger site of a redox-switch protein, and four variants of the classical ββα zinc finger were used. They differ in their coordination set, their sequence length, and their hydrophobic amino acid content. The speciation, metal binding constants, and structure of these peptides have been investigated as a function of pH. The zinc binding constants of peptides, which adopt a well-defined structure, were found to be around 10(15) at pH 7.0. The rates of zinc exchange between EDTA and the peptides were also assessed. We evidenced that the packing of hydrophobic amino acids into a well-defined hydrophobic core can have a drastic influence on both the binding constant and the kinetics of metal exchange. Notably, well-packed hydrophobic amino acids can increase the stability constant by 4 orders of magnitude. The half-life of zinc exchange was also seen to vary significantly depending on the sequence of the zinc finger. The possible causes for this behavior are discussed. This work will help in understanding the dynamics of zinc exchange in zinc-containing proteins.     

The effects of individual amino acids on the fast folding dynamics of alpha-helical peptides

Nanosecond temperature jump experiments coupled to time-resolved infrared spectroscopy were carried out on a series of alanine-based peptides containing different guest amino acids to study the effects of residues with different helix propensities on the helix-coil dynamics.     

Encoded peptide libraries and the discovery of new cell binding ligands

Cells over-expressing integrins or CCR6 were incubated on a DNA microarray, pre-hybridized with a 10,000 member PNA-encoded peptide library allowing novel cell specific ligands for integrins and CCR6 to be identified.     

ZiCo: a peptide designed to switch folded state upon binding zinc

We describe a novel approach to the design of a metal-triggered conformational switch. Specifically, two distinct protein-folding motifs were merged into one polypeptide sequence. The target structures were an alpha-helical coiled-coil trimer and zinc-bound monomer. Solution-phase spectroscopic, sedimentation, and binding studies confirmed the key aspects of the design. Both forms of the peptide were cooperatively folded, and the switch between them was reversible. This design process potentially presents a novel route to peptide-based biosensors.     

Marine metabolites: metal binding and metal complexes of azole-based cyclic peptides of marine origin

Azole-based cyclic peptides found in ascidians ("sea squirts") of the genus Lissoclinum have a high propensity to chelate metal ions. This Highlight summarises the current evidence for marine cyclic peptide-metal congruence, and the structural and stereochemical features in cyclic peptides which seem necessary to facilitate metal complexation. The biological relevance of the metal ions in these associations, including their possible role in the assembly of cyclic peptides in the marine milieu, is also briefly considered. Finally, the synthesis of natural, and some novel non-natural, azole-based cyclic peptides from the cyclooligomerisation and assembly of azole-based amino acids, including in the presence of metal ions, is presented.     

Phosphorylation of an alpha-synuclein peptide fragment enhances metal binding

By using Tb3+ as a luminescent probe, we demonstrate that the phosphorylation state of a 14-residue peptide fragment of alpha-synuclein, a protein implicated in Parkinson's Disease, dramatically affects the metal ion affinity of the peptide. Whereas the unphosphorylated peptide and its phosphoserine analogue show weak Tb3+ binding, its phosphotyrosine analogue shows tight 1:1 binding as well as 2:1 and 3:1 Tb:peptide adducts. Our data suggest that the phosphorylated amino acid must be appropriately positioned among additional ligating residues to establish this phosphorylation-dependent metal binding.     

Oxazole-based peptide macrocycles: a new class of G-quadruplex binding ligands

Herein we report on the synthesis and DNA binding properties of a new class of water soluble oxazole-based peptide macrocycles that bind selectively to quadruplex DNA, with no detectable binding to duplex DNA. We have recently identified one quadruplex in the proto-oncogene c-kit that is suspected to act as a regulatory element for the expression of the c-kit gene. Here we provide the first example of a ligand binding to and stabilizing the c-kit quadruplex. Moreover, we show that these macrocycles show a preference for the c-kit quadruplex as compared to the human telomeric quadruplex.     

Matrix-assisted laser desorption/ionization mass spectra reflect solution-phase zinc finger peptide complexation

The complexation between an 18-residue zinc finger peptide of CCHC type (CCHC=Cys-X₂-Cys-X₄-His-X₄-Cys, X=variable amino acid) from the gag protein p55 of human immunodeficiency virus type 1 (HIV-1) and various transition metal ions was studied by means of circular dichroism spectroscopy and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). A correlation between the complexation behavior in solution and in MALDI-MS could be established. It was shown that MALDI-MS is a fast method suitable for studying metal binding properties of zinc finger complexes.     

Columnar assembly formation and metal binding of cyclic tri-beta-peptides having terpyridine ligands

[reaction: see text] A novel cyclic tri-beta-peptide having terpyridine (tpy) metal ligands was synthesized to investigate its assembly formation and metal complexation. Microscopic observation revealed that this cyclic peptide formed a rod-shaped molecular assembly. The assembly was able to bind Cu(II) because the tpy ligands covered the surface of the crystal, keeping the tpy plane parallel to the ring plane of the cyclic tri-beta-peptide.     

Diamidodipyrrins: versatile bipyrrolic ligands with multiple metal binding modes

A straightforward, facile synthesis of diamidodipyrromethenes (diamidodipyrrins, DADP (R,R')) is presented. These tetradentate ligands readily form complexes with metal ions such as Ni (2+) and Cu (2+) and can adopt different binding modes with these metals. One version of the ligand (DADP (Ph, iPr )) has been structurally characterized in its "free base" form, as a HBr salt, and as the Ni (2+) and Cu (2+) complexes. A symmetric NNOO donor set is found for the Cu (2+) complex in the solid state, involving two carbonyl oxygen atoms and two dipyrrin nitrogen atoms, and this coordination mode has been confirmed in solution by electron paramagnetic resonance. An asymmetric NNNO binding mode found for the Ni (2+) complex in the solid state persists in solution as revealed by (1)H NMR. The HBr salt form of the ligand shows an intriguing hydrogen-bonded head-to-head dimer arrangement. Experiments show that Cu (2+), but not Ni (2+), can mediate the rapid oxidation of the diamidodipyrromethane precursors to the diamidodipyrromethene ligands in the presence of dioxygen. The work here shows that diamidodipyrrins are a versatile new class of ligands in the area of nonporphyrinic pyrrole-based compounds that merit further investigation.     

The effect of N-substitution on the metal binding properties of peptide binding sites

The influence of methyl- and ethylsubstitution at the nitrogen atom of peptide groups on their interaction with alkali and alkaline earth metal ions has been studied by means of quantum chemical calculations on the complexes of lithium, sodium and beryllium with the different substituted amides, and by means of difference energy surfaces obtained fromab initio calculations employing minimalGaussian basis sets. Characteristic ion specific differences are found to occur in the interaction according to the respective substitutions, which will influence the potential for the metal ion in the field of the peptide groups quite strongly. Binding energies and electron density distribution in the complexes are discussed with respect to recent experimental data obtained by metal nmr spectroscopy. The results of the calculations give some indications to possible ways of influencing the ion specifity and reactivity of peptide and protein metal binding sites in biological systems.

---

Der Effekt der N-Substitution auf die metallbindenden Eigenschaften von Peptiden

Zusammenfassung Der Einfluß von Methyl- und Ethyl-Substitution am Stickstoff der Peptidbindung auf die Wechselwirkung mit Alkali- und Erdalkali-Metallionen wurde mittels quantenchemischer Berechnungen an Komplexen mit Lithium, Natrium und Beryllium mit verschieden substituierten Amiden, und mittels der Differenz-Energie-Flächen vonab initio Berechnungen mit minimalemGauß-Basis-Set, studiert. Es wurden charakteristische ionenspezifische Differenzen in den Wechselwirkungen-entsprechend den verschiedenen Substituenten gefunden, die das Potential der Metallionen im Feld der Peptidbindungsgruppe sehr stark beeinflussen. Es werden Bindungsenergien und Elektronendichten in den Komplexen, bezogen auf neuere experimentelle Daten der Metall-NMR-Spektroskopie, diskutiert. Die Ergebnisse der Berechnungen zeigen mögliche Wege auf, die Ionenspezifität und die Reaktivität von Peptid- und Protein-Metall-Bindungszentren in biologischen Systemen zu beeinflussen.